WO2009055805A2 - Genetic markers and methods for improving swine genetics - Google Patents

Abstract

The present invention provides compositions and methods useful for determining an animal's genotype and selecting animals having a desired genotype. Embodiments of the invention also provide analytical kits that may be used to determine an animal's genotype. Furthermore, the present invention provides methods for improving desirable animal traits including improved growth, enhanced body composition, improved meat color, and improved meat quality using genetic markers. The invention also provides methods for allocating animals for predetermined uses, for picking potential parent animals for breeding, and for producing progeny animals. The instant invention also provides methods for identifying associations between single nucleotide polymorphisms (SNPs) and phenotypic traits.

Description

GENETIC MARKERS AND METHODS FOR IMPROVING SWINE GENETICS

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority under 35 U.S. C. § 119(e) to U.S. Provisional Patent

Application Serial No. 60/982,538 filed October 25, 2007, which is incorporated herein in its entirety by this reference.

FIELD OF THE INVENTION

The invention relates to the enhancement of desirable characteristics in swine. More specifically, it relates to genetic markers and methods for improving swine genetics.

BACKGROUND OF THE INVENTION

The future viability and competitiveness of the Pork Industry depends on improvement in the appearance (e.g., color), nutrient quality (e.g., reduced total fat content) and eating quality (e.g. , water-holding capacity, tenderness) of pork food products. These improvements must be accompanied by continued gains in the efficiency of production. Unfortunately, efficiency traits are often unfavorably correlated with product quality traits. Although these traits all have some degree of underlying genetic variation in commercial pig populations, the accuracy of selecting breeding animals with superior genetic merit for many of them is low due to low heritability or the inability to measure the trait directly on the candidate animal. In particular, meat quality traits can only be measured on the relatives of potential breeding animals. Thus, the accuracy of conventional selection for these traits is low and ability to make genetic change through selection is limited.

Genomics offers the potential for greater improvement in traits of pork production and quality through the discovery of genes, or genetic markers linked to genes, that account for genetic variation and can be used for more direct and accurate selection.

SUMMARY OF THE INVENTION

This section provides a non-exhaustive summary of embodiments of the present invention.

Embodiments of the invention provide methods of evaluating an animal's genotype at one or more genomic locus/loci, the method comprising: determining the animal's genotype for at least one locus; the locus comprising a single nucleotide polymorphism (SNP) having at least two allelic variants; and correlating the identified allele with a phenotype as described in

Table 3; wherein at least one SNP is selected from the SNPs described in Table 3. Embodiments of the invention provide methods for allocating animals for use comprising: determining at least one animal's genotype at one or more locus/loci; wherein the one or more locus/loci contains a single nucleotide polymorphism (SNP), having at least two allelic variants; and wherein at least one SNP is selected from the SNPs described in Table 3; analyzing the determined genotype of the at least one animal at one or more SNPs selected from the SNPs described in Table 3 to determine which allelic variant is present; and allocating the animal for use according to its determined genotype.

Embodiments of the invention provide methods for selecting a potential parent animal for breeding, comprising: determining at least one potential parent animal's genotype at one or more genomic locus/loci; wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from the SNPs described in Table 3; analyzing the determined genotype of the at least one potential parent animal for one or more SNPs selected from the SNPs described in Table 3 to determine which allele is present; correlating the identified allele with a phenotype as described in Table 3; and allocating at least one animal for breeding use based on its genotype.

Embodiments of the invention provide methods of producing progeny animals comprising: identifying at least one animal that has been allocated for breeding in accordance with the methods described herein; producing progeny from the at least one allocated animal through a process comprising: natural breeding; artificial insemination; in vitro fertilization; and/or collecting semen/spermatozoa or at least one ovum from the animal and contacting it, respectively, with ovum/ova or semen/spermatozoa from a second animal to produce a conceptus by any means.

Embodiments of the invention provide methods of identifying at least one phenotypic trait associated with a quantitative trait locus (QTL), the method comprising: measuring one or more phenotypic traits in a plurality of animals; determining the animals' genotype for at least one locus; wherein the locus comprises at least one single nucleotide polymorphism (SNP) having at least two variants, and wherein the SNP is selected from the group of SNPs described in Table 3; statistically correlating the association of at least one phenotypic trait with the presence of an allele of at least one SNP selected from the group of SNPs described in Table 3; wherein the presence of a different allele for that SNP has a different association for the phenotypic trait. Embodiments of the invention provide methods of identifying a genetic marker in allelic association with at least one SNP selected from the group of SNPs described in Table 3, the method comprising: identifying a genetic marker Bi suspected of being in allelic association with a marker Ai selected from the group of SNPs described in Table 3; determining whether Ai and Bi are in allelic association; wherein allelic association exists if r²>0.2 for Equation 1 for a population sample of at least about 100 animals and wherein Equation 1 is: r² = rf(AiBi) - f(Ai)f(Bi)l² [Equation 1] fCAoα-fCAoxfCBoα-fCBO)

and wherein Ai represents an allele of a SNP described in Table 3; Bi represents a genetic marker at another locus; f(AiBi) denotes frequency of having both Ai and B₁; f(Ai) is the frequency of Ai in the population; and f(Bi) is the frequency of Bi in a population.

Embodiments of the invention provide methods of screening animals to identify those which have a genetic predisposition related to a predetermined phenotypic trait, the method comprising: identifying a desired phenotypic trait; obtaining a sample of genomic DNA from an animal; assaying for the presence of a single nucleotide polymorphism (SNP) in the sample; wherein the polymorphism is located within a gene listed in Table 3, and wherein the phenotypic trait is selected from the phenotypic traits listed in Table 3 as being associated with the gene. Alternative embodiments of this invention may also include methods wherein the gene is selected from the group consisting of: Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR23a, GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, and AQP7.

Embodiments of the invention provide methods for selecting a potential parent animal for improvement of one or more traits selected from the group consisting of growth, meat color, meat composition, or meat quality, the method comprising: determining at least one potential parent animal's genotype at one or more genomic locus/loci; wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from: the SNPs described in Table 3 and the Sequence Listing; and/or a SNP located in a gene selected from the group of genes listed in Table 3; analyzing the determined genotype of at least one evaluated animal for one or more SNPs selected from: the SNPs described in Table 3; and/or a SNP located in a gene selected from the group of genes listed in Table 3; correlating the identified allelic variants with a phenotype using the information provided in Table 3 and the Sequence Listing; and allocating at least one animal for breeding use based on its genotype.

Embodiments of the invention also provide methods for evaluating an animal's genotype by determining which of two or more alleles for a SNP are present for one or more SNPs selected from the group consisting of the SNPs described in Table 3 of the instant application, as well as methods of evaluating an animal's genotype by determining which of two or more alleles for a SNP are present for one or more SNPs located within a gene selected from the group consisting of Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR23a, GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, and AQP7. Various embodiments of the invention relate to genetic markers associated with meat color, body composition, growth rate, and/or meat quality. Embodiments of the invention provide methods for identification of animals that are more likely to produce offspring that are leaner, fastest growing and possess superior meat quality (lower shear force, darker meat color and higher water holding capacity). Various embodiments of the invention relate to genetic markers and methods for the identification and selection of pigs more likely to produce offspring with desired meat color, body composition, growth rate, and/or meat quality, by the presence or absence of polymorphism(s) in the GHRH, ALOX15, SLC2A4, TBC1D7, AQP7, Ssc-miR15b, Ssc- miR23a, Ssc-miR27a, and Ssc-miR184 genes. Other embodiments of the invention provide methods for evaluating an animal's genotype at one or more positions in the animal's genome. In various aspects of these embodiments, the animal's genotype is evaluated at a position within a segment of DNA (an allele) that contains at least one SNP selected from the SNPs described in Table 3 and Sequence Listing of the present application. Other embodiments of the invention provide methods for allocating animals for use based on their genotype (e.g. allocating for use as a breeding animal or to be sold for finishing and/or slaughter). Various aspects of this embodiment of the invention provide methods that comprise: a) analyzing at least one animal's genomic sequence at one or more alleles (where the alleles analyzed each comprise at least one SNP) to determine the animal's genotype at each of those alleles; b) analyzing the genotype determined for each allele to determine which allele of a SNP is present; c) allocating the at least one animal for use based on its genotype at one or more of the alleles analyzed. Various aspects of this embodiment of the invention provide methods for allocating animals for use based on a favorable association between the animals' genotype, at one or more SNP alleles disclosed in the present application, and a desired phenotype. Alternatively, the methods provide for not allocating an animal for a certain use because it has one or more SNP alleles that are either associated with undesirable phenotypes or are not associated with desirable phenotypes.

Other embodiments of the invention provide methods for selecting animals for use in breeding to produce progeny. Various aspects of these methods comprise: A) determining the genotype of at least one potential parent animal at one or more locus/loci, where at least one of the loci analyzed contains an allele of a SNP selected from the group of SNPs described in Table 3; B) Analyzing the determined genotype at one or more positions for at least one animal to determine which of the SNP alleles is present; C) Correlating the analyzed allele(s) with one or more phenotypes; D) Allocating at least one animal for use to produce progeny.

Other embodiments of the invention provide methods for producing offspring animals

(progeny animals). Aspects of this embodiment of the invention provide methods that comprise : breeding an animal that has been selected for breeding by methods described herein to produce offspring. The offspring may be produced by purely natural methods or through the use of any appropriate technical means, including but not limited to: artificial insemination; embryo transfer (ET), multiple ovulation embryo transfer (MOET), in vitro fertilization (IVF), or any combination thereof. Other embodiments of the invention provide for databases or groups of databases, each database comprising lists of nucleic acid sequences, which lists include a plurality of the SNPs described in Table 3. Preferred aspects of this embodiment of the invention provide for databases comprising the sequences of about 50 or more SNPs. Other aspects of these embodiments comprise methods for using a computer algorithm or algorithms that use one or more database(s), each database comprising a plurality of the SNPs described in Table 3, to identify phenotypic traits associated with the inheritance of one or more alleles of the SNPs, and/or using such a database to aid in animal allocation.

Still other embodiments of the invention provide diagnostic kits and/or arrays for detecting one or more of the SNPs described in Table 3. Further embodiments of the invention provide methods for identifying associations between one or more of the SNPs described in Table 3 and one or more phenotypic traits. Additional embodiments of the invention provide methods for identifying other genetic markers that are in allelic association with one or more of the SNPs described in Table 3.

DEFINITIONS

The following definitions are provided to aid those skilled in the art to more readily understand and appreciate the full scope of the present invention. Nevertheless, as indicated in the definitions provided below, the definitions provided are not intended to be exclusive, unless so indicated. Rather, they are preferred definitions, provided to focus the skilled artisan on various illustrative embodiments of the invention.

As used herein the term "allelic association" preferably means: nonrandom deviation of f(A3_j) from the product Of^A₁) and f(B,), which is specifically defined by r²>0.2, where r² is measured from a reasonably large animal sample (e.g., > 100) and defined as r² = rf(AiBi) - f(Ai)f(Bi)l² [Equation 1] fCAoα-fCAoxfCBoα-fCBO)

where Ai represents an allele at one locus, Bi represents an allele at another locus; f(AiBi) denotes frequency of having both Ai and Bi, f(Ai) is the frequency of Ai, f(Bi) is the frequency of Bi in a population.

As used herein the terms "allocating animals for use" and "allocation for use" preferably mean deciding how an animal will be used within a herd or that it will be removed from the herd to achieve desired herd management goals. For example, an animal might be allocated for use as a breeding animal or allocated for sale as a non-breeding animal (e.g. allocated to animals intended to be sold for meat). In certain aspects of the invention, animals may be allocated for use in sub-groups within the breeding programs that have very specific goals (e.g. to improve meat color or carcass composition). Accordingly, even within the group of animals allocated for breeding purposes, there may be more specific allocation for use to achieve more specific and/or specialized breeding goals.

As used herein the terms "animal" or "animals" preferably refer to pigs/swine. As used herein the terms "composition" and "body composition" preferably refer to measurements of the physical characteristics of the animal/pig and/or its carcass, or to the characteristics themselves.

As used herein the term "growth" refers to the measurement of various parameters associated with an increase in an animal's size/weight. As used herein the term "linkage disequilibrium" preferably means allelic association wherein Ai and Bi (as used in the above definition of allelic association) are present on the same chromosome.

As used herein the term "meat color" refers to measurements of color of meat obtained from a slaughtered animal.

As used herein the term "meat quality" refers to measurements of the palatability and/or eating qualities (e.g. marbling, texture, and tenderness) of meat from a slaughtered animal.

As used herein the term "natural breeding" preferably refers to mating animals without human intervention in the fertilization process. That is, without the use of mechanical or technical methods such as artificial insemination or embryo transfer. The term does not refer to selection of the parent animals.

As used herein the term "quantitative trait" is used to denote a trait that is controlled by multiple (e.g., two or more, and often many) genes each of which contributes a small to moderate effect on the trait. The observations on quantitative traits often follow a normal distribution.

As used herein the term "quantitative trait locus (QTL)" is used to describe a locus that contains at least one polymorphism that has an effect on a quantitative trait.

As used herein the term "reproductive material" includes, but is not limited to, semen, spermatozoa, ova, and zygote(s).

As used herein the terms "single nucleotide polymorphism" or "SNP" refer to a location in an animal's genome that is polymorphic within the population. That is, within the population some individual animals have one type of base at that position, while others have a different base. For example, a SNP might refer to a location in the genome where some animals have a "G" in their DNA sequence, while others have a "T".

As used herein the terms "hybridization under stringent conditions" and "stringent hybridization conditions" preferably mean conditions under which a "probe" will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g. , at least about 5-fold over background or spurious hybridization). Stringent conditions are target-sequence dependent and will differ depending on the structure of the polynucleotide. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).

Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is at least about 30 ⁰C for short probes (e.g., about 10 to about 50 nucleotides) and at least about 60 ⁰C for long probes (e.g., greater than about 50 nucleotides). Stringency may also be adjusted with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1 % SDS (sodium dodecyl sulphate) at 37⁰C, and a wash in IX to 2X SSC (2OX SSC = 3.0 M NaC 1/0.3 M trisodium citrate) at 50 to 55 ⁰C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1 % SDS at 37 ⁰C, and a wash in 0.5X to IX SSC at 55 to 60 ⁰C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1 % SDS at 37 ⁰C, and a wash in 0. IX SSC at 60 to 65 ⁰C. The duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours.

Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the thermal melting point (T_m) can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: T_m = 81.5 ⁰C + 16.6 (log M) + 0.41 (% GC) - 0.61 (% form) - 500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The T_m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T_m is reduced by about 1⁰C for each 1 % of mismatching; thus, T_m, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with 90% identity are sought, the T_m can be decreased by about 10 ⁰C. Generally, stringent conditions are selected to be about 5°C lower than the T_m for the specific sequence and its complement at a defined ionic strength and pH. However, highly stringent conditions can utilize a hybridization and/or wash at about 1 ⁰C, about 2 ⁰C, about 3 ⁰C, or about 4 ⁰C lower than the thermal melting point (T_m); moderately stringent conditions can utilize a hybridization and/or wash at about 6⁰C, about 7 ⁰C, about 8 ⁰C, about 9 ⁰C, or about 10 ⁰C lower than the thermal melting point (T_m); low stringency conditions can utilize a hybridization and/or wash at about 11 ⁰C, about 12 ⁰C, about 13 ⁰C, about 14 ⁰C, about 15 ⁰C, or about 20⁰C lower than the thermal melting point (T_m). Using the equation, hybridization and wash compositions, and desired T_m, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T_m of less than 45 ⁰C (aqueous solution) or 32 ⁰C (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, N.Y.); and Ausubel et al, eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See also Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

DESCRIPTION OF THE INVENTION Various embodiments of the present invention provide methods for evaluating an animal's (especially a pig's) genotype at one or more positions in the animal's genome. Aspects of these embodiments of the invention provide methods that comprise determining the animal's genomic sequence at one or more locations (loci) that contain single nucleotide polymorphisms (SNPs). Specifically, the invention provides methods for evaluating an animal's genotype by determining which of two or more alleles for a SNP are present for one or more SNPs selected from the group consisting of the SNPs described in Table 3 of the instant application, as well as evaluating an animal's genotype by determining which of two or more alleles for a SNP are present for one or more SNPs located within a gene selected from the group consisting of Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR23a, GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, and AQP7.

In preferred aspects of these embodiments, the animal's genotype is evaluated to determine which allele is present for 1 or more, 2 or more, 3 or more, 4 or more, and/or 5 or more SNPs selected from the group of SNPs described in Table 3.

In alternative embodiments, the animal's genotype is evaluated to determine which allele is present for a SNP in addition to the SNPs listed in Table 3. Additional SNPs beyond those listed in Table 3 which can be used for swine breeding purposes are known in the art. Furthermore, SNPs of particular relevance may be found in US Provisional Patent Application Serial Numbers 60/860,462 and 60/839,404, each of which is incorporated by reference herein in its entirety, including the Sequence Listing of the instant application. More preferably, the animal's genotype is determined for positions corresponding to at least about 25, at least about 50, at least about 100, at least about 200, at least about 500, at least about 1000, or more SNPs, including, without limitation, one or more of the SNPs described in Table 3.

In other aspects of this embodiment, the animal's genotype is analyzed with respect to at least about 1, about 10, about 25, about 50, about 100, about 200, about 500, or more SNPs that have been shown to be associated with growth, composition, meat color, or meat quality, or any combination thereof, wherein at least one of these SNPs is found in Table 3. For example, embodiments of the invention provide methods of genotyping for a single SNP or for genotyping about 10 or more, about 25 or more, about 50 or more, about 100 or more, about 200 or more, or about 500 or more SNPs that have been determined to be significantly associated with growth.

In any embodiment of the invention the genomic sequence at the SNP locus may be determined by any means compatible with the present invention. Suitable means are well known to those skilled in the art and include, but are not limited to, direct sequencing, sequencing by synthesis, primer extension, Matrix Assisted Laser Desorption/Ionization-Time Of Flight (MALDI-TOF) mass spectrometry, polymerase chain reaction-restriction fragment length polymorphism, microarray/multiplex array systems (e.g. those available from Affymetrix, Santa Clara, California), and allele-specifϊc hybridization.

Embodiments of the invention provide methods of evaluating an animal's genotype at one or more genomic locus/loci, the method comprising: determining the animal's genotype for at least one locus; the locus comprising a single nucleotide polymorphism (SNP) having at least two allelic variants; and correlating the identified allele with a phenotype as described in Table 3 ; wherein at least one SNP is selected from the SNPs described in Table 3. Alternative embodiments of this invention may also include methods wherein the animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more positions that contain SNPs, including at least one SNP selected from the SNPs described in Table 3. Alternative embodiments may also include methods wherein the animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more positions that contain SNPs, including at least two SNPs selected from the SNPs described in Table 3. Embodiments of the invention provide methods for allocating animals for use comprising: determining at least one animal's genotype at one or locus/loci; wherein at least one locus contains a single nucleotide polymorphism (SNP) having at least two allelic variants; and wherein at least one SNP is selected from the SNPs described in Table 3; analyzing the determined genotype of at least one evaluated animal at one or more SNPs selected from the SNPs described in Table 3 to determine which allelic variant is present; and allocating the animal for use according to its determined genotype. Alternative embodiments of this invention may also include methods wherein at least one animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs, including at least one SNP selected from the SNPs described in Table 3. Alternative embodiments of this invention may also include methods wherein at least one animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs, including at least two SNPs selected from the SNPs described in Table 3. Embodiments of the invention provide methods for selecting a potential parent animal for breeding comprising: determining at least one potential parent animal's genotype at one or more genomic locus/loci; wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from the SNPs described in Table 3; analyzing the determined genotype of the at least one potential parent animal for one or more SNPs selected from the SNPs described in Table 3 to determine which allele is present; correlating the identified allele with a phenotype as described in Table 3; and allocating at least one potential parent animal for breeding use based on its genotype. Alternative embodiments of this invention may also include methods wherein at least one potential parent animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, or about 1000 or more loci that contain SNPs, including at least one SNP selected from the SNPs described in Table 3. Alternative embodiments of this invention may also include methods wherein at least one potential parent animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs, including at least two SNPs selected from the SNPs described in Table 3.

Embodiments of the invention provide methods of producing progeny animals comprising: identifying at least one animal that has been allocating for breeding in accordance with the methods described herein; producing progeny from the allocated animal through a process comprising: natural breeding; artificial insemination; in vitro fertilization; and/or collecting semen/spermatozoa or at least one ovum from the animal and contacting it, respectively, with ovum/ova or semen/spermatozoa from a second animal to produce a conceptus by any means. Alternative embodiments of this invention may also include methods which include producing progeny through natural breeding as well as methods comprising producing offspring through artificial insemination, embryo transfer, and/or in vitro fertilization. Alternative embodiments of this invention may also include methods wherein at least one potential parent animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs, including at least one SNP selected from the SNPs described in Table 3. Alternative embodiments of this invention may also include methods wherein at least one potential parent animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs, including at least two SNPs selected from the SNPs described in Table 3.

Embodiments of the invention provide methods of identifying at least one phenotypic trait associated with a quantitative trait locus (QTL), the method comprising: measuring one or more phenotypic traits in a plurality of animals; determining the animal's genotype for at least one locus; wherein the locus comprises at least one a single nucleotide polymorphism (SNP) having at least two variants, and wherein the SNP is selected from the group of SNPs described in Table 3; statistically correlating the association of at least one phenotypic trait with the presence of an allele of at least one SNP selected from the group of SNPs described in Table 3; wherein the presence of a different allele for that SNP has a different association for the phenotypic trait. Embodiments of the invention provide methods of identifying a genetic marker in allelic association with at least one SNP selected from the group of SNPs described in Table 3, the method comprising: identifying a genetic marker Bi suspected of being in allelic association with a marker Ai selected from the group of SNPs described in Table 3; determining whether Ai and Bi are in allelic association; wherein allelic association exists if r²>0.2 for Equation 1 for a population sample of at least 100 animals and wherein Equation 1 is: r² = rf(AiBi) - f(Ai)f(Bi)l² [Equation 1] fCAoα-fCAoxfCBoα-fCBO)

and wherein Ai represents an allele of a SNP described in Table 3; Bi represents a genetic marker at another locus; f(AiBi) denotes frequency of having both Ai and B₁; f(Ai) is the frequency of Ai in the population; and f(Bi) is the frequency of Bi in a population. Alternative embodiments of this invention may also include methods wherein the genetic marker Bi is a SNP. Alternative embodiments of this invention may also include methods wherein the genetic marker identified is in linkage disequilibrium with at least one SNP selected from the group of SNPs described in Table 3. Preferred embodiments may also include methods wherein r² > 0.5, r² > 0.8, r² > 0.9, or r² > 0.95. Alternative embodiments may also include methods wherein Bi is a causal mutation underlying a quantitative trait locus.

Embodiments of the invention provide methods of screening animals to identify those which have a genetic predisposition related to a predetermined phenotypic trait, the method comprising: identifying a desired phenotypic trait; obtaining a sample of genomic DNA from an animal; assaying for the presence of a single nucleotide polymorphism (SNP) in the sample; wherein the polymorphism is located within a gene listed in Table 3, and wherein the phenotypic trait is selected from the phenotypic traits listed in Table 3 as being associated with the gene. Alternative embodiments of this invention may also include methods wherein the gene is selected from the group consisting of: Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR23a, GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, and AQP7. Alternative embodiments of this invention may also include methods wherein the SNP is selected from the SNPs described in Table 3 and the Sequence Listing. Alternative embodiments of this invention may also include methods wherein at least one animal's genotype is evaluated at about 10 or more, about 25 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci that contain SNPs.

Embodiments of the invention provide methods for selecting a potential parent animal for improvement of one or more traits selected from the group consisting of growth, meat color, meat composition, or meat quality, the method comprising: determining at least one potential parent animal's genotype at one or more genomic locus/loci; wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from: the SNPs described in Table 3 and the Sequence Listing; and/or a SNP located in a gene selected from the group of genes listed in Table 3; analyzing the determined genotype of at least one evaluated animal for one or more SNPs selected from: the SNPs described in Table 3; and/or SNP located in a gene selected from the group of genes listed in Table 3; correlating the identified allelic variants with a phenotype using the information provided in Table 3 and the Sequence Listing; and allocating at least one animal for breeding use based on its genotype.

Alternative embodiments of this invention may also include methods wherein the potential parent animal's genotype is evaluated at about 10 or more loci, including at least one locus that contains a SNP selected from: the SNPs described in Table 3 ; and/or a SNP located in a gene selected from the group of genes listed in Table 3. Alternative embodiments may also include methods wherein the potential parent animal's genotype is evaluated at about 50 or more loci, about 100 or more loci, about 200 or more loci, about 500 or more loci, about 1000 or more loci, and/or even greater numbers of loci. Alternative embodiments may also include methods wherein the potential parent animal's genotype is evaluated at about 10 or more, about 50 or more, about 100 or more, and/or about 1000 or more loci, including at least two loci that contain SNPs selected from: the SNPs described in Table 3; and/or a SNP located in a gene selected from the group of genes listed in Table 3; Alternative embodiments of this invention may also include methods that comprise whole-genome analysis. Other embodiments of the invention provide methods for allocating animals for subsequent use (e.g. to be used as sire/dams or to be sold for immediate slaughter or to be sold for finishing or any other use). Various aspects of these embodiments of the invention comprise determining at least one animal's genotype for at least one SNP selected from the group of SNPs described in Table 3 (methods for determining animals' genotypes for one or more SNPs are described above).

The instant invention provides embodiments where analysis of the genotypes of the SNPs described in Table 3 is the only analysis done. Other embodiments provide methods where analysis of the SNPs disclosed herein is combined with any other desired type of genomic or phenotypic analysis (e.g. analysis of any genetic markers beyond those disclosed in the instant invention). Moreover, the SNPs analyzed may be selected from those SNPs only associated with growth, only composition, only meat color, only meat quality, or the analysis may be done for SNPs selected from any desired combination of traits. SNPs associated with various traits are described in Table 3.

According to various aspects of these embodiments of the invention, once the animal's genetic sequence for the selected SNP(s) has been determined, this information is evaluated to determine which allele of the SNP is present for at least one of the selected SNPs. Preferably the animal's allelic complement for all of the determined SNPs is evaluated. Finally, the animal is allocated for use based on its genotype for one or more of the SNP positions evaluated. Preferably, the allocation is made taking into account the animal's genotype at each of the SNPs evaluated, but its allocation may be based on any subset or subsets of the SNPs evaluated. The allocation may be made based on any suitable criteria. For any SNP, a determination may be made as to whether one of the allele(s) is associated/correlated with desirable characteristics or associated with undesirable characteristics. This determination will often depend on the animal breed/line, and on the breeding or other herd management goals. Determination of which alleles are associated with desirable phenotypic characteristics can be made by any suitable means. Methods for determining these associations are well known in the art; moreover, aspects of the use of these methods are generally described in the EXAMPLES, below.

Phenotypic traits that may be associated with the SNPs of the current invention include, but are not limited to: growth traits, body and/or carcass composition, meat quality, meat color, health traits (resistance to disease and injury and stress tolerance), breeding traits such as litter size, survival of young, breeding efficiency, and length of reproductive life of the female.

According to various aspects of these embodiments of the invention, allocation for use of the animal may entail either positive selection for the animals having the desired genotype(s) (e.g. the animals with the desired genotypes are selected for breeding purposes), negative selection of animals having undesirable genotypes (e.g. , animals with an undesirable genotypes are culled from the herd), or any combination of these methods. According to preferred aspects of this embodiment of the invention animals identified as having SNP alleles associated with desirable phenotypes are allocated for use consistent with that phenotype (e.g. allocated for breeding based on phenotypes positively associated with improved growth). Alternatively, animals that do not have SNP genotypes that are positively correlated with the desired phenotype (or possess SNP alleles that are negatively correlated with that phenotype) are not allocated for the same use as those with a positive correlation for the trait.

Other embodiments of the invention provide methods for selecting potential parent animals (i.e., allocation for breeding). Various aspects of this embodiment of the invention comprise determining at least one animal's genotype for at least one SNP selected from the group of SNPs described in Table 3. Furthermore, determination of whether and how an animal will be used as a potential parent animal may be based on its genotype at about one or more, about 10 or more, about 25 or more, about 50 or more, about 100 or more, about 300 or more, and/or about 500 or more SNPs, wherein at least one of these SNPs is described in Table 3 and Sequence Listing. Moreover, as with other types of allocation for use, various aspects of these embodiments of the invention provide methods where the only analysis done is to genotype the animal for one or more of the SNPs described in Table 3. Other aspects of these embodiments provide methods where analysis of one or more SNPs disclosed herein is combined with any other desired genomic or phenotypic analysis (e.g. analysis of any genetic markers beyond those disclosed in the instant invention). Moreover, the SNP(s) analyzed may all be selected from those associated only with growth, or only with composition, or only meat color, or only meat quality. Conversely, the analysis may be done for SNPs selected from any desired combination of these or other traits.

According to various aspects of these embodiments of the invention, once the animal's genetic sequence at the site of the selected SNP(s) has been determined, this information is evaluated to determine which allele of the SNP is present for at least one of the selected SNPs. Preferably the animal's allelic complement for all of the sequenced SNPs is evaluated. Additionally, the animal's allelic complement is analyzed and correlated with the probability that the animal's progeny will express one or more phenotypic traits. Finally, the animal is allocated for breeding use based on its genotype for one or more of the SNP positions evaluated and the probability that it will pass the desired genotype(s)/allele(s) to its progeny. Preferably, the breeding allocation is made taking into account the animal's genotype at each of the SNPs evaluated. However, its breeding allocation may be based on any subset or subsets of the SNPs evaluated. The breeding allocation may be made based on any suitable criteria. For example, breeding allocation may be made so as to increase the probability of enhancing a single certain desirable characteristic in a population (in preference to other characteristics); alternatively, the selection may be made so as to generally maximize overall production based on a combination of traits. The allocations chosen are dependent on the breeding goals.

Other embodiments of the instant invention provide methods for producing progeny animals. According to various aspects of these embodiments of the invention, the animals used to produce the progeny are those that have been allocated for breeding according to any of the embodiments of the current invention. Those using the animals to produce progeny may perform the necessary analysis or, alternatively, those producing the progeny may obtain animals that have been analyzed by another. The progeny may be produced by any appropriate means, including, but not limited to using: (i) natural breeding, (ii) artificial insemination, (iii) in vitro fertilization (IVF) or (iv) collecting semen/spermatozoa and/or at least one ovum from the animal and contacting it, respectively with ova/ovum or semen/spermatozoa from a second animal to produce a conceptus by any means.

According to preferred aspects of this embodiment of the invention the progeny are produced by a process comprising natural breeding. In other aspects of this embodiment the progeny are produced through a process comprising the use of standard artificial insemination

(AI), in vitro fertilization, multiple ovulation embryo transfer (MOET), deep intrauterine insemination (DIUI), or any combination thereof.

Other embodiments of the invention provide for methods that comprise allocating an animal for breeding purposes and collecting/isolating genetic material from that animal: wherein genetic material includes but is not limited to: semen, spermatozoa, ovum, zygotes, blood, tissue, serum, DNA, and/or RNA.

It is understood that most efficient and effective use of the methods and information provided by the instant invention employ computer programs and/or electronically accessible databases that comprise all or any portion of the sequences disclosed in the instant application. Accordingly, the various embodiments of the instant invention provide for databases comprising all or any portion of the sequences corresponding to at least about 10

SNPs described in Table 3. In preferred aspect of these embodiments the databases comprise sequences for at least about 25 or more, about 50 or more, about 100 or more, about 200 or more, about 500 or more, and/or about 1000 or more SNPs, wherein at least one of these SNPs is described in Table 3 and sequence listing.

Likewise, any method of identification of the presence of absence for the polymorphisms may be used, including for example TaqMan^®, gene sequencing (for example from library, PCR product), restriction fragment length polymorphism (RFLP), heteroduplex analysis, temperature gradient electrophoresis, denaturing gradient gel electrophoresis, and/or single-strand conformation polymorphism (SSCP).

It is further understood that efficient analysis and use of the methods and information provided by the instant invention will employ the use of automated genotyping; particularly when large numbers (e.g. 100s) of markers are evaluated. Any suitable method known in the art may be used to perform such genotyping, including, but not limited to, the use of micro- arrays.

Other embodiments of the invention provide methods wherein one or more of the SNP sequence databases described herein are accessed by one or more computer executable programs. Such methods include, but are not limited to, use of the databases by programs to analyze for an association between the SNP and a phenotypic trait, or other user-defined trait (e.g. traits measured using one or more metrics such as gene expression levels, protein expression levels, or chemical profiles), and programs used to allocate animals for breeding or market.

Other embodiments of the invention provide methods comprising collecting genetic material from an animal that has been allocated for breeding. Wherein the animal has been allocated for breeding by any of the methods disclosed as part of the instant invention.

Other embodiments of the invention are drawn to isolated nucleic acids comprising about 17 or more contiguous nucleotides corresponding to any one of the SNP sequences described in Table 3 (i.e. any of SEQ ID NOs: 1-1 9 and Table 3). In preferred aspects of this embodiment of the invention the isolated nucleic acid comprises a nucleotide corresponding with the polymorphic site in the sequence (i.e. it contains the site that defines the SNP 's polymorphism as described in Table 3). Various embodiments of the invention provide isolated nucleic acids having the sequence of alleles comprising single nucleotide polymorphisms (SNPs) that are provided by the present invention. Aspects of these embodiments of the invention provide for isolated nucleic acids identical to all or a portion of the genomic sequences surrounding the SNPs (described in Table 3), or identical to all or portion of the complementary strands of the genomic sequences surrounding the SNPs (described in Table 3). For example the sequence may be 100% identical or greater than about 99%, about 98%, about 97%, about 96%, about 95%, or about 90% with all or a portion of the sequences described in Table 3 and the SEQUENCE LISTING. Alternatively, the isolated nucleic acid sequence maybe 100% , greater than about 99%, greater than about 98%, greater than about 97%, greater than about 96%, greater than about 95%, or greater than about 90% identical with a contiguous segment of about 17 or more nucleotides, about 25 or more, about 50 or more, or about 100 or more nucleotides. Other embodiments of the invention provide isolated nucleic acid molecules comprising about 100 or more contiguous nucleotides which are at least about 90 percent identical with any of SEQ ID NOs: 1-19. In preferred aspects of these embodiments of the invention, the isolated nucleic acid molecules comprise the polymorphic site for one or more SNPs selected from the group of SNPs described in Table 3. Other embodiments of the invention provide for diagnostic kits or other diagnostic devices for determining which allele of a SNP is present in a sample; wherein the SNP(s) are selected from the group of SNPs described in Table 3. In various aspects of these embodiments of the invention, the kit or device provides reagents/instruments to facilitate a determination as to whether a nucleic acid corresponding to a given SNP is present. Such kit or device may further facilitate a determination as to which allele of the SNP is present. In certain aspects of these embodiments of the invention, the kit or device comprises at least one nucleic acid oligonucleotide suitable for DNA amplification (e.g. through polymerase chain reaction). In other aspects of the invention the kit or device comprises a purified nucleic acid fragment capable of specifically hybridizing, under stringent conditions, with at least one allele of at least one SNP described in Table 3.

In particularly preferred aspects of these embodiments of the invention, the kit or device comprises at least one nucleic acid array (e.g. DNA micro-arrays) capable of determining which allele of one or more of the SNPs described in Table 3 is present in a sample. Preferred aspects of these embodiments of the invention provide DNA microarrays capable of simultaneously determining which allele is present in a sample for at least about 10 or more SNPs. Preferably, the DNA micro-array is capable of determining which SNP allele is present in a sample for at least about 25 or more, about 50 or more, about 100 or more, about 200 or more, about 500 or more, or about 1000 or more SNPs, wherein at least one of these SNPs is described in Table 3 and sequence listing. Methods for making such arrays are known to those skilled in the art and such arrays are commercially available (e.g. from Affymetrix, Santa Clara, California). Other embodiments of the present invention provide methods for identifying, within a plurality of animals, an association between one or more of the SNPs described in Table 3 and at least one phenotypic trait. In various aspects of these embodiments of the invention, the method comprises: (a) measuring one or more phenotypic traits in a plurality of animals; (b) determining the genotype for at least one SNP for a plurality of animals, wherein at least one SNP genotype determined is selected from the group of SNPs described in Table 3; and (c) statistically correlating the presence of at least one phenotypic trait with the presence of an allele of at least one SNP selected from the group of SNPs described in Table 3; wherein the presence of different alleles for that SNP is associated with different phenotypic attributes or with distinguishable phenotypic variation. That is, where the presence of different alleles, for at least one SNP, is associated with a statistically distinct phenotypic difference in the animals possessing them. The distinct phenotype may be detectable either between individual animals or it may be detectable when pluralities of the animals having different genotypes are compared as groups. Additional embodiments of the invention provide for genetic markers that are in allelic association with one or more of the SNPs described in Table 3. Markers provided as part of this embodiment of the invention may be identified by any suitable means known to those of ordinary skill in the art. A marker falls within this embodiment of the invention if it is determined to be in allelic association with one or more of the SNPs described in Table 3 as defined by Equation 1, supra, where r² is greater than about 0.2, greater than about 0.5, greater than about 0.7, or greater than about 0.9. In preferred aspects of these embodiments of the invention the markers are in linkage disequilibrium with one or more of the SNPs described in Table 3.

Genetic markers that are in allelic association with any of the SNPs described in Table 3 may be identified by any suitable means known to those skilled in the art. For example, a genomic library may be screened using a probe specific for any of the sequences of the SNPs described in Table 3. In this way clones comprising at least a portion of that sequence can be identified and then up to 300 kilobases of 3' and/or 5' flanking chromosomal sequence can be determined. By this means, genetic markers in allelic association with the SNPs described in Table 3 will be identified.

Other embodiments of the present invention provide methods for identifying genes that may be associated with phenotypic variation. According to various aspects of these embodiments, the chromosomal location of a SNP associated with a particular phenotypic variation can be determined by means well known to those skilled in the art. Once the chromosomal location is determined, genes suspected to be involved with determination of the phenotype can be analyzed. Such genes may be identified by sequencing adjacent portions of the chromosome or by comparison with analogous sections of the human genetic map (or known genetic maps for other species). An early example of the existence of clusters of conserved genes is reviewed in Womack (1987), where genes mapping to the same chromosome in one species were observed to map to the same chromosome in other, closely related, species. As mapping resolution improved, reports of the conservation of gene structure and order within conserved chromosomal regions were published (see, for example, Grosz et al, 1992). More recently, large scale radiation hybrid mapping and BAC sequence have yielded chromosome-scale comparative mapping predictions between human and bovine genomes (Everts-van der Wind et al., 2005), between human and porcine genomes (Yasue et al., 2006) and among vertebrate genomes (Demars et al., 2006). Other embodiments of the invention provide methods for identifying causal mutations that underlie one or more quantitative trait loci (QTL). Various aspects of these embodiments of the invention provide for the identification of QTL that are in allelic association with one or more of the SNPs described in Table 3. Once these SNPs are identified, it is within the ability of skilled artisans to identify mutations located proximal to such SNP(s). Further, one skilled in the art can identify genes located proximate to the identified SNP(s) and evaluate these genes to select those likely to contain the causal mutation. Once identified, these genes and the surrounding sequence can be analyzed for the presence of mutations, in order to identify the causal mutation.

In still further embodiments of the invention, a DNA sample is obtained from a pig and it is used as template for amplification of the region containing the polymorphism(s) of interest, using any known techniques such as, for example, polymerase chain reaction (PCR). The DNA sample can be obtained from any source, such as blood, tissue, semen, etc. Examples of the PCR technique useful with embodiments of the present invention are described in U.S. Patent No. 4,683,195 issued JuI. 28, 1987 to Mullis et al, U.S. Patent No. 4,683,202 issued JuI. 28, 1987 to Mullis, U.S. Patent No. 4,800,159 issued Jan. 24, 1989 to Mullis et al, U.S. Patent No. 4,889,818 issued Dec. 26, 1989 to Gelfand et al, and U.S. Patent No. 4,902,624 issued Feb. 20, 1990 to Clumbus et al, all of which are incorporated herein by reference.

In various embodiments of the invention, specific primers are designed to amplify a DNA region of interest around a desired area of polymorphism, using PCR technology. Suitable DNA primers can be first optimized by gradient PCR reactions to determine optimal annealing temperature for a set of primers, by running and visualizing the PCR products on 2% agarose gel. By way of example, a standard PCR reaction can contain 5μL of JUMPSTART™ READYMIX™ Taq DNA polymerase, 1.5 to 2.5 mM MgCl (Sigma), 3μL dH2θ, lμL 10 mM forward and reverse primers (IDT), and lμL of template DNA (20ng/μL). The termocycler program for the gradient PCR can consist of the following cycles: (1) 95 ⁰C for 15 minutes, (2) 94 ⁰C for 45 seconds, (3) gradient temperature for 45 seconds (which can be a temperature range of from 45 ⁰C to 56 ⁰C, from 55 ⁰C to 66 ⁰C, or from 62 ⁰C to 73 ⁰C, depending on primer melting temperature), (4) 72⁰C for 45 seconds, (5) repeat steps (2) to (4) 34 times, (6) 72 ⁰C for 10 minutes, and (7) hold at 4 ⁰C forever. Once a optimal annealing temperature is identified, a regular PCR amplification protocol can consist of the following cycles: (1) 95°C for 15 minutes, (2) 94°C for 45 seconds, (3) optimal annealing temperature for 45 seconds, (4) 72 ⁰C for 60 seconds, (5) repeat steps (2) to (4) 35 times, (6) 72 ⁰C for 10 minutes, and (7) hold at 4 ⁰C forever. There are several ways the PCR products can be processed and sequenced. As an example, PCR products can be purified using Magic PCR Preps (Promega; by following supplier's specifications) and then sequenced with the AmpliTaq Cycle Sequencing Kit (Perkin Elmer) by manufacturer specifications.

Visualization of sequences, with SEQUENCHER™ (Gene Code) for example, allows for determination of the allele variants carried by the individual. Genetic marker association for growth and meat quality traits is identified by determining the allele variants carried by a number of individuals (preferably, at least about 300) with phenotypic data (such as for example, growth and meat quality traits) and identifying an association of an allelic variant of a polymorphism with the trait.

EXAMPLES The following examples are included to demonstrate general embodiments of the invention and are not intended to be limiting. It will be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art will, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and a like or similar result will be obtained without departing from the invention. All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied without departing from the concept and scope of the invention. Example 1 : Determining Associations between Genetic Markers and Phenotypic Traits

Simultaneous discovery and fine-mapping on a genome-wide basis of genes underlying quantitative traits (Quantitative Trait Loci: QTL) requires genetic markers densely covering the entire genome. As described in this example, a whole-genome, dense-coverage marker map was constructed from microsatellite and single nucleotide polymorphism (SNP) markers with previous estimates of location in the pig genome, and from SNP markers with putative locations in the pig genome based on homology with human sequences and the human/pig comparative map. A new linkage-mapping software package was developed, as an extension of the CRIMAP software (Green et al., Washington University School of Medicine, St. Louis, MO, 1990), to allow more efficient mapping of densely-spaced markers genome- wide in a pedigreed livestock population (Liu and Grosz Abstract CO 14; Grapes et al. Abstract W244; 2006 Proceedings of the XIV Plant and Animal Genome Conference, www.intl-pag.org). The new linkage mapping tools build on the basic mapping principles programmed in CRIMAP to improve efficiency through partitioning of large pedigrees, automation of chromosomal assignment and two-point linkage analysis, and merging of sub- maps into complete chromosomes. The resulting whole-genome discovery map (WGDM) included -5,926 markers and a map length of 2,373.6 cM for an average map density of 2.41 markers/cM. The average gap between markers was 0.44 cM and the largest gap was 11.1 cM. This map provided the basis for whole-genome discovery and fine-mapping of QTL contributing to variation in pig growth, efficiency, carcass composition and meat quality. Discovery and Mapping Populations

Systems for discovery and mapping populations can take many forms. The most effective strategies for determining population- wide marker/QTL associations include a large and genetically diverse sample of individuals with phenotypic measurements of interest collected in a design that allows accounting for non-genetic effects and includes information regarding the pedigree of the individuals measured. In the present example, three populations were used to discover and map QTL: a population derived from the Pietrain breed, a population derived from the Duroc breed, and a composite of the other two populations produced by crossing followed by several generations of inter se mating. DNA samples were collected from approximately 1,000 to 2,000 progeny per population; representing multiple sire and grandsire families. DNA samples were also collected from the sire of each progeny, and in some cases from additional members of the pedigree. The progeny sampled from these populations had been measured for several phenotypic traits including average daily gain in weight, ultrasonically-measured fat thickness and loin muscle area, fat and muscle depth at slaughter, pH and water-holding capacity of the meat, color of the meat, intra-muscular fat or marbling in the meat, and tenderness of the meat. DNA samples collected from the progeny and members of the pedigree were genotyped for approximately 4,600 SNP markers that are approximately evenly distributed across the WGDM and that were previously determined to be informative for mapping purposes in these populations. For each animal, and each SNP marker, a genotype was generated reflecting the alleles present on the chromosome pair at that locus (e.g. , AA, AB or BB) and is used in subsequent marker/trait association analyses. Phenotypic Analyses

The phenotypic measurements on individual animals for growth, body composition and meat quality were subjected to standard statistical procedures to remove erroneous and biologically impossible data, and to account for non-genetic sources of variation. For example, in a first step, upper and lower biological limits can be determined for each trait by examining the upper and lower 2.5% and excluding data that are known to exceed the range of biological possibilities for the trait. In a second step, a general linear statistical model can be used for each trait that includes adjustment for known potential non-genetic effects. For example, all traits can be adjusted for the on- farm contemporary group to which the animal belonged (season-year- farm-building) and the sex of the animal. Measurements of periodic growth rate can be adjusted for the beginning age of the animal and the number of days measured. Body composition measurements (e.g., lean percentage) can be adjusted for the weight of the animal at measurement. Data collected after slaughter are typically adjusted for the effect of day of slaughter. Meat quality data can be adjusted for other relevant information (e.g., extended time to reach the cooler or excessive skinning). After adjustments for these non-genetic factors, the data can again be examined for outliers and values with a residual standard deviation of 4.0 or more excluded from analyses. QTL Discovery and Mapping Analyses

Mapping the location of QTL through associations between marker genotypes and phenotypic traits (pre-adjusted for non-genetic effects) can be approached in several ways, including simple regressions of each trait on the genotype for each SNP marker (e.g., trait regressed on number of "A" alleles: 0, 1 , or 2) or analyses of families within the population to detect linkage between markers and QTL . The marker/trait associations most useful as animal selection tools are those of markers tightly linked to a QTL and based on marker/QTL allele configurations that are present in most individuals across the population.

These types of population- wide results can be obtained from linkage disequilibrium (LD) mapping. When a mutation that can cause a trait difference first occurs, that mutation is in complete LD with all other alleles on that chromosome. Over time recombination breaks down the LD, but there is a relatively small frequency of recombination between the QTL and loci in very close proximity. Hence, individuals that share an allele of the QTL transmitted from some common ancestor (Identical By Decent: IBD) are likely to share alleles of closely linked markers. By using ordered marker genotypes along the chromosome (marker haplotypes with known parental origin) to determine the probabilities at each locus that individuals with phenotypic data are IBD, marker alleles in population- wide linkage with valuable QTL alleles can be identified.

In the present example, LD mapping was performed in the aforementioned discovery population using statistical analyses that require knowledge of ordered genotypes. Ordered genotypes of an individual can be inferred partially or with certainty conditional on pedigree information and observed genotype data (Du and Hoeschele, 2000). With simple pedigrees such as a nuclear family and small numbers of linked markers, exact calculation of the probabilities of linkage phases is achievable, by evaluating all possible genotype configurations. The exact calculation quickly becomes infeasible as the size and complexity of the pedigree and number of linked markers increases. For example, there are totally 2^{k l} linkage phases when a parent has k linked heterozygous loci. In part due to this computational difficulty, most methods have focused on identifying the most probable linkage phase. Windig and Meuwissen (2004) provide a computationally efficiency method for phase construction. They start with a likely phase derived with a simple rule based method, calculate the parental origin of the two alleles at a marker, and perform a switch if the probability of the switch is greater than 0.5. The process is repeated until the probability of a switch is less than 0.5 for all linked markers. In the present example, probabilities of parental linkage phases for the entire set of linked loci were determined by choosing small subsets of markers (e.g. , 5 to 10) and considering all possible phases for these markers by calculating their probability conditional on the observed genotypes for all markers under evaluation. Only phases with a likelihood ratio greater than some pre-specified threshold are retained, and the iteration of the method over the entire marker set produces a collection of likely phases and their probabilities conditional on the observed data.

To determine associations between haplotypes probabilities and trait phenotypes, haplotypes of neighboring (and/or non-neighboring) markers across each chromosome were defined by setting the maximum length of a chromosomal interval and minimum and maximum number of markers to be included. Clearly, one needs to set similar parameters to form or define groups of marker loci for haplotype evaluation. The association between pre- adjusted trait phenotypes and haplotype was evaluated via a regression approach with the following model: Y_k = Ep₁[P(H₈₁O + P(H_dlk)] + e_k [Equation 2] where Y_k is the preadjusted phenotype of one of the traits described above for individual k, and e_k is the residual; P(H_slk) and P(H_dlk) are the probability of paternal and maternal haplotype of individual k being haplotype i; P(H_slk, (H_dlk)is the probability of individual k having paternal haplotype i and maternal haplotype j; all β are corresponding regression coefficients.

Least-squares methods were used to estimate the effect of a haplotype on a phenotypic trait and the regular F-test used to test the significance of the effect. Permutation tests were performed based on phenotype permutation (10,000 to 50,000) within the whole sample for Type I error rate (p value) estimation.

Example 2: Use of single nucleotide polymorphisms to improve offspring traits To improve the average genetic merit of a population for a chosen trait, one or more of the markers with significant association to that trait can be used in selection of breeding animals. In the case of each discovered locus, use of animals possessing a marker allele (or a haplotype of multiple marker alleles) in population- wide LD with a favorable allele will increase the breeding value of animals used in breeding, increase the frequency of that allele in the population over time and thereby increase the average genetic merit of the population for that trait. This increased genetic merit can be disseminated to commercial populations for full realization of value.

For example, a closed genetic nucleus (GN) population of pigs may be maintained to produce boars for use in commercial production of market hogs. A GN herd of 200 sows would be expected to produce approximately 4,000 offspring per year (2,000 boar offspring per year), typically according to a weekly breeding and farrowing schedule. A commercial sow herd of 300,000 would be expected to produce more than 6,000,000 market pigs per year and might maintain a boar stud with inventory of 1,500 boars to service the 300,000 sows. Hence the GN herd of 200 sows could support boar replacements for the 300,000 sows of commercial production by shipping 500 boars every six months to the commercial boar stud (assumes inventory in the commercial boar stud is turned over every 1.5 years and the top half of boar candidates from the GN are selected for commercial breeding).

The first step in using a SNP for estimation of breeding value and selection in the GN is collection of DNA from all offspring that will be candidates for selection as breeders in the GN or as breeders in other commercial populations (in the present example, the 4,000 offspring produced in the GN each year). One method is to capture shortly after farrowing a small bit of tail tissue from each piglet into a labeled (bar-coded) tube. The DNA extracted from this tissue can be used to assay an essentially unlimited number of SNP markers and the results can be included in selection decisions before the animal reaches breeding age.

One method for incorporating into selection decisions the markers (or marker haplotypes) determined to be in population- wide LD with valuable alleles (see Example 1) is based on classical quantitative genetics and selection index theory (Falconer and Mackay, 1996; Dekkers and Chakraborty, 2001 ). To estimate the effect of the marker in the population targeted for selection, a random sample of animals with phenotypic measurements for the trait of interest can be analyzed with a mixed animal model with the marker fitted as a fixed effect or as a covariate (regression of phenotype on number of allele copies). Results from either method of fitting marker effects can be used to derive the allele substitution effects, and in turn the breeding value of the marker:

(Xi = q[a + d(q - p)] [Equation 3]

(X₂ = -p[a + d(q - p)] [Equation 4]

(X = a + d(q - p) [Equation 5]

gAiAi = 2((X₁) [Equation 6]

g_AiA2 = (⁽X₁) + (⁽X₂) [Equation 7]

g_A2A2 = 2((X₂) [Equation 8]

where (Xi and (X₂ are the average effects of alleles 1 and 2, respectively; (X is the average effect of allele substitution; p and q are the frequencies in the population of alleles 1 and 2, respectively; a and d are additive and dominance effects, respectively; §AIAI, §AIA2 and

§A2A2 are the (marker) breeding values for animals with marker genotypes AlAl, A1A2 and

A2A2, respectively. The total trait breeding value for an animal is the sum of breeding values for each marker (or haplotype) considered and the residual polygenic breeding value: EBV_1J = Σ g_j + lX [Equation 9]

where EB Vy, is the Estimated Trait Breeding Value for the 1^th animal, Σ g, is the marker breeding value summed from j = 1 to n where n is the total number of markers (haplotypes) under consideration, and U₁ is the polygenic breeding value for the 1^th animal after fitting the marker genotype(s). These methods can readily be extended to estimate breeding values for selection candidates for multiple traits, the breeding value for each trait including information from multiple markers (haplotypes), all within the context of selection index theory and specific breeding objectives that set the relative importance of each trait. Other methods also exist for optimizing marker information in estimation of breeding values for multiple traits, including random models that account for recombination between markers and QTL (e.g. , Fernando and Grossman, 1989), and the potential inclusion of all discovered marker information in whole- genome selection (Meuwissen et al., Genetics 2001). Through any of these methods, the markers reported herein that have been determined to be in population- wide LD with valuable alleles may be used to provide greater accuracy of selection, greater rate of genetic improvement, and greater value accumulation in the pork production chain. Example 3 : Identification of SNPs A nucleic acid sequence contains a SNP of the present invention if it comprises at least about 20 consecutive nucleotides that include and/or are adjacent to a polymorphism described in Table 3 and the Sequence Listing. Alternatively, a SNP of the present invention may be identified by a shorter stretch of consecutive nucleotides which include or are adjacent to a polymorphism which is described in Table 3 and the Sequence Listing in instances where the shorter sequence of consecutive nucleotides is unique in the pig genome. A SNP site is usually characterized by the consensus sequence in which the polymorphic site is contained, the position of the polymorphic site, and the various alleles at the polymorphic site. "Consensus sequence" means a DNA sequence constructed as the consensus at each nucleotide position of a cluster of aligned sequences. Such clusters are often used to identify SNP and Indel (insertion/deletion) polymorphisms in alleles at a locus. Consensus sequence can be based on either strand of DNA at the locus, and states the nucleotide base of either one of each SNP allele in the locus and the nucleotide bases of all Indels in the locus, or both SNP alleles using degenerate code (IUPAC code: M for A or C; R for A or G; W for A or T; S for C or G; Y for C or T; K for G or T; V for A or C or G; H for A or C or T; D for A or G or T; B for C or G or T; N for A or C or G or T; Additional code used in the present invention includes I for "-"or A; O for "-" or C; E for "-" or G; L for "-" or T; where "-" means a deletion). Thus, although a consensus sequence may not be a copy of an actual DNA sequence, a consensus sequence is useful for precisely designing primers and probes for actual polymorphisms in the locus. Such SNPs have a nucleic acid sequence having at least about 90% sequence identity, more preferably at least about 95% or even more preferably for some alleles at least about 98% and in many cases at least about 99% sequence identity, to the sequence of the same number of nucleotides in either strand of a segment of pig DNA which includes or is adjacent to the polymorphism. The nucleotide sequence of one strand of such a segment of pig DNA may be found in a sequence in the group consisting of SEQ ID NO:1 through SEQ ID NO:23. It is understood by the very nature of polymorphisms that, for at least some alleles, there will be no identity at the polymorphic site itself. Thus, sequence identity can be determined for sequence that is exclusive of the polymorphism sequence. The polymorphisms in each locus are described in Table 3.

Shown below are examples of public porcine SNPs that match each other: SNP ssl6337002 (SEQ IDNO:20) was determined to be the same as ssl6337593 (SEQ IDNO:21) because 41 bases (with the polymorphic site at the middle) from each sequence match one another perfectly (match length=41, identity=100%). ss 16337002: gcaacctacaccacagctcayggcaaggcccaatccttaac ss 16337593: glclalalclcltlalclalclclalclalglcltlclalylglglclalalglglclclclalaltlclcltltlalalcl

SNP ssl6337555 (SEQ ID NO:22) was determined to be the same as ssl6338279 (SEQ ID NO:23) because 41 bases (with the polymorphic site at the middle) from each sequence match one another at all bases except for one base (match length=41, identity=97%). ssl6337555: gaaccatgaagttgcgggttsgatccctggcctcgmtcagt ss 16338279: glalalclclaltlglalrlgltltlglclglglgltltlslglaltlclclcltlglglclcltlclglmltlclalgltl

Example 4: Quantification of the animal's body and/or carcass composition Quantifying an animal's body and/or carcass composition can be accomplished by measuring a number of phenotypes including, but not limited to: average backfat thickness {e.g. in inches or centimeters) measured on the carcass or on the live animal using ultrasound; loin muscle (eye) area {e.g. in²) measured on the carcass or on the live animal using ultrasound; fat depth, loin depth (millimeters) and carcass weight (pounds) measured on-line after slaughter using industry standard equipment {e.g., Fat-0-Meater); predicted lean percentage (%) calculated from backfat thickness, loin muscle depth or area, and body or carcass weight; carcass length {e.g. in inches); National Pork Producers Council (NPPC) marbling quality score {i.e., 1-5); Intramuscular fat content of the loin (%); primal cuts (loin, shoulder, belly, etc) as a percent of carcass weight (%); carcass yield as a percentage of live weight (%).

Example 5 : Quantification of the animal's growth

Quantifying an animal's growth can be accomplished by measuring phenotypes including, but not limited to: average daily weight gain {e.g. lbs/day); average daily feed intake (lbs/day); feed conversion ratio (lbs feed per Ib gain); growth from birth to any desired age (Ib); and growth during a specified test period (e.g. from 21 to 165 days of age). Example 6: Quantification of Meat color

Quantifying meat color can be accomplished by measuring phenotypes including, but not limited to: Hunter colorimeter scores; change in Hunter colorimeter score over a 24 hour period; Japanese color score (1-5); and NPPC color quality score (1-5). Example 7: Quantification of meat quality

Quantifying meat quality can be accomplished by measuring phenotypes including, but not limited to: Drip loss (%); purge loss (%); pH of loin or ham; moisture content in the loin (%); NPPC firmness quality score (1-5); Werner-Bratzler shear force (kg); and cooking loss (%). Example 8: Identification of Protein-coding Genes and Markers with Associated Traits

QTL regions for meat quality and performance traits were selected for candidate gene

SNP discovery. A human-swine comparative map was used to estimate the correspondent region in the human genome. Ensemble (www.ensembl.org/index .html) was then used to identify genes in the genomic region of interest, which were then further filtered by biological meaning, i.e., candidate genes for SNP analysis were selected by their function and probable involvement in the trait affected by the QTL. The NCBI (www.ncbi.nlm.nih.gov/) nucleotide and protein databases were searched for availability of public information on the swine candidate genes sequences. If mRNA and genomic sequence were available, primers were designed in the intronic regions in order to amplify the gene exons and regulatory regions

(promoter).

If only cDNA sequence was available for swine, a database was used to compare genomic sequence with the cDNA sequence to obtain genomic sequence. If no swine sequence was available, the human cDNA sequence was blasted against a swine cDNA database. BAC (Bacterial Artificial Chromosome) clones from a swine BAC library were also sequenced to obtain genomic sequence of genes of interest, using standard DNA extraction and sequencing techniques. Once genomic (flanking) sequences for the genes of interest were available, primers were designed in the flanking regions in order to amplify the gene exons and regulatory regions.

A total of 24 animals, 12 Pietrain and 12 Duroc, were used as a discovery panel to identify novel genetic markers (SNPs) by sequencing the candidate genes and comparing forward and reverse strand sequences between all 24 samples. Standard protocols for DNA extraction were used to extract DNA. Standard laboratory PCR was used to amplify DNA fragments containing the coding region and regulatory regions of the genes prior to sequencing. Standard direct PCR product sequencing was conducted and resolved on an ABI 3730x1 Automated Sequencer (Applied Biosystems, Foster City, CA).

Selected SNPs were then genotyped (TAQMAN™) in a larger panel of animals (at least 300), and association analyses for the candidate genes were performed using two widely used approaches: the allelic model (which estimates average allele substitution effects for each locus) and the genotype model (which models the genotypic effects). Association analyses for the candidate genes were performed using a series of fixed and mixed models with the general structure given by: y = X_/# + Xgg + Zv + e [Equation 10] where y is a vector of phenotypic measures; β is a vector of fixed nongenetic effects including off-test age, contemporary group and slaughter age (for carcass traits); g is a vector of fixed SNP effects; v = a vector of litter effects assuming v ~ n(0,I (T_c ²), where I is the identity matrix and G_c ² is the common environmental variance for each litter; e is a vector of random errors assuming e ~ n(0,I G_e ²) and G_e ² is the error variance; X^, X_g and Z are the corresponding design variances. The SNP effects were estimated as average allele substitution effects for each locus or genotypic effects. The allelic model consisted of a regression approach that assumes a pure additive linear relationship between the depended and independent variables. The genotype model fitted the 3 genotypic effects for each locus, and the heterozygous represented the interaction between alleles at that particular locus. For fixed and random models, the fixed effects of SNPs, off-test age, contemporary group and slaughter age (for carcass traits) were included, and for the random models the common environment of each litter was added.

Table 1 : The following table lists protein-coding genes along with their correlated NCBI GeneID numbers.

Example 9: Identification ofmicroRNA Genes and Markers with Associated Traits

The swine miRNA stemloop sequences from the miRBase were compared to the Monsanto sequence database to obtain genomic flanking sequences. PCR primer pairs were designed around the flanking region to amplify the surrounding and the stemloop sequences.

A total of 24 animals, 12 Pietrain and 12 Duroc, were used as a discovery panel to identify novel genetic markers (SNPs) by sequencing the candidate genes and comparing forward and reverse strand sequences between all 24 samples. Standard protocols for DNA extraction were used to extract the samples DNA. Standard laboratory PCR was used to amplify DNA fragments containing the coding region and regulatory regions of the genes prior to sequencing. Standard direct PCR product sequencing was conducted and resolved on an ABI 3730x1 Automated Sequencer (Applied Biosystems, Foster City, CA).

Selected SNPs were then genotyped (TAQMAN™) a larger panel of animals (at least 300), and association analyses for the candidate genes were performed using two widely used approaches: the allelic model (which estimates average allele substitution effects for each locus) and the genotype model (which models the genotypic effects).

Association analyses for the candidate genes were performed using a series of fixed and mixed models with the general structure given by: y = X_/# + Xgg + Zv + e [Equation 11] where y is a vector of phenotypic measures; β is a vector of fixed nongenetic effects including off-test age, contemporary group and slaughter age (for carcass traits); g is a vector of fixed

SNP effects; v = a vector of litter effects assuming v ~ n(0,I (T_c ²), where I is the identity matrix and G_c ² is the common environmental variance for each litter; e is a vector of random errors assuming e ~ n(0,I G_e ²) and G_e ² is the error variance; X^, X_g and Z are the corresponding design variances. The SNP effects were estimated as average allele substitution effects for each locus or genotypic effects. The allelic model consisted of a regression approach that assumes a pure additive linear relationship between the depended and independent variables. The genotype model fitted the three genotypic effects for each locus, and the heterozygous represented the interaction between alleles at that particular locus. For fixed and random models, the fixed effects of SNPs, off-test age, contemporary group and slaughter age (for carcass traits) were included, and for the random models the common environment of each litter was added.

Table 2: The following table lists miRNA stem- loop sequences along with their correlated MiRbase accession numbers (www.microrna.sanger.ac.uk).

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DESCRIPTION OF TABLE 3

Table 3 : provides a list of phenotypic traits and the assigned identification numbers of SNPs found to be associated with each trait. The left column provides a counter to allow easier reading of the table. The "Trait" column lists the following traits: "CL" (meat color), "CP" (body composition); "GR" (growth rate); and "Q" (meat quality). Table 3 also provides the SEQ ID NO of the sequence associated with each of the SNPs listed. The "SNP POSITION" column provides the position (nucleotide number) of the SNP within the associated sequence (SEQ ID NO) and the "SNP ALLELE 1 " and "SNP ALLELE 2" columns provide the identity of the two nucleotides that occur most frequently at the SNP POSITION within the population analyzed.

TABLE 3

The principles, preferred embodiments and modes of operation of the present invention have been described in the foregoing specification. The invention which is intended to be protected herein should not, however, be construed as limited to the particular forms disclosed, as these are to be regarded as illustrative rather than restrictive. Variations and changes may be made by those skilled in the art without departing from the spirit of the present invention. Accordingly, the foregoing best mode of carrying out the invention should be considered exemplary in nature and not as limiting to the scope and spirit of the invention as set forth in the appended claims.

Claims

What is claimed is:

1. A method of evaluating an animal's genotype at one or more genomic locus or loci, the method comprising: determining the animal's genotype for at least one locus, said locus comprising a single nucleotide polymorphism (SNP) having at least two allelic variants, and correlating an identified allele with a phenotype selected from the group consisting of meat color, body composition, growth rate, and meat quality; wherein at least one SNP is selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

2. The method of claim 1 , wherein the animal's genotype is evaluated at at least about 10 or more positions that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

3. The method of claim 1 , wherein the animal's genotype is evaluated at at least about 50 or more positions that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

4. The method of claim 1 , wherein the animal's genotype is evaluated at at least about 100 or more positions that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

5. The method of claim 1 , wherein the animal's genotype is evaluated at at least about 100 or more positions that contain SNPs, including at least two SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

6. A method for allocating animals for use, comprising: a) determining at least one animal's genotype at one or more locus or loci; wherein the at least one locus or loci contains a single nucleotide polymorphism (SNP) having at least two allelic variants; and wherein at least one SNP is selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc- miR23a, and Ssc-miR23a_l; b) analyzing the determined genotype of the at least one animal at one or more SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l, to determine which allelic variant is present; and c) allocating the at least one animal for use according to its determined genotype.

7. The method of claim 6, wherein at least one animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

8. The method of claim 6, wherein at least one animal's genotype is evaluated at at least about 50 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

9. The method of claim 6, wherein at least one animal's genotype is evaluated at at least about 100 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc- miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

10. The method of claim 6, wherein at least one animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least two SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

11. A method for selecting a potential parent animal for breeding, comprising: a) determining at least one potential parent animal's genotype at one or more genomic locus; wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc- miR184_l, Ssc-miR23a, and Ssc-miR23a_l; b) analyzing the genotype of the at least one potential parent animal for one or more SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l to determine which allele is present; c) correlating the determined allele with a phenotype selected from the group consisting of meat color, body composition, growth rate, and meat quality; and d) allocating the at least one potential parent animal for breeding based on its genotype.

12. The method of claim 11, wherein the at least one potential parent animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6,

GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

13. The method of claim 11, wherein the at least one potential parent animal's genotype is evaluated at at least about 50 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

14. The method of claim 11, wherein the at least one potential parent animal's genotype is evaluated at at least about 100 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

15. The method of claim 11, wherein the at least one potential parent animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least two SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

16. A method of producing progeny animals comprising: a) identifying at least one potential parent animal that has been allocating for breeding in accordance with the method of claim 11 ; b) producing progeny from the at least one potential parent animal through a process comprising a member of the group consisting of: i) natural breeding; ii) artificial insemination; iii) in vitro fertilization; and ii) collecting semen/spermatozoa or at least one ovum from the animal and contacting it, respectively, with ovum/ova or semen/spermatozoa from a second animal to produce a conceptus by any means.

17. The method of claim 16, comprising producing progeny through natural breeding.

18. The method of claim 16, comprising producing offspring through a member of the group consisting of artificial insemination, embryo transfer, and in vitro fertilization.

19. The method of claim 16, wherein the at least one potential parent animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

20. The method of claim 16, wherein the at least one potential parent animal's genotype is evaluated at at least about 50 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

21. The method of claim 16, wherein the at least one potential parent animal's genotype is evaluated at at least about 100 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

22. The method of claim 16, wherein the at least one potential parent animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least two SNPs selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

23. A method of identifying at least one phenotypic trait associated with at least one quantitative trait locus (QTL), the method comprising: a) measuring one or more phenotypic traits in a plurality of animals; b) determining the genotype of the plurality of animals for at least one locus, wherein the locus comprises at least one a single nucleotide polymorphism (SNP) having at least two variants and wherein the SNP is selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l; and c) statistically correlating the association of at least one phenotypic trait with the presence of an allele of at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc- miR23a, and Ssc-miR23a_l; wherein the presence of a different allele for the at least one SNP has a different association for the phenotypic trait.

24. A method of identifying a genetic marker in allelic association with at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l, the method comprising: a) identifying a genetic marker B 1 suspected of being in allelic association with a marker Al selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH_7,SLC2A4,TBC1D7,TBC1D7_1,ALOX15,ALOX15_1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc- miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l; b) determining whether Al and Bl are in allelic association, wherein allelic association exists if r² > 0.2 for Equation 1 for a population sample of at least about 100 animals and wherein Equation 1 is: r² = rf(AiBi) - f(Ai)f(Bi)l² [Equation 1] fCAoα-fCAoxfCBoα-fCBO) and wherein Ai represents an allele of a SNP described in Table 3; Bi represents a genetic masker at another locus; f( AiBi) denotes frequency of having both Ai and Bi; f(Ai) is the frequency of Ai in the population; and f(Bi) is the frequency of Bi in a population.

25. The method of claim 24, wherein the genetic marker Bi is a SNP.

26. The method of claim 24, wherein the genetic marker identified is in linkage disequilibrium with at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, AL0X15, AL0X15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

27. The method of claim 24, wherein Bi is a causal mutation underlying a quantitative trait locus.

28. The method of claim 26, wherein r² > 0.5.

29. The method of claim 26, wherein r² > 0.9.

30. A method of screening animals to identify those that have a genetic predisposition related to a predetermined phenotypic trait, the method comprising: a) identifying a desired phenotypic trait; b) obtaining a sample of genomic DNA from an animal; c) assaying for the presence of a single nucleotide polymorphism (SNP) in the sample; wherein said polymorphism is located within a gene selected from the group consisting of GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, AQP7, Ssc-miR15b, Ssc- miR27a, Ssc-miRl 84, and Ssc-miR23a, and wherein said phenotypic trait is selected from the group consisting of meat color, body composition, growth rate, and meat quality and is associated with the gene.

31. The method of claim 30, wherein said gene is selected from the group consisting of: Ssc-miRl 5b, Ssc-miR27a, Ssc-miRl 84, Ssc-miR23a, GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, and AQP7.

32. The method of claim 30, wherein said SNP is selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, Ssc-miR23a_l, SEQ IDNO:1, SEQ IDNO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO: 17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23..

33. The method of clam 30, wherein at least one animal's genotype is evaluated at at least about 10 or more loci that contain SNPs.

34. The method of clam 30, wherein at least one animal's genotype is evaluated at at least about 25 or more loci that contain SNPs.

35. The method of clam 30, wherein at least one animal's genotype is evaluated at at least about 50 or more loci that contain SNPs.

36. The method of clam 30, wherein at least one animal's genotype is evaluated at at least about 100 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc- miR27a, Ssc-miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

37. The method of clam 30, wherein at least one animal's genotype is evaluated at at least about 10 or more loci that contain SNPs, including at least one SNP selected from the group consisting of GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l.

38. A method for selecting a potential parent animal for improvement of one or more traits selected from the group consisting of growth, meat color, meat composition, and meat quality, the method comprising: a) determining at least one potential parent animal's genotype at one or more genomic locus, wherein at least one locus contains a single nucleotide polymorphism (SNP) that has at least two allelic variants, and wherein at least one SNP is selected from the group consisting of: i) GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7,

TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, Ssc-miR23a_l, SEQ IDNO:1, SEQ IDNO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO: 17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23.; and ii) a SNP located in a gene selected from the group consisting of GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, AQP7, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, and Ssc-miR23a; b) analyzing the determined genotype of the at least one potential parent animal for one or more SNPs selected from the group consisting of: i) GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC 1D7,

TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc- miR184, Ssc-miR184_l, Ssc-miR23a, and Ssc-miR23a_l; and ii) a SNP located in a gene selected from the group consisting of GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, AQP7, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, and Ssc-miR23a; c) correlating the identified allelic variants with a phenotype selected from the group consisting of meat color, body composition, growth rate, and meat quality; and d) allocating at least one animal for breeding based on its genotype. 39. The method of claim 38, wherein the potential parent animal's genotype is evaluated at at least about 10 or more loci, including at least one locus that contains a SNP selected from: a) GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc- miR184_l, Ssc-miR23a, and Ssc-miR23a_l; and b) a SNP located in a gene selected from the group consisting of GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, AQP7, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, and Ssc- miR23a; 40. The method of claim 38, wherein the potential parent animal's genotype is evaluated at at least about 50 or more loci.

41. The method of claim 38, wherein the potential parent animal's genotype is evaluated at at least about 100 or more loci.

42. The method of claim 38, wherein the potential parent animal's genotype is evaluated at at least about 200 or more loci.

43. The method of claim 39, wherein the potential parent animal's genotype is evaluated at at least about 10 or more loci, including at least two loci that contain SNPs selected from the group consisting of: a. GHRH, GHRH 4, GHRH 5, GHRH 6, GHRH 7, SLC2A4, TBC1D7, TBC1D7 1, ALOX15, ALOX15 1, BMPRlB, BMPR1B 2, BMPR1B 4, BMPR1B 5, BMPR1B 6, BMPR1B 9, AQP7, AQP7 1, AQP7 3, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, Ssc- miR184_l, Ssc-miR23a, and Ssc-miR23a_l; and b. a SNP located in a gene selected from the group consisting of GHRH, SLC2A4, TBC1D7, ALOX15, BMPRlB, AQP7, Ssc-miR15b, Ssc-miR27a, Ssc-miR184, and Ssc- miR23a.

44. The method of any of claims 38 to 43 , wherein the method comprises whole- genome analysis.