WO2011118549A1

WO2011118549A1 - Vertnin gene that controls number of vertebrae in pigs, and use of same

Info

Publication number: WO2011118549A1
Application number: PCT/JP2011/056711
Authority: WO
Inventors: 智美川; 周史佐藤; 武司林; 崇粟田; 雅宏新居; 直樹森; 史雄谷; 静柏岡; 岳哉両角
Original assignee: 独立行政法人農業生物資源研究所
Priority date: 2010-03-23
Filing date: 2011-03-22
Publication date: 2011-09-29
Also published as: JP5717272B2; JP2011193825A

Abstract

Provided is a method for assessing the presence of a genotype that increases the number of vertebrae in pigs, which uses as an indicator the polymorphic marker on or in the proximity of the Vertnin (VRTN) gene on the 7th chromosome of pigs. The inventors successfully identified a novel Vertnin gene related to an increase in the number of vertebrae in pigs, on the seventh chromosome of pigs. The inventors also discovered that it is possible to assess the presence of a genotype that increases the number of vertebrae in pigs, by using a polymorphic marker on or in the proximity of said gene, thereby completing this invention.

Description

Vertnin gene that controls the number of vertebrae in pigs, and its use

The present invention relates to a method for determining the presence or absence of an inherited trait with increased vertebral number in pigs using as an index a polymorphic marker present on or near the Vertnin gene on chromosome 7 of pigs.

The pig is said to have been domesticated in several areas of the Eurasian continent, with wild boars as its ancestors. In Europe from the middle of the 19th century, pigs with good growth and physique were selected and bred, and the current commercial varieties were formed based on them.

The present inventors have been proceeding with the isolation of loci involved in economic traits for the purpose of improving pigs. Many of the economic traits such as meat quality and growth are quantitative traits, and the loci that govern them are called quantitative trait loci (QTL). Currently, there are about 1800 reports in about 110 articles on various QTLs in pigs (PigQTLdb, http://www.animalgenome.org/cgi-bin/QTLdb/SS/index). However, since quantitative traits are dominated by multiple loci and are also greatly influenced by environmental factors, accurate mapping of QTL is difficult, identifying the responsible gene, and polymorphisms that cause diversity It is very difficult to identify. In the QTL elucidated at the gene level in pigs, there are a PRKAG3 gene (non-patent document 1) involved in meat quality (glycogen content) and an IGF2 gene (non-patent document 2) involved in meat content.

The present inventors created a plurality of F2 experimental families and conducted QTL analysis on various economic traits such as growth, meat production, and meat quality (Non-Patent Documents 3 to 10). As a result, various QTLs were detected. Among them, QTLs related to the number of vertebrae shown by the sum of the number of thoracic vertebrae and the number of lumbar vertebrae (Fig. 1) were distributed in two genomic regions (first chromosome q It was detected at the end of the arm and the center of the chromosome 7 q arm, and its existence was judged to be probable (Table 2 (F2 experimental family and vertebral number QTL), FIG. 2).

[Table 2]

The two vertebra number QTLs have alleles that increase the number of vertebrae, and the effects are almost equal, and the average of the results of each family increased about 0.5 to 0.6 vertebrae per allele. In addition, the two QTLs worked independently of each other, and when all alleles were increased in vertebral number, the average number of vertebrae increased by about 2.3 (Table 3 (Effects of two QTLs on porcine vertebral number). ).

[Table 3]

The number of cervical vertebrae in pigs is 7 as in other mammals, but the number of thoracic vertebrae and lumbar vertebrae varies, with 13 to 16 thoracic vertebrae and 5 to 7 lumbar vertebrae (non-patent literature). 11). The total number of these (vertebral vertebrae) is 19 in the boar ancestor wild boar, but in the current meat variety, it is 20 to 23. In pigs only (Figure 1). Pigs were selected to grow in size to increase meat volume and improve fertility, and it is thought that the number of vertebrae increased in the process, and in fact, the increase in the number of vertebrae increased the body length on average by about 1.5 cm (Non-Patent Document 12).

In the analysis of the F2 experimental family so far, the vertebral number QTL in the q-arm end region of chromosome 1 has not been observed to increase in alleles of Asian native species such as Umeyama pig and Kinka pig, and Japanese wild boar. In addition, all the alleles of Western varieties such as Landrace, Large Yorkshire, Duroc, and Berkshire had an effect of increasing the number of vertebrae (Table 2, Table 4 (vertebral number QTL genotype)).

[Table 4]

Regarding the number of vertebrae on the first chromosome, QTL, a region of about 300 kb fixed by a western variety with an increased number of vertebrae was found, and the responsible gene NR6A1 located there was identified (Non-patent Document 13). In connection with this, a patent application was filed (Patent Document 1).

In the QTL at the center of chromosome 7 q vertebrae number QTL, some alleles derived from Western varieties used in F2 experimental families had an effect of increasing the number of vertebrae (Tables 2 and 4) (non-patented) Reference 14). In addition, using a large Yorkshire breed pig in Tokushima Prefecture, we conducted a half sibling analysis of the number of vertebrae QTLs on chromosome 7 of the pig so that individuals with heterozygous QTL were detected (Fig. 4) (non-patented) Reference 14). From these results, it was clarified that the number of vertebrae QTL on chromosome 7 is also diverse in Western varieties currently used for pork production.

The prior art document information related to the invention of the present application is shown below.

JP2006-101871

The present invention has been made in view of the above situation, and an object of the present invention is to provide a method for determining a pig having an increased vertebral number inheritance. More specifically, the present invention is to provide a method for determining the presence or absence of an inherited trait with increased vertebral number in pigs, using a polymorphism on or near the Vertnin (VRTN) gene on chromosome 7 of the pig as an index. And

In general, linkage disequilibrium analysis is used to identify the location of the causative gene from the range narrowed down by linkage analysis using F2 experimental family. Because livestock has a short generation interval and related and tabular values are recorded, a method of mapping common chromosomal regions derived from the same ancestor related to the difference in traits using the trait data of existing animals (identical by decent analysis) ; (IBD analysis) is commonly used. However, in quantitative traits, the relationship between traits and genotypes is not as great as qualitative traits such as genetic diseases, and it is difficult to elucidate responsible genes in IBD analysis using trait values, which is the responsibility of various QTLs. This is the cause of unidentified genes.

Therefore, the present inventors tried the IBD analysis using the QTL type determined not by the trait value but by the half sibling analysis. In this case, the QTL type and the genotype of the responsible gene are completely identical. A strain pig was used as an individual to determine the QTL type. This is derived from 10 males and 65 females, and after being constructed by 7-generation closed group breeding, it is maintained in 9 males and 35 females, and is expected to have a large number of chromosome recombination. The The individuals introduced at the start of creation are independent of each other and are genetically distantly related. In other words, both mapping by homologous chromosome region recombination and searching for a small common genetic region that exists between independent individual samples are expected.

Specifically, the present inventors determined the number of vertebrae QTL type in the sow of large Yorkshire breed pigs by semisidy analysis, and matched the QTL type using microsatellite markers arranged at high density. A genomic region having a haplotype was searched. In addition, in the vicinity of the found region, the genomic region having a haplotype that matches the QTL type was further narrowed down using F2 experimental parental pigs including other breeds that had previously been determined to have the QTL type. As a result, a novel gene VRTN that reaches the region of about 45 kb and controls the number of vertebrae located there was isolated.

In the 45-kb region containing the VRTN gene, a polymorphism search was performed using large Yorkshire breed pigs. As a result, 42 polymorphic sites corresponding to the QTL type were revealed. There are two haplotypes composed of these polymorphisms in this large Yorkshire breed pig, and these two haplotypes are also analyzed in haplotype analysis using field samples (Landrace, Large Yorkshire, and Duroc hybrids). Was a major haplotype.

As a result of the analysis of VRTN gene expression in heterozygous pig embryos, the wild type allele was expressed in the limited period from 8.5 to 10 days after mating, whereas the allele with increased vertebral number Expression was confirmed from day 8 to day 14. From these results, it is determined that the VRTN increased vertebral number allele increases the number of vertebrae by changing the control of the expression time.

The present inventors succeeded in identifying a novel Vertnin gene associated with an increase in the number of vertebrae in pigs on the seventh chromosome of pigs. Furthermore, the present inventors have found that by using a polymorphic marker present on or near the gene, it is possible to determine the presence or absence of an inherited trait with increased number of vertebrae in pigs, thereby completing the present invention.

That is, the present invention relates to a method for determining the presence or absence of swine vertebral number-inherited genetic traits, using as a marker a polymorphic marker present on or near the Vertnin gene on chromosome 7 of swine, more specifically,
[1] A method for determining the presence or absence of an inherited trait of increased number of vertebrae in pigs, wherein one or more of the following (A) (1) to (25) present on the seventh chromosome of pigs A method of determining by the step (B) below using the polymorphic marker of
(A)
(1) Position 40 of the base sequence described in SEQ ID NO: 1 (2) Position 207 of the base sequence described in SEQ ID NO: 2 (3) Position 68 of the base sequence described in SEQ ID NO: 3 (4) SEQ ID NO: : Position 47 or 101 of the base sequence described in (5) Position 81 of the base sequence described in SEQ ID NO: 5 (6) Position 355 of the base sequence described in SEQ ID NO: 6 (7) SEQ ID NO: 7 (8) 42nd position of the base sequence described in SEQ ID NO: 8 (9) 152th or 185th position of the base sequence described in SEQ ID NO: 9 (10) described in SEQ ID NO: 10 (11) Positions 95 to 385 of the base sequence set forth in SEQ ID NO: 11 (12) Position 49 of the base sequence set forth in SEQ ID NO: 12 (13) Base sequence set forth in SEQ ID NO: 13 Position 31, 116, 335, or 421 of (14) SEQ ID NO: 127 of the base sequence described in 14 (15) 78, 154, 173, 187, 217, 320, 433 of the base sequence described in SEQ ID NO: 15 (16) SEQ ID NO: 16 111 of the base sequence described in (17) 71 or 192 of the base sequence described in SEQ ID NO: 17 (18) 80 to 82 of the base sequence described in SEQ ID NO: 18 (19) SEQ ID NO: 19 285 or 300 to 301 of the base sequence described in (20) 55th, 65th, 75th, or 150th position of the base sequence described in SEQ ID NO: 20 (21) The base sequence described in SEQ ID NO: 21 (22) 75th position of the base sequence described in SEQ ID NO: 22 (23) 217th position of the base sequence described in SEQ ID NO: 23 (24) 91 of the base sequence described in SEQ ID NO: 24 Rank (25) Based on the determination table of the following [Table 1] in which the base type of each polymorphic marker of (B) above (A) is described, position 136 of the base sequence described in column number 25: Step of determining presence / absence [Table 1]

[2] Judgment of presence or absence of a genetic character with increased vertebral number in pigs characterized by detecting the microsatellite sequence described in any of (a) to (d) below on chromosome 7 of pigs Method,
(a) a microsatellite sequence at positions 180 to 195 or 196 to 216 in the base sequence set forth in SEQ ID NO: 26
(b) a microsatellite sequence at positions 311 to 323, 380 to 388, 389 to 396, or 400 to 406 in the nucleotide sequence set forth in SEQ ID NO: 27
(c) a microsatellite sequence at positions 393 to 413 in the nucleotide sequence set forth in SEQ ID NO: 28
(d) a microsatellite sequence at positions 96 to 107 or 309 to 325 in the nucleotide sequence set forth in SEQ ID NO: 29 [3] DNA comprising the polymorphic marker or microsatellite sequence present on pig chromosome 7 The method according to [1] or [2], comprising a step of amplifying a region and detecting a polymorphism or a microsatellite sequence of the amplification product,
[4] A method for determining the presence or absence of an inherited trait with increased vertebral number in pigs, characterized by using the expression level of a Vertnin gene present on pig chromosome 7 as an index,
I will provide a.

Elucidation of the genes that control the number of vertebrae enables the control of the number of vertebrae, so that efficient improvement of pig meat production and reproduction is realized. In particular, the number of vertebrae QTL in the center of chromosome 7 q is the cause of variability in the number of vertebrae in western varieties used for pork production, and the information provided by the elucidation of this responsible gene is directly related to today's pork production. And can contribute greatly to the efficiency improvement.

It is a figure which shows the number of the cervical vertebrae, the thoracic vertebrae, the lumbar vertebrae, the sacral vertebrae, and the caudal vertebrae in humans, horses, cows / sheeps / pigs, and pigs. Western varieties (Landlace, Great Yorkshire, Duroc, Berkshire) have 20, 21, 22, 23 vertebrae, 19 Asian varieties (Umeyama and Kinka) and 19 wild boar. It is a figure which shows the result of the QTL analysis (JD family line) regarding the number of vertebrae. QTLs related to the number of two vertebrae were detected in the end region of chromosome 1 q arm and the center of chromosome 7 q arm. It is a figure which shows the effect of two vertebra number QTL in a JD family. The average number of vertebrae of F2 individuals with the respective genotypes of the two QTLs is shown. There are significant differences between different alphabets (a, b, c, d). Each QTL has mainly additive effects, and the two QTLs work independently. It is a figure which shows the result of the half sibling analysis of the number of vertebrae QTL on the 7th chromosome using the pig of Tokushima Prefecture large Yorkshire breed (AY). The transmission of the QTL region on the homologous chromosome of the pig to piglets was analyzed using microsatellite markers. Divided into two groups (arbitrarily indicated in black and white) according to the QTL region of the sow derived pigs, the average value of the number of vertebrae for each was plotted. The number of piglets and the standard error were also shown. In the t-test, the QTL of the sow was judged to be heterozygous at P <0.01 (**). The Z test was performed according to the method of Nezer et al. With an effect of increasing the number of vertebrae of 0.43, and Z <−2.0 was made homozygous. In addition, the number of vertebrae of each pig of homozygous pigs was multiple-tested with the number of vertebrae of piglets (Q: 371, q: 383) that were transmitted by heterozygous pigs with increased vertebral number and wild-type alleles. (Steel test) and vertebral number increased type or wild type was determined. It is a figure which shows the confidence interval (three prefectures joint, JD family) of the vertebra number QTL on the 7th chromosome. The 95% confidence interval where the QTL is located was obtained by Bootstrap method (10000 times). The 95% section is shown in black and the others in gray. The 95% confidence interval was 83 cM to 88 cM. It is a figure which shows development of the microsatellite marker in the vertebra number QTL vicinity region. A BAC clone was isolated by porcine STS developed using human gene information, and a microsatellite marker was developed. The developed microsatellite markers were compared with the ongoing pig genome draft sequence by SGSC (International Swine Genome Sequencing Consortium), and their chromosomal positions were confirmed. Underlined markers indicate those not yet found in the pig genome draft sequence. It is a figure which shows the QTL type and the homoeologous chromosomal area | region in the pig of Tokushima Prefecture large Yorkshire breed pig (AY). In FIG. 4, the haplotype of the microsatellite marker was analyzed for each chromosome of the sow whose QTL type was determined. Regions that are homoeologous (the same type of haplotype) are shown in the same color. The vertebral number increasing allele Q and the wild type allele wt are shown in red letters in the region that is transmitted to both loci. It was between SJ7106 and SJ7008 that the homologous chromosomal region did not transmit to both Q and wt. L and R represent any two chromosomal regions of each individual. It is a figure which shows the result of the genome structure analysis of the vertebra number QTL vicinity region. (A) BAC clone whose base sequence is decoded by SGSC (International Swine Genome Sequencing Consortium). (B) Gene map created from the base sequence of the BAC clone. The position of the microsatellite marker is shown. Those underlined were newly developed from the base sequence of the BAC clone. (C) Polymorphic site near the VRTN gene. Polymorphic sites consistent with QTL in large Yorkshire pigs were shown. It is a figure which shows the QTL type and the homoeologous chromosomal region in a large Yorkshire breed pig and F2 experimental family parental pig. A newly developed microsatellite marker (underlined) was added from the BAC clone sequence, and haplotype analysis was performed. L: Land Race, W: Large Yorkshire, B: Berkshire, D: Duroc, Wb: Amber, M: Umeyama Pig, J: Jinhua Pig, C: Crown Mini Pig. L and R represent any two chromosomal regions of each individual. It is a figure which shows the result of the relevance analysis with the number of vertebrae using the polymorphism of the vertebra number QTL vicinity area, and the haplotype block analysis. A polymorphic marker was developed in the area near the QTL of vertebrae. Using 199 heads sampled from the field, analysis of variance was performed on the relationship between the genotype and the number of vertebrae, and F values were plotted. Haplotype blocks were also analyzed for these polymorphisms. Numbers indicate R ² values. It is a figure which shows the expression comparison analysis between the alleles of the VRTN gene using a hetero pig pig. After mating, heterozygous (Q / wt) embryos were collected from the uterus on the 8th, 8.5th, 10th, 12th, and 14th days, and total RNA was prepared. NV062 was amplified by RT-PCR and TA cloning was performed. The nucleotide sequence of the cloned 192 colonies was determined, and the expression level of each allele was evaluated by measuring the frequency of the polymorphic pattern of NV062.

The present invention relates to a method for determining the presence or absence of a porcine vertebral number-increasing genetic trait using as an index a polymorphic marker present on or in the vicinity of the Vertnin (VRTN) gene on the seventh chromosome of pig (in the present specification, “ May be described as “the determination method of the present invention”).

The nucleotide sequence of the Vertnin gene found by the present inventors and the amino acid sequence of the protein encoded by the gene are described in SEQ ID NOs: 88 and 89, respectively.

In the present invention, “determination” usually means that a test pig (pig used in the determination method of the present invention) has or does not have a vertebral number wild-type genetic trait.

Further, it refers to discriminating between pigs having an increased vertebral number-inherited genetic trait and other pigs. The term “determination” in the present invention is, for example, “appraisal”, “discrimination” or “discrimination”, “ It may be expressed as “inspection” or the like.

In addition, the determination method of the present invention is not necessarily limited to the method for determining a pig individual, for example, meat or processed meat (for example, ham), or a biological sample derived from a test pig. And a method for determining the presence or absence of an inherited trait with increased vertebral number.

In the present invention, “polymorphism” refers to, for example, single nucleotide polymorphism (SNP), deletion mutation, insertion mutation, microsatellite and the like.

A preferred embodiment of the determination method of the present invention is a method characterized by using a polymorphic marker present in the pig genome.

In the present invention, the polymorphic marker refers to a DNA site (polymorphic site) capable of determining the presence or absence of an inherited trait with increased vertebral number in pigs. Therefore, using a polymorphic marker in the method of the present invention usually means determining the presence or absence of an inherited trait of increased swine vertebral number based on the difference in DNA sequence (base species) at the polymorphic site of the present invention. Say.

Specifically, the polymorphic marker used in the present invention is a polymorphic marker present on porcine chromosome 7, which is a polymorphic marker at the following site (in the present specification, “polymorphic marker of the present invention”). May be indicated).
(1) Position 40 of the base sequence described in SEQ ID NO: 1 (2) Position 207 of the base sequence described in SEQ ID NO: 2 (3) Position 68 of the base sequence described in SEQ ID NO: 3 (4) SEQ ID NO: : Position 47 or 101 of the base sequence described in (5) Position 81 of the base sequence described in SEQ ID NO: 5 (6) Position 355 of the base sequence described in SEQ ID NO: 6 (7) SEQ ID NO: 7 (8) 42nd position of the base sequence described in SEQ ID NO: 8 (9) 152th or 185th position of the base sequence described in SEQ ID NO: 9 (10) described in SEQ ID NO: 10 (11) Positions 95 to 385 of the base sequence set forth in SEQ ID NO: 11 (12) Position 49 of the base sequence set forth in SEQ ID NO: 12 (13) Base sequence set forth in SEQ ID NO: 13 Position 31, 116, 335, or 421 of (14) SEQ ID NO: 127 of the base sequence described in 14 (15) 78, 154, 173, 187, 217, 320, 433 of the base sequence described in SEQ ID NO: 15 (16) SEQ ID NO: 16 111 of the base sequence described in (17) 71 or 192 of the base sequence described in SEQ ID NO: 17 (18) 80 to 82 of the base sequence described in SEQ ID NO: 18 (19) SEQ ID NO: 19 285 or 300 to 301 of the base sequence described in (20) 55th, 65th, 75th, or 150th position of the base sequence described in SEQ ID NO: 20 (21) The base sequence described in SEQ ID NO: 21 (22) 75th position of the base sequence described in SEQ ID NO: 22 (23) 217th position of the base sequence described in SEQ ID NO: 23 (24) 91 of the base sequence described in SEQ ID NO: 24 Rank (25) Column number: 136 of the nucleotide sequence of 25

In a preferred embodiment of the present invention, the presence or absence of an inherited trait with increased vertebral number in pigs is determined by evaluating a polymorphic site in the polymorphic marker (for example, determining a base type (DNA sequence) in the polymorphic site). It is a method to do.

More specifically, the determination method of the present invention uses each of the polymorphic markers described above using one or a plurality of polymorphic markers described in any one of (1) to (25) present in the porcine genome. Is a method for determining the presence or absence of an inherited trait with increased vertebral number of pigs based on the following determination table in which the base species (DNA sequence) is described.

[Table 1]

In Table 1 above, “del” represents a deletion mutation and “ins” represents an insertion mutation.

In the method of the present invention, the accuracy of determination usually increases as more polymorphic markers are used. Therefore, the method of the present invention is not necessarily essential, but a plurality of polymorphic markers may be used. The polymorphic marker used in the method of the present invention is usually one or a small number (for example, about 1 to 9). One embodiment of the method of the present invention is a method using the polymorphic marker in combination, that is, one selected from the group consisting of a plurality of polymorphic markers described in (1) to (25) above. Alternatively, a method characterized by using a plurality of polymorphic markers is also included in the present invention.

A preferred embodiment of the determination method of the present invention is a method characterized by detecting a mutation at a polymorphic site in the polymorphic markers (1) to (25).
In the present invention, the site for detecting a mutation is preferably a polymorphic site in the polymorphic marker described in any of (1) to (25) above.

In the present invention, the mutation is, for example, a mutation to the increased vertebral number type (Q) at the polymorphic site in the polymorphic markers (1) to (25).
Specifically, in the test pig, when the polymorphic site in the polymorphic markers (1) to (25) is “increased Q” described in the determination table, the test pig is vertebral bone. It is determined to have a number-increasing genetic trait.
In the method of the present invention, when the polymorphic site in the polymorphic markers (1) to (25) is not “increased Q” described in the determination table, ”, It is determined that the test pig does not have an increased vertebral number inheritance.

That is, as a preferred embodiment of the method of the present invention, there is provided a method for determining the presence or absence of a porcine vertebral number-increasing genetic trait, which is one or more of the above (1) to (25) present in the porcine genome. Using a plurality of polymorphic markers, if the base type (DNA sequence) in the polymorphic marker is not “increased Q” in the above determination table, or “wild type wt”, the test pig has the number of vertebrae This is a method for determining that there is no increased genetic trait.

In a preferred embodiment of the present invention, the number of vertebrae in pigs is increased by detecting the microsatellite sequence described in any of (a) to (d) below on the seventh chromosome of pigs: The present invention relates to a method for determining the presence or absence of type inheritance.
(a) a microsatellite sequence at positions 180 to 195 or 196 to 216 in the base sequence set forth in SEQ ID NO: 26
(b) a microsatellite sequence at positions 311 to 323, 380 to 388, 389 to 396, or 400 to 406 in the nucleotide sequence set forth in SEQ ID NO: 27
(c) a microsatellite sequence at positions 393 to 413 in the nucleotide sequence set forth in SEQ ID NO: 28
(d) a microsatellite sequence at positions 96 to 107 or 309 to 325 in the nucleotide sequence set forth in SEQ ID NO: 29

In this method, when any one of the microsatellite sequences (a) to (d) above is detected in the chromosome of the test pig, the test pig is determined to have an increased vertebral number inheritance trait. . On the other hand, if the microsatellite sequence is not detected, it is determined that the test pig does not have an increased vertebral number inheritance.
Details of the microsatellite arrangement are described in Tables 6-1 and 6-2 below.

Also, in the examples described later, it was shown that the expression of porcine Vertnin gene is responsible for the increase in the number of vertebrae. Accordingly, the present invention provides a method for determining the presence or absence of an inherited trait with increased vertebral number in pigs, characterized by using the expression level of the Vertnin gene present on the seventh chromosome of pigs as an index. Here, gene expression includes transcription and translation.

The detection of the gene expression level is usually performed by comparing the amount of RNA transcribed from the Vertnin gene with a control. Examples of such methods include Northern blotting using a probe that hybridizes to a polynucleotide encoding the Vertnin gene, or RT-PCR using a primer that hybridizes to the Vertnin gene (polynucleotide). Can do. In addition, a DNA array (new genetic engineering handbook, Masaaki Muramatsu, Masaru Yamamoto, Yodosha, p280-284) can be used for detection of the expression level of the Vertnin gene.

Furthermore, it is also possible to detect the expression level of the Vertnin gene by evaluating the translation level. The detection is performed by comparing the amount of the polypeptide transcribed and translated from the Vertnin gene with a control. Such methods include SDS polyacrylamide electrophoresis and Western blotting, dot blotting, immunoprecipitation, enzyme linked immunoassay (ELISA), and antibodies that bind to Vertnin (polypeptide), and An immunofluorescence method can be exemplified.

In the above method, when the expression level of the RNA or polypeptide derived from the Vertnin gene is increased as compared to the control (wild type), the individual (test pig) from which the gene is derived has an increased number of vertebrae. Determined to have genetic traits.

In the determination method of the present invention, various known methods can be used as a method for detecting a mutation (evaluating the base type (DNA sequence) of a polymorphic site in a polymorphic marker). That is, any method can be used in the determination method of the present invention as long as it can detect a mutation.

Examples of methods capable of detecting a mutation at a polymorphic site in the polymorphic marker of the present invention are illustrated below, but are not necessarily limited to these methods. A person skilled in the art can appropriately detect the mutation in consideration of the type and position of the mutation.

First, a method of directly determining a polymorphic mutation (base species) in the polymorphic marker of the present invention can be mentioned. That is, a method including the following steps, characterized in that a base sequence including a polymorphic site is directly determined.
(A) a step of preparing DNA from a test pig (b) a step of amplifying a DNA region containing the polymorphic marker of the present invention (c) a step of determining the base sequence of the amplified DNA

In this method, first, a DNA sample is prepared from a test pig. The DNA sample can be prepared based on chromosomal DNA extracted from, for example, an organ or tissue of a test pig, cells, blood, oral mucosa, skin, hair, or the like.

In this method, a DNA region containing the polymorphic marker of the present invention is then isolated. The DNA can also be isolated by PCR or the like using a primer that hybridizes to DNA containing the polymorphic marker of the present invention and using chromosomal DNA as a template. In this method, the base sequence of the isolated DNA (base type of polymorphic site) is then determined. The base sequence of the isolated DNA can be determined by a method known to those skilled in the art.

In this method, the presence or absence of porcine vertebral number-increasing genetic traits is then determined based on the determined DNA base sequence (base type of the polymorphic site) based on the determination table.

The determination method of the present invention can be performed by various methods capable of detecting the polymorphic mutation other than the method for directly determining the base sequence of DNA derived from the test pig as described above.

For example, the detection of the polymorphic mutation in the present invention can also be performed by a method including the following steps.
(A) Step of preparing DNA from test pig (b) Step of amplifying DNA region containing polymorphic marker of the present invention (c) Step of cleaving amplified DNA with restriction enzyme (d) Size of DNA fragment (E) a step of comparing the size of the detected DNA fragment with a control

First, a DNA sample is prepared from the test pig. Next, DNA containing the polymorphic marker of the present invention is amplified. Furthermore, the amplified DNA is cleaved with a restriction enzyme. The DNA fragments are then separated according to their size. The size of the detected DNA fragment is then compared to a control.

Examples of such methods include a method using restriction enzyme fragment length polymorphism (Restriction Fragment Length Polymorphism / RFLP) and a PCR-RFLP method. Specifically, when a mutation is present in the recognition site of a restriction enzyme, the size of the fragment generated after the restriction enzyme treatment changes compared to the control. By amplifying a portion containing this mutation by PCR and treating with each restriction enzyme, these mutations can be detected as a difference in mobility of bands after electrophoresis. Alternatively, the presence or absence of mutation can be detected by treating chromosomal DNA with these restriction enzymes, performing electrophoresis, and performing Southern blotting using the probe DNA of the present invention. The restriction enzyme used can be appropriately selected according to each mutation. Furthermore, it is also possible to amplify the genomic DNA by PCR using a fluorescently labeled primer, cleave the restriction enzyme, and then detect the mutation with a detector such as a sequencer.

The restriction enzyme used in the above method is usually an enzyme that recognizes a DNA sequence containing the polymorphic marker of the present invention.
As a preferred embodiment of the above method using a restriction enzyme, for example, a DNA fragment amplified using a forward primer and a reverse primer described in Tables 8-1 to 8-7 described later is treated with a restriction enzyme. The PCR-RFLP method carried out by

A person skilled in the art can appropriately select appropriate primers and restriction enzymes that can be used in the determination method of the present invention based on information such as the polymorphic site of the polymorphic marker and the base type of the site. It is.

In a preferred embodiment of the method of the present invention, the step of amplifying a DNA region containing the polymorphic marker according to any one of (1) to (25) present in the porcine genome and detecting the polymorphism of the amplified product It is a method including.

The detection of polymorphism in the above method is preferably performed by treating the amplified product with a restriction enzyme. The restriction enzyme to be used can be appropriately selected by those skilled in the art based on information on the base type of the target polymorphic marker and the base sequence of the surrounding DNA region.

Still another method includes a method including the following steps.
(A) a step of preparing DNA from a test pig (b) a step of amplifying a DNA region containing the polymorphic marker of the present invention (c) a step of dissociating the amplified DNA into single strands (d) a dissociated one Step of separating single-stranded DNA on non-denaturing gel (e) Step of comparing the mobility of the separated single-stranded DNA on the gel with the control

First, a DNA sample is prepared from the test pig. Next, a DNA region containing the polymorphic marker of the present invention is amplified. Furthermore, the amplified DNA is dissociated into single-stranded DNA. The dissociated single-stranded DNA is then separated on a non-denaturing gel. The mobility of the separated single-stranded DNA on the gel is compared with the control.

Examples of the method include PCR-SSCP (single-strand conformation polymorphism) method (Cloning and polymerase chain reaction-single-strand conformation polymorphism analysis of anonymous Alu repeats on chromosome 11. Genomics. 1992 Jan 1; 12 (1): 139-146., Detection of p53 gene mutations in human brain tumors by single-strand conformation polymorphism analysis of polymerase chain reaction products. Oncogene. 1991 Aug 1; 6 (8): 1313-1318. , Multiple fluorescence-based PCR-SSCP analysis with postlabeling. PCR, Methods Appl. 1995 Apr 1; 4 (5): 275-282.). This method is suitable for screening a large number of DNA samples in particular because it is relatively easy to operate and has advantages such as a small amount of test sample. The principle is as follows. When a double-stranded DNA fragment is dissociated into single strands, each strand forms a unique higher-order structure depending on its base sequence. When this dissociated DNA strand is electrophoresed in a polyacrylamide gel containing no denaturing agent, single-stranded DNA having the same complementary strand length moves to a different position according to the difference in each higher-order structure. The higher-order structure of this single-stranded DNA also changes by substitution of a single base, and shows different mobility in polyacrylamide gel electrophoresis. Therefore, by detecting this change in mobility, it is possible to detect the presence of mutation due to deletion or the like in the DNA fragment.

Specifically, first, a DNA region containing the polymorphic marker of the present invention is amplified. The amplification range is usually preferably about 200 to 400 bp. Those skilled in the art can perform PCR by appropriately selecting reaction conditions and the like. During PCR, the amplified DNA product can be labeled by using a primer labeled with an isotope such as ³² P, a fluorescent dye, or biotin. Alternatively, the amplified DNA product can be labeled by performing PCR by adding a substrate base labeled with an isotope such as ³² P, a fluorescent dye, or biotin to the PCR reaction solution. Furthermore, labeling can also be performed by adding a substrate base labeled with an isotope such as ³² P, a fluorescent dye, or biotin to the amplified DNA fragment using Klenow enzyme or the like after the PCR reaction. The labeled DNA fragment thus obtained is denatured by applying heat or the like and electrophoresed on a polyacrylamide gel containing no denaturing agent such as urea. At this time, conditions for separating DNA fragments can be improved by adding an appropriate amount (about 5 to 10%) of glycerol to the polyacrylamide gel. Electrophoretic conditions vary depending on the nature of each DNA fragment, but are usually performed at room temperature (20 to 25 ° C). If favorable separation cannot be obtained, the temperature at which the optimal mobility is obtained at temperatures from 4 to 30 ° C. Review. After electrophoresis, the mobility of the DNA fragments is detected and analyzed by autoradiography using an X-ray film, a scanner that detects fluorescence, or the like. When a band with a difference in mobility is detected, this band can be directly excised from the gel, amplified again by PCR, and directly sequenced to confirm the presence of the mutation. Even when the labeled DNA is not used, the band can be detected by staining the gel after electrophoresis with ethidium bromide or silver staining.

Still another method includes a method including the following steps.
(A) Step of preparing DNA from test pig (b) Step of amplifying a DNA region containing the polymorphic marker of the present invention (c) Step of providing a substrate on which a nucleotide probe is immobilized (d) Step (b) (E) contacting the DNA of step (c) with the substrate in step (c) (e) detecting the strength of hybridization between the DNA and the nucleotide probe immobilized on the substrate (f) detecting the intensity detected in step (e) Process to compare with control

First, a DNA containing a polymorphic marker of the present invention prepared from a test pig and a substrate on which a nucleotide probe that hybridizes with the DNA is immobilized are provided. Next, the DNA is brought into contact with the substrate. Furthermore, the “mutation” is detected by detecting DNA hybridized to the nucleotide probe immobilized on the substrate.

An example of such a method is a DNA array method. A DNA sample containing the polymorphic marker of the present invention can be prepared by a method well known to those skilled in the art. In a preferred embodiment of the preparation of the DNA sample, for example, it can be prepared based on chromosomal DNA extracted from tissues or cells of blood, skin, oral mucosa and the like of a test pig. In order to prepare a DNA sample of the present method from chromosomal DNA, for example, using a primer that hybridizes to a DNA region containing the polymorphic marker of the present invention, PCR using chromosomal DNA as a template, etc. It is also possible to prepare DNA containing a marker. The prepared DNA sample can be labeled for detection by a method well known to those skilled in the art, if necessary.

In the present invention, the “substrate” means a plate-like material capable of fixing nucleotides. In the present invention, the nucleotide includes oligonucleotides and polynucleotides. The substrate of the present invention is not particularly limited as long as nucleotides can be immobilized, but a substrate generally used in DNA array technology can be preferably used.

Generally, a DNA array is composed of thousands of nucleotides printed on a substrate at high density. Usually these DNAs are printed on the surface of a non-porous substrate. The surface layer of the substrate is generally glass, but a porous membrane such as a nitrocellulose membrane can be used.

In the present invention, examples of the nucleotide immobilization (array) method include an oligonucleotide-based array developed by Affymetrix. In an array of oligonucleotides, the oligonucleotides are usually synthesized in situ. For example, in-situ synthesis methods of oligonucleotides using photolithographic technology (Affymetrix) and ink-jet (RosettapharmaInpharmatics) technology for immobilizing chemical substances are already known. Can be used.

The nucleotide probe immobilized on the substrate is not particularly limited as long as it can detect the “mutation”. That is, the probe is, for example, a probe that specifically hybridizes with DNA containing the polymorphic marker of the present invention. If specific hybridization is possible, the nucleotide probe need not be completely complementary to the DNA containing the polymorphic marker to be detected.

In the present invention, the length of the nucleotide probe to be bound to the substrate is usually 10 to 100 bases, preferably 10 to 50 bases, more preferably 15 to 25 bases when oligonucleotides are immobilized.

In the present invention, the DNA sample is then brought into contact with the substrate. By this step, the DNA sample is hybridized to the nucleotide probe. The hybridization reaction solution and reaction conditions may vary depending on various factors such as the length of the nucleotide probe immobilized on the substrate, but can generally be performed by methods well known to those skilled in the art.

In the present invention, the presence / absence or intensity of hybridization between the DNA sample and the nucleotide probe immobilized on the substrate is then detected. This detection can be performed, for example, by reading the fluorescence signal with a scanner or the like. In a DNA array, DNA fixed on a slide glass is generally called a probe, while labeled DNA in a solution is called a target. Therefore, the nucleotide immobilized on the substrate is referred to as a nucleotide probe in this specification.

Still another method includes a method including the following steps.
(A) Step of preparing DNA from test pig (b) Step of hybridizing with nucleotide hybridizing to DNA region containing polymorphic marker of the present invention (c) Step of detecting degree of hybridization (d) Step Comparing the degree detected in (c) with a control

First, a DNA containing a polymorphic marker of the present invention prepared from a test pig and a nucleotide that hybridizes with the DNA are prepared. Next, the DNA and nucleotide are hybridized. Further, the mutation is detected by detecting the degree of hybridization and comparing to the control.

Specifically, for the purpose of detecting only a defect at a specific position, an allele-specific oligonucleotide (Aligonucleotide / ASO) hybridization method can be used. When an oligonucleotide containing a base sequence that is considered to have a polymorphic mutation is prepared and hybridized with the sample DNA, the efficiency of hybridization is reduced when the mutation is present. It can be detected by Southern blotting, a method using the property of quenching by intercalating a special fluorescent reagent into the hybrid gap, or the like.

Also, detection by Invader method is possible. Specifically, two kinds of oligonucleotides (allelic oligo and Invader oligo) that hybridize to the polymorphic site in the polymorphic marker of the present invention are prepared. At this site, the Invader oligo invades only one base below the allele oligo. By cleaving the part that recognizes the invasion structure by an enzymatic reaction, an allele oligo fragment is released. The reaction is repeated with excess allele oligo and the amount of fragments is amplified. Mutation can be detected by detecting the amount of fragments using an oligonucleotide corresponding to the mutation.

Also, detection by the TaqMan probe method is possible. Specifically, an oligonucleotide that hybridizes to a DNA containing the polymorphic marker of the present invention, in which the 5 ′ end is modified with a special fluorescent substance (such as FAM) and the 3 ′ end is modified with a quencher substance (such as TAMRA) ( In the presence of the TaqMan probe), the DNA containing the polymorphic marker of the present invention is amplified by PCR or the like. When the TaqMan probe hybridized to the template DNA is decomposed during the PCR extension reaction step, the fluorescent dye is released from the probe, and the suppression by the quencher is released and fluorescence is emitted. Mutations can be detected by measuring the amount of fluorescence using TaqMan ™ probes that emit different fluorescence for different mutations.

Still another method includes a method including the following steps.
(A) a step of preparing DNA from a test pig (b) a step of amplifying a DNA region containing the polymorphic marker of the present invention (c) a step of applying the DNA amplified in step (b) to a mass spectrometer and measuring the molecular weight Step (d) Step of comparing the molecular weight measured in step (c) with a control

First, DNA is prepared from a test pig, and then a DNA region containing the polymorphic marker of the present invention is amplified. The amplified DNA is then subjected to a mass analyzer and the molecular weight is measured. The measured molecular weight is then compared to a control. Examples of such a method include the MALDI-TOF-MS method (Trends Biotechnol (2000): 18: 77-84).

In addition, the method of the present invention can be carried out using a PCR-SSP (sequence-specific primers) method. The PCR-SSP method is a method in which a DNA site having a specific sequence is selectively amplified by PCR.

For example, a primer capable of selectively amplifying the “enhanced Q” base species (DNA sequence) in the polymorphic marker of the present invention is set and PCR is performed. Based on the presence or absence of the PCR amplification product, it is possible to determine the presence or absence of an inherited trait with an increased number of vertebrae in pigs. For example, when an amplification product of the PCR is detected, it is determined that the test pig has an increased number of vertebrae. On the other hand, when the PCR amplification product is not detected, it is determined that the test pig does not have an increased vertebral number inheritance.
When PCR-SSP is performed, the primer is preferably designed so that the sequence to be detected (polymorphic marker of the present invention) is located on the 3 ′ end side.

A preferred embodiment of the above method includes a method including the following steps.
(A) Step of preparing DNA from test pig (b) DNA containing the polymorphic marker using the PCR-SSP primer designed so that the polymorphic marker of the present invention is located on the 3 ′ end side A step of amplifying the region by PCR (c) A step of detecting the amplified DNA

The present invention also provides a polymorphic marker according to any one of (1) to (25) above, which is a polymorphic marker present on porcine chromosome 7. More specifically, the present invention relates to the genetic marker described in any of (1) to (25) below.
(1) A genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 1, comprising a polymorphic site at position 40, and the base type of the polymorphic site is T Genetic marker (2) is a genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 2, comprising a polymorphic site at position 207, and the base type of the polymorphic site is C (3) A genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 3, comprising a polymorphic site at position 68, wherein the base type of the polymorphic site is A (4) a genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 4, comprising a polymorphic site at position 47 or 101, and the polymorphism The base type of the site is A genetic marker characterized by being A or G (5) A genetic marker comprising the whole or a partial sequence of the base sequence set forth in SEQ ID NO: 5, comprising a polymorphic site at position 81, and the polymorphism (6) a genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 6, comprising a polymorphic site at position 355; Genetic marker (7) characterized in that the base type of the polymorphic site is T, a genetic marker consisting of all or a partial sequence of the base sequence set forth in SEQ ID NO: 7, wherein the polymorphic site at position 87 is A genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 8, wherein the polymorphic site is A and the base type of the polymorphic site is A. Including mold part And a genetic marker (9) comprising the whole or a partial sequence of the base sequence set forth in SEQ ID NO: 9, characterized in that the base type of the polymorphic site is G, which is at position 152 or 185 A genetic marker comprising a polymorphic site, wherein the base type of the polymorphic site is C or C, respectively (10) a genetic marker comprising the entire or partial sequence of the base sequence set forth in SEQ ID NO: 10 A genetic marker comprising the polymorphic site at position 82 and the base type of the polymorphic site is A (11) consisting of all or a partial sequence of the base sequence set forth in SEQ ID NO: 11 A genetic marker comprising a whole or a partial sequence of the base sequence set forth in SEQ ID NO: 12, wherein the genetic marker comprises a polymorphic site at positions 95 to 385 A genetic marker comprising a polymorphic site at position 49 and the base type of the polymorphic site is G (13) consisting of all or a partial sequence of the base sequence set forth in SEQ ID NO: 13 A genetic marker comprising a polymorphic site at position 31, 116, 335, or 421, and the base type of the polymorphic site is A, T, C, or T, respectively Genetic marker (14) A genetic marker comprising the whole or a partial sequence of the base sequence set forth in SEQ ID NO: 14, comprising a polymorphic site at position 127, and the base type of the polymorphic site is C Characteristic genetic marker (15) A genetic marker comprising all or a partial sequence of the base sequence described in SEQ ID NO: 15, which is the 78th, 154th, 173th, 187th, 217th, 320th, or 433 Place A genetic marker comprising a polymorphic site and wherein the base type of the polymorphic site is a deletion mutation (deletion mutation of A), A, A, G, G, C, or T, respectively (16 ) A genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 16, comprising a polymorphic site at position 111, and the base type of the polymorphic site is A Marker (17) A genetic marker comprising the entire or partial sequence of the base sequence set forth in SEQ ID NO: 17, comprising a polymorphic site at position 71 or 192, and the base type of the polymorphic site is T or Genetic marker (18), characterized in that it is a genetic marker consisting of all or a partial sequence of the base sequence set forth in SEQ ID NO: 18, comprising a polymorphic site at positions 80 to 82, and the polymorphism The base type of the site is AA (19) A genetic marker comprising the whole or a partial sequence of the nucleotide sequence set forth in SEQ ID NO: 19, comprising a polymorphic site at position 285 or positions 300 to 301, and Genetic marker (20) characterized in that the base type of the polymorphic site is T or GA, respectively, which is a genetic marker consisting of all or a partial sequence of the base sequence set forth in SEQ ID NO: 20, A genetic marker (21) comprising a polymorphic site at positions 75, 150, and 150, and the base type of the polymorphic site is T, T, G, or G, respectively, A genetic marker comprising all or a partial sequence of the nucleotide sequence, comprising a polymorphic site at position 99 or 138, and the base type of the polymorphic site is C or G Genetic marker (22) A genetic marker comprising the whole or a partial sequence of the base sequence set forth in SEQ ID NO: 22, comprising a polymorphic site at position 75, and the base type of the polymorphic site is G Characteristic genetic marker (23) A genetic marker comprising all or a partial sequence of the base sequence set forth in SEQ ID NO: 23, comprising a polymorphic site at position 217, and the base type of the polymorphic site is C A genetic marker (24) comprising a whole or a partial sequence of the nucleotide sequence set forth in SEQ ID NO: 24, comprising a polymorphic site at position 91, wherein said polymorphic site is deleted Genetic marker (25) characterized by being a mutation (deletion mutation of C), a genetic marker comprising the whole or a partial sequence of the nucleotide sequence set forth in SEQ ID NO: 25, comprising a polymorphic site at position 136 , Genetic markers One polymorphic site nucleotide species characterized in that it is a C

The length of the genetic marker is not particularly limited, but is, for example, 300 bp or less, preferably 100 bp or less, more preferably 50 bp or less, and further preferably 30 or 20 bp.

Note that all prior art documents cited in the present specification are incorporated herein by reference.

Hereinafter, the present invention will be specifically described with reference to examples, but the present invention is not limited to these examples.

[Example 1] Fine mapping of QTLs using large Yorkshire pigs
(1) Judgment of QTL type for large pigs from the Yorkshire breed (AY) in Tokushima Prefecture The Great Yorkshire breed (AY) in Tokushima Prefecture introduced 10 males and 65 females in 1987, followed by 7 generations. Breeded in a closed group. The number of males and females between them is 8-11 and 28-36. Thereafter, 9 males and 35 females were maintained. The number of vertebrae in each piglet (18 to 167) was measured for 9 large Yorkshire breed male pigs and 6 breed sows, and a half sibling analysis was performed using microsatellite markers. QTL was detected with the microsatellite marker SW252 as a peak (Fig. 2), and all swine and piglets were typed together with SW263 and S0115 in the vicinity, and which QTL region on the two piglets of the pig was It was determined whether it was transmitted to the pig. For each pig, the difference in the average value of the number of vertebrae between the piglet groups to which the two QTL regions were transmitted was examined by t-test. If a significant difference was found, the QTL of the pig was heterozygous It was. When no difference was observed, it was determined to be homozygous at Z <−2.0 by Z test (Nezer C. 2003 Genetics 165: 277-285). At that time, the average value 0.43 in the analysis of the F2 experimental family so far was used for the effect of increasing the number of vertebrae. In addition, the number of vertebrae of the homozygous piglets was transferred to the piglets (Q; 371, wt; 383) transmitted by the heterozygous pigs with increased vertebral number (Q) and wild type alleles (wt) ) And multiple tests (Steel test), and Q / Q type or wt / wt type was determined (FIG. 4). As a result, 9 were shown to be Q / wt heterotype. Six were homozygous, 5 were QQ, and 1 was wt / wt (FIG. 4).

(2) Development of microsatellite markers in the QTL region The 95% confidence interval of the number 7 vertebrae QTL was analyzed using QTL express (Seaton G. 2002 Bioinformatics 18: 339-340). The region was between 83 cM and 88 cM between SW632 (Fig. 5). Next, in order to develop a new microsatellite marker in this region, a homology search was first performed using gene sequences on the human genome, and homologous porcine sequences (mainly EST sequences) were obtained. PCR primers were prepared for these, and microsatellite sequences were isolated from a BAC clone (Suzuki K. 2000 Anim. Genet. 31: 8-12) obtained by a screening system using PCR. The isolated microsatellite sequences are compared with the pig genome draft sequence in progress by SGSC (International Swine Genome Sequecing Consortium, http://piggenome.org/), and the position of the BAC clones with these microsatellite sequences on the pig genome. Was confirmed by FPC (Finger Print Contig) map. The development of 55 microsatellite markers derived from 39 genes is shown in Tables 5-1 to 5-2 (microsatellite markers developed in the QTL region of the number of vertebrae on chromosome 7), FIG.

[Table 5-1]

Table 5-2 is a continuation of Table 5-1.
[Table 5-2]

(3) Analysis of the haplotypes of microsatellite markers on each chromosome of the pigs of the Tokushima prefecture large Yorkshire breed pig (AY) Genotyping of the above microsatellite markers for large Yorkshire breed pigs and their piglets The haplotype in pigs was determined. Haplotypes were compared between sows, and the genomic regions derived from common ancestors (homologous) and their recombination positions on the chromosomes were analyzed. As a result of analyzing the relationship between the haplotype of the microsatellite marker on each chromosome of a large Yorkshire breed pig and the allele (Q or wt) of QTL, only in the range of SJ7106, SJ7101, and J7008, the vertebral augmentation type allele Q, there was no common haplotype (homogeneous genomic region) in both chromosomes where the wild type allele wt was located (FIG. 7). Therefore, the candidate region is a region between the microsatellite markers SJ7088 and SJ7040 outside the candidate region.

(4) Creation of genetic map of QTL region and development of new microsatellite marker Bases of 5 BAC clones, CH242-31K14, CH242-238O9, CH242-92H3, CH242-154M12, CH242-313I6, which were decoded by SGSC Using the sequence (FIG. 8A), a genetic map of the region near the QTL was created (FIG. 8B). In addition, using the nucleotide sequences of CH242-92H3 and CH242-154M12, we searched for new microsatellite sequences and developed nine microsatellite markers SJ7099, SJ7103, SJ7107, SJ7113, SJ7114, SJ7121, SJ7126, SJ7136, and SJ7139.

(5) Fine mapping using pigs from the large Yorkshire breed pigs Using the above-mentioned Tokushima prefecture pig breeds (AY), new microsatellite markers SJ7099, SJ7103, SJ7107, SJ7113, SJ7114, SJ7121, SJ7126 , SJ7136, SJ7139, and the result of analysis was that the common haplotype indicating the homoeologous genomic region is between SJ7121 and SJ7008, where the vertebral number increasing allele Q and the wild type allele wt are not present on both chromosomes. The region where the haplotype was conserved in the vertebral number increasing type Q was in the range of SJ7121 to SJ7103 (FIG. 9).

[Example 2] Fine mapping using F2 experimental family parent generation pigs For nine generation F2 experimental family parent generation pigs, the vertebral number QTL genotype was determined (Table 2), and a previous report (Mikawa S. 2005 J Anim. Sci. 83: 2247). Using the microsatellite marker near the QTL region narrowed down by the Tokushima prefecture large Yorkshire breed pigs, haplotype analysis was also conducted on F2 experimental family parent generation pigs to search for regions matching the QTL. As a result, haplotypes associated with increased vertebral number allele Q in large Yorkshire breed pigs were also detected in F2 experimental family parental pigs, and in F2 experimental family parental pigs, increased vertebral number increased The conserved range in the chromosome to which allele Q is located was SJ7088 to SJ7114 (FIG. 9). When combining the analysis of both the Tokushima prefecture large Yorkshire breed pig (AY) and the F2 experimental family parent generation pig, the common region was SJ7121 to SJ7114, and the QTL region was successfully narrowed down to the outer marker, SJ7126 to SJ7099. (Tables 6-1 to 6-2 (microsatellite sequence information)). It is possible to determine the number of vertebrae QTL by the haplotype consisting of these microsatellite markers.

[Table 6-1]

Table 6-2 is a continuation table of Table 6-1.
[Table 6-2]

In Tables 6-1 and 6-2 above, the underline indicates the primer, the italic letters and the underline indicate the microsatellite sequences.

[Example 3] Haplotype block analysis in the QTL vicinity region The polymorphism search of the QTL vicinity region is performed, and NV101, NV102, orf45-i2, orf45-i4, ALDH6A1-i11, LIN52-i4, LIN52-i5, LIN52- e6, NV103, ABCD4-i15, NV038, NV032, NV004, NV015, NV090, NV025, NV035, NV062, NV067, NV071, NV106, NV108, NV109, NV111, NPC2-i2, ISCA2-i3 were detected (FIG. 10). These were subjected to genotyping using the DNA of 199 beef pigs (Landrace, Large Yorkshire, and Duroc cross) randomly selected from the field, and Haploview 4.0 (Barrett et al. 2005). The haplotype block was analyzed by Bioinformatics 21: 263-265). As a result, about 60 kb from ABCD4-i15 to NV067 became the same haplotype block (FIG. 10). There are two major haplotypes of this haplotype block, which coincided with the haplotypes in the large vertebral allele Q and wild-type allele wt in Tokushima Prefecture, Yorkshire pig (AY). In addition, it was confirmed that the polymorphisms (NV004, NV015, NV090, NV025, NV035, NV062) located downstream of the ABCD4 gene were higher than the surrounding polymorphic sites in relation to the number of vertebrae in beef pigs (Fig. 10). ). These polymorphisms are located between SJ7126 and SJ7099 (FIG. 8C). The additive effect on the increase in the number of vertebrae due to genotype in the field sample was 0.53, which was almost equal to the effect observed so far (Table 7 (Distribution of the number of vertebrae in the field sample (Western variety))) . The frequency of the increased vertebral allele was 55.5%.

[Table 7]

[Example 4] Identification of genes governing the number of vertebrae There was no gene whose function was elucidated between SJ7126 and SJ7099, and there was a locus encoding hypothetical protein named LOC55237 in humans and LOC432677 in mice. Also in pigs, the transcript of this region was isolated, and the gene encoding it was named Vertnin (VRTN), which was the gene that controls the number of vertebrae (FIG. 8C). The VRTN gene consists of two exons (Figure 8C) and encodes 698 amino acids. As a result of homology search, there was no similar gene. The cDNA sequence of the VRTN gene and the amino acid sequence encoded by the gene are shown in SEQ ID NOs: 88 and 89, respectively.

[Example 5] Polymorphism analysis of porcine VRTN gene Regarding the region from SJ7126 to SJ7099 containing the VRTN gene, polymorphism in all regions except for the repeat sequence such as PRE1 sequence in the pig of the Tokushima prefecture large Yorkshire breed pig As a result of the analysis, the 42 polymorphisms shown in FIG. 8C and Tables 8-1 to 8-7 (SNP sequence information) coincided with the QTL type. The 42 polymorphism patterns are shown in Table 9 (Haplotype of porcine VRTN gene). Among these, NV064 is a non-synonymous substitution and the wild type is GAC (Asp), while the augmented type is substituted with GGC (Gly).

[Table 8-1]

Table 8-2 is a continuation table of Table 8-1.
[Table 8-2]

Table 8-3 is a continuation table of Table 8-2.
[Table 8-3]

Table 8-4 is a continuation table of Table 8-3.
[Table 8-4]

Table 8-5 is a continuation of Table 8-4.
[Table 8-5]

Table 8-6 is a continuation table of Table 8-5.
[Table 8-6]

Table 8-7 is a continuation of Table 8-6.
[Table 8-7]

In the above Tables 8-1 to 8-7, the letters enclosed in squares indicate the polymorphic sites.

[Table 9]

In Table 9, “del” represents a deletion mutation and “ins” represents an insertion mutation.

[Example 6] Analysis of expression of responsible gene in pig embryo Since there is a polymorphism that matches QTL in the promoter region of VRTN gene, the difference in the expression pattern between alleles is considered to be the cause of QTL. It is done. Therefore, the promoter regions of the porcine VRTN gene increased vertebral number and wild type alleles were linked to a plasmid using luciferase as a reporter gene, and the promoter activity was compared using CGR8 cells and P19 cells. There was no difference. CGR8 cells are mouse ES cells and P19 cells are mouse embryonic tumor cells, both expressing the endogenous mouse VRTN gene.

Also, in order to analyze the expression pattern of endogenous VRTN gene in pigs, the expression difference of VRTN gene in pig embryos due to alleles was analyzed. A breeding pig with a VRTN gene of increased Q / Q and a breeding pig with a wild type wt / wt were crossed to produce a heterozygous Q / wt embryo. The expressed mRNA can distinguish alleles derived from polymorphisms of NV062, NV064, MV065 located on exons. After mating, embryos are collected from the uterus on the 8th, 8.5th, 10th, 12th, 14th, RT-PCR is performed on the VRTN gene, the region containing NV062 is amplified, and the TOPO TA cloning kit (Invitrogen) is used. Were used for cloning. For each of 192 colonies cloned, the nucleotide sequence was determined and the frequency of NV062 polymorphism pattern was measured to evaluate the expression level of each allele (FIG. 11). As a result, the relative frequency of the increased vertebral number allele Q and the wild type allele wt was almost the same on day 10 after mating, but in other cases, the increased number of vertebral numbers was frequently expressed, and on the 12th and 14th days, the wild type Was not observed (Table 10 (VRTN gene expression analysis in pig embryo)). It was suggested that the change in the expression time of the VRTN gene was responsible for the increase in the number of vertebrae.

[Table 10]

These results revealed that the VRTN gene controls the number of vertebrae in pigs. The polymorphism information of VRTN gene has high utility value for breeding. This gene increases the number of vertebrae by about 0.6 per allele within the improved variety. Since the number of vertebrae correlates with carcass length, genetic diagnosis of VRTN gene is widely used for genetic improvement such as meat production and fertility (number of pups, number of nipples). In addition, it is possible to improve the breeding method using this genetic diagnosis. It is also possible to change the number of vertebrae and various traits associated therewith by using VRTN gene transcripts and proteins.

Claims

One or more polymorphisms according to any one of (1) to (25) in the following (A), which is a method for determining the presence or absence of an inherited trait with increased number of vertebrae in pigs The method of determining by the process of the following (B) using a marker.
(A)
(1) Position 40 of the base sequence described in SEQ ID NO: 1 (2) Position 207 of the base sequence described in SEQ ID NO: 2 (3) Position 68 of the base sequence described in SEQ ID NO: 3 (4) SEQ ID NO: : Position 47 or 101 of the base sequence described in (5) Position 81 of the base sequence described in SEQ ID NO: 5 (6) Position 355 of the base sequence described in SEQ ID NO: 6 (7) SEQ ID NO: 7 (8) 42nd position of the base sequence described in SEQ ID NO: 8 (9) 152th or 185th position of the base sequence described in SEQ ID NO: 9 (10) described in SEQ ID NO: 10 (11) Positions 95 to 385 of the base sequence set forth in SEQ ID NO: 11 (12) Position 49 of the base sequence set forth in SEQ ID NO: 12 (13) Base sequence set forth in SEQ ID NO: 13 Position 31, 116, 335, or 421 of (14) SEQ ID NO: 127 of the base sequence described in 14 (15) 78, 154, 173, 187, 217, 320, 433 of the base sequence described in SEQ ID NO: 15 (16) SEQ ID NO: 16 111 of the base sequence described in (17) 71 or 192 of the base sequence described in SEQ ID NO: 17 (18) 80 to 82 of the base sequence described in SEQ ID NO: 18 (19) SEQ ID NO: 19 285 or 300 to 301 of the base sequence described in (20) 55th, 65th, 75th, or 150th position of the base sequence described in SEQ ID NO: 20 (21) The base sequence described in SEQ ID NO: 21 (22) 75th position of the base sequence described in SEQ ID NO: 22 (23) 217th position of the base sequence described in SEQ ID NO: 23 (24) 91 of the base sequence described in SEQ ID NO: 24 Rank (25) Based on the determination table of the following [Table 1] in which the base type of each polymorphic marker of (B) above (A) is described, position 136 of the base sequence described in column number 25: Step of determining presence / absence [Table 1]
A method for determining the presence or absence of an inherited trait with increased vertebral number in pigs, comprising detecting the microsatellite sequence according to any one of the following (a) to (d) on the seventh chromosome of pigs.
(a) a microsatellite sequence at positions 180 to 195 or 196 to 216 in the base sequence set forth in SEQ ID NO: 26
(b) a microsatellite sequence at positions 311 to 323, 380 to 388, 389 to 396, or 400 to 406 in the nucleotide sequence set forth in SEQ ID NO: 27
(c) a microsatellite sequence at positions 393 to 413 in the nucleotide sequence set forth in SEQ ID NO: 28
(d) a microsatellite sequence at positions 96 to 107 or 309 to 325 in the nucleotide sequence set forth in SEQ ID NO: 29
The method comprises the steps of amplifying a DNA region containing the polymorphic marker or microsatellite sequence present on pig chromosome 7, and detecting the polymorphism or microsatellite sequence of the amplified product. Method.
A method for determining the presence or absence of an inherited trait with increased vertebral number in pigs, characterized in that the expression level of the Vertnin gene present on the seventh chromosome of the pig is used as an index.