KR101897808B1 - Method for Predicting Meat quality of Bos taurus africanus - Google Patents

Abstract

The present invention provides a method for providing information necessary for predicting meat quality of an African marsupial ( Bos taurus africanus ) for the production of high quality meat. (b) The present invention provides markers relating to high quality meat flesh, intramuscular fat, meat color, juice loss, and food intake and efficiency. The markers can be used for marker-assisted selection and will be useful for meat production and pedigree improvement programs.

Description

{Method for predicting Meat quality of Bos taurus africanus}

The present invention relates to a method for predicting meat quality in African dumplings.

Africa, with its diverse agricultural environment, is home to a variety of small cattle varieties adapted to the local environment. Because the cow has evolved to survive in poor food conditions, high temperatures, internal and ex vivo parasites, and high disease environments, the cattle are better able to tolerate higher temperature tolerance, environmental adaptability, tick tolerance, reproduction It has maternal characteristics such as longevity and fertility. Despite these advantages, African cattle meat is generally believed to have low quality meat with low tenderness and marbling characteristics.

The African bell tower , also known as Bos taurus africanus , is a heterozygous hybrid of Bos taurus and Bos indicus in East Africa, Central Africa and South Africa. Generally, the marsupial bovine can be identified by long and thin horns, cervico-thoracic hump, and small spreading jaws. Thirty varieties of African varieties are subdivided into East African and South African varieties based on geographical location. Despite previous myths about low quality meat produced by African cattle, the quality of carcass and meat produced by African varieties and varieties derived from varieties is higher than indigenous cattle in Africa, The research results that the quality is lower than the species are claimed. Commercial varieties in South Africa (eg, Bonsmara, Afrikaner, and Nguni) reported low shear forces, short root fibers, thick ribs, high water soluble collagen, and high juice loss rates compared to indigenous (Brahman) .

Meat quality is a general term describing the characteristics of meat, such as the composition and form of carcass, eating quality of meat, health problems associated with meat, production and environmental issues. Meat sensory characteristics of meat, such as year, flavor, juice, and meat color, are important meat quality-related factors that are influenced by muscle biological and proteolytic activities. Muscle biology, such as fiber type, collagen, intramuscular fat tissue and protease activity, is known to regulate the age and flavor of meat and to be influenced by genetic and breeding factors. However, difficulties in measuring low heritability and meat quality are difficult to apply to traditional breeding selection methods, which take a long time when necessary results are obtained in a short time. MAS (marker-assisted selection), which is more effective than traditional selection processes for properties that are difficult to measure under a variety of conditions, is a relatively beneficial genetic selection approach. Recently, a selection signature is an approach that detects related genes based on the evolutionary and biological understanding of the phenotype. Studies on several genes related to immune system, reproduction, energy metabolism, coat coloration, thermoregulation and tick resistance have been reported on selection of positive selection of African cattle. Selection signals associated with reproduction and temperature control are adaptations to heat stress conditions, while detection of immunologically related genes is associated with selective pressure of the effects of long-term presence of pathogenic agents in the continent. However, none of the studies clearly identified the genes associated with the meat characteristics of African cattle, especially the marsupial species.

Numerous papers and patent documents are referenced and cited throughout this specification. The disclosures of the cited papers and patent documents are incorporated herein by reference in their entirety to better understand the state of the art to which the present invention pertains and the content of the present invention.

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The inventors of the present invention have made efforts to analyze the genetic characteristics of the high quality meat produced by the barnyardgrass in comparison with African native African beef which has excellent environmental adaptability. As a result, the present invention has been accomplished by identifying markers related to meat flesh, fat intakes, meat color, and feeding efficiency, which can predict high quality meat quality of African bovine species.

Accordingly, it is an object of the present invention to provide a method for providing information necessary for predicting meat quality of African dumplings.

Another object of the present invention is to provide a meat quality prediction kit

Other objects and advantages of the present invention will become more apparent from the following detailed description of the invention, claims and drawings.

According to one aspect of the present invention, the present invention provides a method of providing information necessary for predicting meat quality of an African marsupial ( Bos taurus africanus ) comprising the steps of:

(a) separating a nucleic acid molecule of a biological sample separated from an African phylogenetic tree; And

(b) the nucleic acid PIK3CB (NCBI Gene ID 517948) in the molecule, MRAS (NCBI Gene ID 540803) , PLA2G2A (NCBI Gene ID 507201), CAPZB (NCBI Gene ID 338052), COL9A2 (NCBI Gene ID 505942), LIMA1 (NCBI Gene ID 540637), SLC48A1 (NCBI Gene ID 784685), MB (NCBI Gene ID 280695), APOL6 (NCBI Gene ID 616957), ATP8A1 (NCBI Gene ID 317692), PDGFRA (NCBI Gene ID 282301), MAP3K5 (NCBI Gene ID 537380), PARK2 (NCBI Gene ID 530858), ZNF410 (NCBI Gene ID 507530), AHSA1 (NCBI Gene ID 539220), MAP4K4 (NCBI Gene ID 509109), NFATC2 (NCBI Gene ID 530401), WWP1 (NCBI Gene ID 513789) , OR2D2 (NCBI Gene ID 504498) , OR10A4 (NCBI Gene ID 617571), OR2D3 (NCBI Gene ID 513635), MAP2K3 (NCBI Gene ID 516039), PLCD3 (NCBI Gene ID 513057), TIMP2 (NCBI Gene ID 282093), PLCD1 (NCBI Gene ID 281986) , ROCK1 (NCBI Gene ID 785911) And And PRKG1 (NCBI Gene ID 282004).

The inventors of the present invention have made efforts to analyze the genetic characteristics of the high quality meat produced by the barnyardgrass in comparison with African native African beef which has excellent environmental adaptability. As a result, we have identified markers related to meat flesh, muscle fat, meat color, and food efficiency that can predict high quality meat quality in African marsupials.

In the present invention, the African mall species to which the meat quality is to be predicted is a heterozygous hybrid of Bos taurus and Bos indicus . The African marsupial bellows have a small breeding horn and are distinguished from native ones with high thoracic humps (see https://en.wikipedia.org/wiki/Sanga_cattle).

The method of predicting the meat quality of the African dumplings of the present invention will be described step by step.

Step (a): Separation of nucleic acid molecules

First, we isolate nucleic acid molecules from biological specimens isolated from african amphibia.

As used herein, the term " nucleic acid molecule " has the meaning inclusive of DNA (gDNA and cDNA) and RNA molecules, and nucleotides which are basic constituent units in nucleic acid molecules are not only natural nucleotides, Also included are analogues (Scheit, Nucleotide Analogs, John Wiley, New York (1980); Uhlman and Peyman, Chemical Reviews, 90: 543-584 (1990)).

According to one embodiment of the present invention, the nucleic acid molecule is genomic DNA.

In the method of the present invention, the nucleic acid molecule can be obtained from a biological sample of African amphibian species.

As used herein, the term " biological sample " refers to a biological sample of an animal that has been separated from the body of a subject, such as blood, plasma, serum, urine, bone marrow, cells, hair or tissue sample. According to one embodiment of the present invention, Is a blood sample.

In order to isolate the genomic DNA from the biological sample, the separation of the gDNA can be carried out according to conventional methods known in the art (Rogers & Bendich (1994)). When the starting material is mRNA, the total RNA is isolated by a conventional method known in the art (see Sambrook, J. et al., Molecular Cloning, A Laboratory Manual, 3rd ed. Cold Spring Harbor Press (1987); and Chomczynski, P. et al., Anal. Biochem. 162: 156 (1987)). The isolated total RNA is synthesized by cDNA using reverse transcriptase. Because the total RNA is isolated from animal cells, it has a poly-A tail at the end of mRNA. CDNA can be easily synthesized using oligo dT primers and reverse transcriptase using such a sequence characteristic (see PNAS USA, 85: 8998 (1988); Libert F, et al., Science, 244: 569 (1989); and Sambrook, J. et al., Molecular Cloning, A Laboratory Manual, 3rd ed. Cold Spring Harbor Press )).

According to one embodiment of the present invention, the African animal species species is an animal species.

Step (b): Measurement of gene expression

Next, the above-mentioned genomic DNA, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta, NCBI Gene ID 517948) , MRAS (Muscle RAS Oncogene Homolog, NCBI Gene ID 540803) , PLA2G2A (Phospholipase A2 Group IIA, NCBI Gene ID 507201) , CAPZB (Capping Actin Protein Of Muscle Z-Line Beta Subunit, NCBI Gene ID 338052) , COL9A2 (Collagen Type IX Alpha 2, NCBI Gene ID 505942) , LIMA1 (LIM domain and actin binding 1, NCBI Gene ID 540637), SLC48A1 (solute carrier family 48 member 1, NCBI Gene ID 784685), MB (Myoglobin, NCBI Gene ID 280695), APOL6 (Apolipoprotein L6, NCBI Gene ID 616957), ATP8A1 (ATPase Phospholipid Transporting 8A1, NCBI Gene ID 317692 ) , PDGFRA (Platelet Derived Growth Factor Receptor Alpha, NCBI Gene ID 282301) , MAP3K5 (Mitogen-Activated Protein Kinase Kinase Kinase 5, NCBI Gene ID 537380) , PARK2 (Parkin RBR E3 Ubiquitin Protein Ligase, NCBI Gene ID 530858) , ZNF410 (Zinc Finger Protein 410, NCBI Gene ID 507530) , AHSA1 (Activator of Hsp90 ATPase activ (Nuclear Factor of activated T-cells 2, NCBI Gene ID 530401) , WWP1 (WW Domain Containing E3 (NCBI Gene ID 530401) , MAP4K4 (Mitogen-activated protein kinase kinase kinase 4, NCBI Gene ID 509109) , NFATC2 Ubiquitin Protein Ligase 1, NCBI Gene ID 513789), OR2D2 (Olfactory receptor Family 2 Subfamily D Member 2, NCBI Gene ID 504498), OR10A4 (Olfactory receptor 10A4, NCBI Gene ID 617571), OR2D3 (olfactory receptor family 2 subfamily D member 3 , NCBI Gene ID 513635) , MAP2K3 (Mitogen-Activated Protein Kinase Kinase 3, NCBI Gene ID 516039) , PLCD3 (Phospholipase C Delta 3, NCBI Gene ID 513057) , TIMP2 (TIMP metallopeptidase inhibitor 2, NCBI Gene ID 282093) PLCDl (Phospholipase C Delta 1, NCBI Gene ID 281986) , ROCK1 (Rho Associated Coiled-Coil Containing Protein Kinase 1, NCBI Gene ID 785911) And The expression level of one or more genes selected from the group consisting of PRKG1 (Protein Kinase, cGMP-Dependent, Type I, NCBI Gene ID 282004) is measured.

The PIK3CB has the nucleotide sequence of 131351896 to 131530834 of the chromosome 1 (NCBI Accession Number AC_000158.1) of the dendritic cell, and related known sequences include NM_001206047 and XM_005201871. The MRAS has a nucleotide sequence of 131765942 to 131834773 nucleotides of the chromosome 1 of the gastric flank, and related known sequences include XM_005201891, XM_005201889, XM_010801552 and NM_001098118. The PLA2G2A has a nucleotide sequence of 133289295 to 133295334 of NCBI Accession Number AC_000159.1 of the dendritic cell, and a related known sequence is NM_001025324. The CAPZB has 133789485 to 133926415 nucleotide sequences of the chromosome 2 of the dendritic cell, and related known sequences include NM_176648, XM_005203083 and XM_010802525. COL9A2 has a nucleotide sequence of 106396680 to 106411482 of the chromosome 3 of the dendritic cell (NCBI Accession Number AC_000160.1), and related known sequence is XM_015466616. The LIMA1 has a nucleotide sequence of 29804632 to 29898282 of the chromosome 5 of NCBI Accession Number AC_000162.1. The SLC48A1 has a nucleotide sequence of 32667466 to 32676306 nucleotides in chromosome 5 of the dendritic cell, and the known sequence is NM_001191205. The MB has a 74170468 to 74181260th nucleotide sequence of the chromosome 5 of the dendritic cell, and a known sequence is NM_173881. The APOL6 has the nucleotide sequence of 74222672 to 74230749 of the chromosome 5 of the dendritic cell, and the known sequence is XM_002687677. The ATP8A1 has a nucleotide sequence of 62893072 to 63128208 of the chromosome 6 of the dendritic cell (NCBI Accession Number AC_000163.1), and the known sequence is NM_174838. The PDGFRA has the nucleotide sequence of 71373513 to 71421283 of the chromosome 6 of the dendritic cell, and known sequences include NM_001192345, XM_010806122 and XM_005207944. The MAP3K5 has 75549283 to 75778418th nucleotide sequence of the chromosome 9 (NCBI Accession Number AC_000166) of the dendritic cell, and known sequences include NM_001144081 and NM_001076890. The PARK2 has 98421510 to 98453799th nucleotide or 98612089 to 99648791th nucleotide sequence of the chromosome 9 of the oligosaccharide, and the known sequence is NM_001199065. The ZNF410 has a nucleotide sequence of 85669037 to 85711375 nucleotides of the chromosome 10 of NCBI Accession Number AC_000167.1, and known nucleotides XM_010809485, XM_0005211999, XM_005212002 and NM_001024491. The AHSA1 has the nucleotide sequence of 89715736 to 89723196 nucleotides of chromosome 10 of the dendritic cell, and the known sequence is NM_001034666. The MAP4K4 has the 6610535 to 6660310th nucleotide sequence of the chromosome 11 of the dendritic cell (NCBI Accession Number AC_000168.1), and the known sequence is XM_010809817. The NFATC2 has the nucleotide sequence of 79971109 to 80131232 of the chromosome 13 of NCBI Accession Number AC_000170.1, and known sequences include XM_005215066, XM_002692357 and XM_005215064. The WWP1 has a nucleotide sequence of 78599363 to 78699730 of the chromosome 14 of the dendritic cell (NCBI Accession Number AC_000171.1), and the known sequence is NM_001037463. The OR2D2 has the 46438275 to 46439222 nucleotide sequence of the chromosome 15 of the dendritic cell (NCBI Accession Number AC_000172), and the known sequence is XM_002693141. The OR10A4 has 46440583 to 46468575th nucleotide sequence of the chromosome 15 of the dendritic cell, and known sequences include XM_010812585 and XM_015474715. The OR2D3 has the 46418054 to 46419025th nucleotide sequence of the chromosome 15 of the dendritic cell, and the known sequence is XM_002693134. The MAP2K3 has a nucleotide sequence of 35859039 to 35876875 of the chromosome 19 of NCVI accession number AC_000176.1, and the known sequence is NM_001083693. The PLCD3 has the 45411512 to 45432420 nucleotide sequence of the chromosome 19 sequence of the dendritic cell, and the known sequences include NM_001193028 and XM_005220854. The TIMP2 has the 54079297 to 54131054 nucleotide sequence of the chromosome 19 sequence of the dendritic cell, and the known sequence is NM_174472. The PLCD1 has the nucleotide sequence of 11497066 to 11518465 nucleotides of the chromosome 22 (NCBI Accession Number AC_000179.1) of the dendritic cell, and known sequences include XM_010817408, XM_005222372 and NM_001081576. The ROCK1 has 35459250 to 35520489th nucleotide sequence of the chromosome 24 of the dendritic cell (NCBI Accession Number AC_000181.1), and known sequences include NM_009071 and XM_006525725. PRKG1 has the nucleotide sequence of nucleotides 6901760 to 8343635 of the chromosome 26 of NCVI Accession Number AC_000183.1.

The gene is associated with various properties of meat quality.

According to one embodiment of the present invention, the CAPZB , LIMA1 , ROCK1 , WWP1 , PARK2 , NFATC2 , COL9A2 , PDGFRA , MAP3K5 and ZNF410 are related to meat quality tenderness.

According to one embodiment of the present invention, the PLA2G2A , PRKG1 , MAP4K4 , APOL6 , PARK2 , ZNF410 , MAP2K3 , PLCD3 , PLCD1 , ROCK1 and AHSA1 are associated with intramuscular fat.

According to one embodiment of the present invention, the MB (Myoglobin) and SLC48A1 are related to meat color.

According to one embodiment of the present invention, the MAP4K4 is associated with drip loss.

According to one embodiment of the present invention, the TIMP2 , PRKG1 , MAP3K5 and ATP8A1 are related to food intake and efficiency of an individual.

The degree of expression of the gene is carried out using an amplification reaction.

As used herein, the term " amplification reaction " means a reaction that amplifies a gene or a nucleic acid molecule. A variety of amplification reactions have been reported in the art, including polymerase chain reaction (PCR) (US Pat. Nos. 4,683,195, 4,683,202, and 4,800,159), reverse transcription-polymerase chain reaction (RT- , The method of Miller, HI (WO 89/06700) and Davey, C. et al (EP 329,822), the method of ligase chain reaction (Sambrook et al., Molecular Cloning, A Laboratory Manual, 3rd ed. Cold Spring Harbor Press ligase chain reaction (LCR), Gap-LCR (WO 90/01069), repair chain reaction (EP 439,182), transcription-mediated amplification (TMA) (WO 88/10315) (WO 90/06995), selective amplification of target polynucleotide sequences (U.S. Patent No. 6,410,276), consensus sequence priming sequence replication (consensus sequence) primed polymerase chain reaction (CP-PCR) 4,437,975), arbitrarily primed polymerase chain reaction (AP-PCR) (U.S. Patent Nos. 5,413,909 and 5,861,245), nucleic acid sequence based amplification (NASBA) U.S. Patent Nos. 5,130,238, 5,409,818, 5,554,517, and 6,063,603), strand displacement amplification and loop-mediated isothermal amplification. (LAMP) 23, but is not limited thereto. Other amplification methods that may be used are described in U.S. Patent Nos. 5,242,794, 5,494,810, 4,988,617 and U.S. Patent No. 09 / 854,317.

Polymerase chain reaction (PCR) is the best known gene or nucleic acid amplification method, and many variations and applications thereof have been developed. The predictive methods of the present invention include touchdown PCR 24, hot start PCR 25, 26, which modified conventional PCR procedures to enhance the specificity or sensitivity of the PCR as well as traditional PCR methods, , Nested PCR (2) and booster PCR (27) can be used. In addition, real-time PCR, differential display PCR (DD-PCR), rapid amplification of cDNA ends (RACE), multiplex PCR, inverse polymerase chain reaction chain reaction (IPCR), vectorette PCR, thermal asymmetric interlaced PCR (TAIL-PCR), and multiplex PCR.

For more information on PCR see McPherson, M.J., and Moller, S.G. PCR. BIOS Scientific Publishers, Springer-Verlag New York Berlin Heidelberg, N.Y. (2000), the teachings of which are incorporated herein by reference.

In addition, the degree of expression of the gene can be performed by a hybridization method.

The hybridization method uses PIK3CB , MRAS , PLA2G2A , CAPZB , COL9A2 , LIMA1 , SLC48A1 , MB (Myoglobin), APOL6 , ATP8A1 , PDGFRA , MAP3K5 , PARK2 , ZNF410 , AHSA1 , MAP4K4 , NFATC2 , WWP1 , OR2D2 , OR10A4 , OR2D3 , MAP2K3 , PLCD3 , TIMP2 , PLCD1 , ROCK1 And Lt ; RTI ID = 0.0 > PRKG1 . ≪ / RTI >

As used herein, the term " probe " refers to a linear oligomer of natural or modified monomer or linkages and includes deoxyribonucleotides and ribonucleotides and can specifically hybridize to a target nucleotide sequence, Present or artificially synthesized. The probe of the present invention is preferably a single strand, and is an oligodioxyribonucleotide.

When the method of the present invention is carried out in a microarray manner among the hybridization methods, the probe is used as a hybridizable array element and immobilized on a substrate. Preferred substrates include rigid or semi-rigid supports such as membranes, filters, chips, slides, wafers, fibers, magnetic beads or non-magnetic beads, gels, tubing, plates, polymers, microparticles and capillaries. The hybridization array elements are arranged and immobilized on the substrate. Such immobilization is carried out by a chemical bonding method or a covalent bonding method such as UV. For example, the hybridization array element may be bonded to a glass surface modified to include an epoxy compound or an aldehyde group, and may also be bound by UV on a polylysine coating surface. In addition, the hybridization array element can be coupled to the substrate via a linker (e.g., ethylene glycol oligomer and diamine).

On the other hand, the sample DNA to be applied to the microarray of the present invention can be labeled and hybridized with the array elements on the microarray. The hybridization conditions can be varied. Further, the detection and analysis of hybridization degree can be variously performed depending on the labeling substance.

The label of the probe may provide a signal to detect hybridization, which may be linked to an oligonucleotide. Suitable labels include fluorescent moieties (e.g., fluorescein, phycoerythrin, rhodamine, lissamine, and Cy3 and Cy5 (Pharmacia)), chromophores, chemiluminescent moieties, magnetic particles, (Such as P32 or S35), mass labels, electron dense particles, enzymes (alkaline phosphatase or horseradish peroxidase), joins, substrates for enzymes, heavy metals such as gold and antibodies, streptavidin, biotin , Hapten having specific binding partners such as digoxigenin and chelating groups. Markers can be generated using a variety of methods routinely practiced in the art such as the nick translation method, the Multiprime DNA labeling systems booklet (Amersham, 1989) and the kaination method (Maxam & Gilbert, Methods in Enzymology, 65: 499 (1986)). The label provides signals that can be detected by fluorescence, radioactivity, color measurement, weighing, X-ray diffraction or absorption, magnetism, enzymatic activity, mass analysis, binding affinity, hybridization high frequency, and nanocrystals.

The nucleic acid sample to be analyzed in the hybridization method can be prepared using mRNA obtained from various biological samples (biosamples). The biological sample is preferably a blood cell. Instead of the probe, the cDNA to be analyzed may be labeled and subjected to a hybridization reaction-based analysis.

When a probe is used, the probe is hybridized with the cDNA molecule. In the present invention, suitable hybridization conditions can be determined by a series of procedures by an optimization procedure. This procedure is performed by a person skilled in the art in a series of procedures to establish a protocol for use in the laboratory. Conditions such as, for example, temperature, concentration of components, hybridization and washing time, buffer components and their pH and ionic strength depend on various factors such as probe length and GC amount and target nucleotide sequence. Detailed conditions for hybridization are described in Joseph Sambrook, et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y. (2001); And M.L.M. Anderson, Nucleic Acid Hybridization, Springer-Verlag New York Inc .; N.Y. (1999).

After the hybridization reaction, a hybridization signal generated through the hybridization reaction is detected. The hybridization signal can be carried out in various ways depending on, for example, the type of label attached to the probe. For example, when a probe is labeled with an enzyme, the substrate of the enzyme can be reacted with the result of hybridization reaction to confirm hybridization. The combination of enzymes / substrates that may be used is a combination of a peroxidase (e.g., horseradish peroxidase) with a chloronaphthol, aminoethylcarbazole, diaminobenzidine, D-luciferin, lucigenin (bis- Acetyl-3,7-dihydroxyphenox), HYR (p-phenylenediamine-HCl and pyrocatechol), TMB (tetramethylbenzidine), ABTS (2, 2 sulfonate]), o-phenylenediamine (OPD), and naphthol / pyronine; (BCIP), nitroblue tetrazolium (NBT), naphthol-AS-B1-phosphate, and ECF substrate; alkaline phosphatase and bromochloroindoleyl phosphate; Glucose oxidase and t-NBT (nitroblue tetrazolium) and m-PMS (phenzaine methosulfate). When the probe is labeled with gold particles, it can be detected by a silver staining method using silver nitrate.

In biological samples, PIK3CB , MRAS , PLA2G2A , CAPZB , COL9A2 , LIMA1 , SLC48A1 , MB ( Myoglobin ), APOL6, ATP8A1 , PDGFRA , MAP3K5 , PARK2 , ZNF410 , AHSA1 , MAP4K4 , NFATC2 , WWP1 , OR2D2 , OR10A4 , OR2D3 , MAP2K3, PLCD3 , TIMP2 , PLCD1 , ROCK1 And If the hybridization signal for the nucleotide sequence of one or more genes selected from the group consisting of PRKG1 is higher than the corresponding gene of the nucleic acid molecule isolated from the indigenous sample, it is determined to be of African genus having high quality meat.

According to one embodiment of the present invention, there is provided a method for predicting meat quality in an African gastroenterologist of the present invention, comprising the steps of: (a) providing a PIK3CB , MRAS , PLA2G2A , CAPZB , COL9A2 , LIMA1 , SLC48A1 , MB ( Myoglobin ) , APOL6, ATP8A1 , PDGFRA , MAP3K5 , PARK2 , ZNF410 , AHSA1 , MAP4K4 , NFATC2 , WWP1 , OR2D2 , OR10A4 , OR2D3 , MAP2K3, PLCD3 , TIMP2 , PLCD1 , ROCK1 And And one or more genes selected from the group consisting of PRKG1 are highly expressed in comparison to African indigenous species ( Bos taurus indicus ).

As used herein, the term " high expression (or overexpression) " means that the expression level of the subject nucleotide sequence is higher than that of the African indigenous from the comparison of the conditions under investigation, which is a positive selected gene. For example, expression analysis methods conventionally used in the art, such as RT-PCR or ELISA methods (see Sambrook, J. et al., Molecular Cloning, A Laboratory Manual, 3rd ed. Cold Spring Harbor Press (2001) In the case of expression analysis, it means that the expression is analyzed to be high.

According to one embodiment of the present invention, the African indigenous species is a boran species, an organism species or a kenana species species.

According to another aspect of the invention there is provided PIK3CB (NCBI Gene ID 517948), MRAS (NCBI Gene ID 540803), PLA2G2A (NCBI Gene ID 507201), CAPZB (NCBI Gene ID 338052), COL9A2 (NCBI Gene ID 505942) , LIMA1 (NCBI Gene ID 540637) , SLC48A1 (NCBI Gene ID 784685), MB (NCBI Gene ID 280695), APOL6 (NCBI Gene ID 616957), ATP8A1 (NCBI Gene ID 317692), PDGFRA (NCBI Gene ID 282301), MAP3K5 (NCBI Gene ID 537380), PARK2 (NCBI Gene ID 530858), ZNF410 (NCBI Gene ID 507530), AHSA1 (NCBI Gene ID 539220), MAP4K4 (NCBI Gene ID 509109), NFATC2 (NCBI Gene ID 530401), WWP1 (NCBI Gene ID 513789) , OR2D2 (NCBI Gene ID 504498) , OR10A4 (NCBI Gene ID 617571 ) , OR2D3 (NCBI Gene ID 513635) , MAP2K3 (NCBI Gene ID 516039) , PLCD3 (NCBI Gene ID 513057) , TIMP2 282093) , PLCD1 (NCBI Gene ID 281986) , ROCK1 (NCBI Gene ID 785911) And PRKG1 (NCBI Gene ID 282004) that a nucleotide sequence, said nucleotide sequence encoding at least one gene selected from the group comprising the complementary sequence or probe specifically binding to fragments of said nucleotide African commercial species consisting of cattle (Bos taurus africanus ).

The kit may be a microarray kit or a gene amplification kit.

Since the kit of the present invention uses the above method, the description common to both is omitted in order to avoid the excessive complexity of the present specification.

The features and advantages of the present invention are summarized as follows:

(a) The present invention provides a method for providing information necessary for predicting meat quality of the African marsupial ( Bos taurus africanus ) for the production of high quality meat.

(b) The present invention provides markers relating to high quality meat flesh, intramuscular fat, meat color, juice loss, and food intake and efficiency.

(c) The markers may be used for marker-assisted selection and will be useful for meat production and lineage improvement programs.

Figure 1 shows the phylogenetic tree of maximum likelihood derived from autosomal SNPs of 38 African beasts. The data set (26,427,196 base pairs) was analyzed using maximum likelihood and neighbor-joining methods and showed the same topology. The robustness of the systematic genomics analysis is shown in each node (the left number of maximum likelihood trees is the bootstrap value and the right number of the neighbor-joining tree number is the quadruple puzzle ring reliability).
Fig. 2 is a clustering of GO terms annotated by DAVID gene presence analysis. XP-EHH and XP-CLR statistics. Clusters associated with meat quality characteristics were highlighted in red.
Figure 3 is an analysis of the presence of CluGo gene in 354 positive selected genes in an Angkor species population. CluGo visualizes selected terms in functionally distinct annotation work that reflects the relationship between terms based on the similarity of the genes involved. The node represents the GO terms, and the size of the node reflects the statistical significance of the term. The most important GO terms for each group are highlighted in color, and the circular GO terms are associated with meat quality characteristics.
Figures 4a-4d are Fst and Tajima's D plots of positive selection gene sites in adherent species and indigenous populations. Figures 4A-4D are graphs showing CAPZB , MB , PDGFRA And the AHSA1 gene. The Tajima's D plot (top plot) for each gene region represents the Tajima's D value between the 50 kb windows displayed in each population. The small (negative) Tajima's D value in the mosquito species indicates the gene region considered positive. The Fst plot (bottom plot) represents the Fst value calculated within 50 kb divided by the 5 kb window step.

Hereinafter, the present invention will be described in more detail with reference to Examples. It is to be understood by those skilled in the art that these embodiments are only for describing the present invention in more detail and that the scope of the present invention is not limited by these embodiments in accordance with the gist of the present invention .

Example

Experimental Method

Sample preparation and full-field genome resequencing

In order to carry out the next-generation sequencing of NGS, we selected a publicly available material for the analysis of WGS (shole-genome requencing) data for five species of cattle.

Five species of small breeds (10 Ankole, 9 Boran, 9 Ogaden, 10 Kenana and 10 Nama Daama) and four commercial cows Blood was collected from [Holstein, Angus, Jersey and Hanwoo] and used as a screening material.

DNA was extracted from whole blood according to the manual using G-DEXTMIIb genomic DNA extraction kit (iNtRoN Biotechnology, Seoul, Korea). To produce inserts of less than 300 bp, 3 지 genomic DNA was arbitrarily sheared using the Covaris system. The library was constructed using the TruSeq DNA sample prep kit (Illumina, Sandiego, Calif.) According to the manufacturer's guidelines and sequencing of the entire genome was performed using the Illumina HiSeq 2000 platform. The quality of the raw sequence data was confirmed using fastQC software. Pair-end sequence leads were mapped to reference subgenomes using Bowtie2 with basic parameters. The overall alignment rate of the leads to the reference sequence was 98.51% and the average read depth was 10.8x. In the whole sample, the lid covered 98.51% of the genome.

SAMartools and Genome Analysis Toolkit (GATK) from Picard tools (http://picard.sourceforge.net) for downstream processing and variant calling. Picard tools were used to eliminate potential PCR duplicates. Samtools was used to generate an index file for the reference and snake (bam) files. Genome Analysis Toolkit 1.4 was used to perform local reordering of leads to correct misalignment due to the presence of indels ("" and "" Genome Analysis Toolkit (GATK) to extract candidate SNPs. To avoid false positives and avoid possible false positives, we used the same software "" argument with the following options: 1) phred less than 30 SNP removal with -scaled score; 2) MQ0 (Mapping Quality Zero; total number of all MQ0)> 4 and quality depth (non-filtering depth of non-reference sample; low score indicates false positives and artifacts) <5 SNP removal; 3) The FS (Phish-scaled P-value of Fisher's exact test) represents the forward or reverse strand variant, which means false positive extraction. BEAGLE was used to infer the haplotyping step and to transfer missing alleles for the entire set of small groups.

Phylogenetic reconstruction

To understand the genetic distance between the varieties under consideration, systematic genomic analysis was performed using neighbor-joining (NJ) and maximum likelihood (ML) methods. A total of 26,427,196 autosomal SNPs of 38 species of 5 varieties were used for phylogenetic tree composition.

ML analysis was performed using the TREE-PUZZLE 5.2 program of the GTR model. For the quadruple puzzle ring method (1,000 puzzle ring steps), the nucleotide frequency and the Ts / Tv ratio (3.18) were estimated from the data set. The quadruple puzzle ring provides a confidence value for the ML analysis.

NJ analysis was performed using PHYLIP package 3.69 based on Kimura's 2-parameter distance. The Ts / Tv ratio (3.18) was estimated from the data set using TREE-PUZZLE 5.2 and used as the input values for the SEQBOOT, DNADIST, NEIGHBOR, and CONSENS programs in the PHYLIP package. To obtain statistical support for each node in the NJ tree, a bootstrap test (1,000 false copies) was performed.

Detection of Positive Selection Signal

To detect genomes with extensive selective sweeps, cross-population Extended Haplotype Homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR) statistics were used. XP-EHH was designed to assess the difference in haplotypes between the two populations and to detect an allele with an increased frequency of fixation in one of the two populations to be compared.

The inventors used Ankole as a test group and compared them with indigenous species ( indicus , grouped grouped species, Ogadenjon and Kenana species) as a reference group. The integrated EHH between the two groups for the representation of the XP-EHH score, which determines the direction of selection with each SNP and the extremum indicating the choice in the test genome, was compared using XP-EHH. To compare genomic regions throughout the population, the genome was divided into 50 kb non-overlapping segments and the maximum XP-EHH score of each segment was calculated. To define the empirical p-value, we removed the increased intrinsic window of 500 SNPs (combining all the windows above 1000 SNPs) according to the method used previously. The area with a P-value less than 0.01 (1%) in the ANCOOL group was judged to be a strong signal.

The present inventors conducted an XP-CLR to identify potential sites that were separately screened between the two groups. XP-CLR is a top-priority method for detecting a selection point that includes joint modeling of frequency differences of multi-locus alleles between two populations. The XP-CLR score was calculated using a script on the web page ( http://genepath.med.harvard.edu/reich) . The present invention reduced XP-CLR results to 0.95, taking into account the non-overlapping sliding window of 50 kb, the maximum number of SNPs in each window (600) and the degree of relationship of the SNPs. The candidate sweeps were defined as those with XP-CLR values in the top 1% of the empirical distribution (XP-CLR> 97.86), and the genes containing the window regions were defined as candidate genes. A significant genomic region identified from XP-EHH and XP-CLR was identified as the closest gene (UMD 3.1).

Using these two statistics, Tajima's D and FST for the candidate gene region were calculated to confirm the positive selection of the detected genes. By detecting the same gene site using other methods, it is possible to provide clear evidence of the intra-site selection effect. Tajima's D, which was used to detect a fixed selection spot in a population with very rare alleles, was consequently negative Tajima's D. Population differentiation; Fst (Fixation index)] is based on the principle that natural selection can change the amount of differentiation between different groups of species. If the population is differentiated, the amount of genetic differentiation within a site containing the selected locus will increase if the genomic differentiation within the genomic region is greater than the expected level of neutrality resulting from natural selection. To calculate the Tajima's D and FST values for the candidate gene region, VCFtool was used with a window size of 50 kb with a spacing of 5 kb steps.

Characteristics of selected candidate genes

The present invention uses the DAVID GO (Database for Annotation, Visualization and Integrated Discovery Gene Ontology) and annotation tools for gene-extent analysis to further understand the biological function and pathway of the selected gene. A significant GO term (Gene Ontology term) provides an understanding of the functional characteristics of the annotated gene. In order to identify a significant pathway, we cross-referenced DAVID with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. R software (version 3.2.1) was used for hierarchical clustering of GO terms from DAVID. In addition, we used the ClueGo plugin from Saitoscape software (version 3.2.0) to establish the GO term as well as the integration of the KEGG path, and established a functionally organized GO / path term network.

result

Data Description

The bovine genome project consists of five species of African bovine lines (Boran species, Ogaden species, Kenanas species, Angkor species and Endama species) sequenced to the ~ 11 × genome range and four species of commercial bovines (Holsters, Species, and species). Using standard sample preparation and an entire genome re-sequencing pipeline, genomic data was obtained containing 98.56% of the small reference genome and a total alignment rate of 98.84%. Finally, false cloning was eliminated through several filtering steps to retain a total of ~ 37 million SNPs. Here, 38 genomes of 4 African species (9 boron species, 9 Ogaden species, 10 kenan species and 10 anchor species) were used.

Phylogenetic tree

The maximum likelihood and neighbor-joining methods show consistent characteristics of the genetic distance between the subject lineages (Fig. 1). The anchor colony was completely separated from the three indigenous sites (100% bootstrap value / quadruple puzzle ring reliability value). Within the indigenous cattle, the three lineages were also drawn as a single lineage group with a high significance value.

The African indigenous cattle appeared on the continent after 1500 BC, but the mausoleum originated from the crossing of the taurine and the taurine in about 700 AD. More than 30 lines per week of mosquito species are distributed throughout the Great Lakes region of Eritrea, Ethiopia, South Sudan, East Africa, and South Africa. The Ancol species are one of the three genera of marsupials represented in Uganda, Rwanda, Burundi, Tanzania and the Democratic Republic of the Congo, and are widely used as valuable genetic resources in the region.

Positive selection signal

The XP-EHH and XP-CLR analyzes were performed to detect positive selection signals in the subspecies. The genomes of the ancols species were compared with those of the three indigenous pedigrees grouped into a single group. On the basis of the above analysis, XP-EHH and XP-CLR analysis statistics were used to obtain positive preselected genes of 238 and 213 respectively. Of these, 98 genes were detected in two statistics. In addition, Tajima's D for candidate genes showing selective maintenance of alleles in the anchor species was also analyzed (Table 1 and Figure 4), with significant deviation from neutral compared to indigenous cattle.

Candidate gene chromosome Windows (Mbp) XP-CLR Max XP-EHH XP-EHH P-value Tajima'D Weighted FST Mean FST characteristic PIK3CB One 131.50 - 131.55 - 2.21 1.69.E-03 -1.06 0.27 0.17 RFI MRAS One 131.73 - 131.78 112.25 - - -1.87 0.16 0.08 FCE PLA2G2A 2 133.28 -133.33 117.48 - - 0.70 0.27 0.18 IMF CAPZB 2 133.78 - 133.83 142.50 - - -0.47 0.22 0.13 year COL9A2 3 106.38 - 106.43 107.14 1.93 5.95.E-03 -1.30 0.18 0.11 year LIMA1 5 29.78 - 29.83 117.18 - - -0.33 0.39 0.24 year SLC48A1 5 32.63 - 32.68 101.45 - - -0.35 0.26 0.14 Color MB 5 74.18 - 74.23 129.86 1.96 5.00.E-03 -0.98 0.20 0.12 Color APOL6 5 74.20 - 74.25 - 2.00 5.00.E-03 -0.91 0.13 0.07 IMF ATP8A1 6 62.90 - 62.95 264.27 2.02 4.00.E-03 -1.39 0.36 0.20 FCE PDGFRA 6 71.35 - 71.40 408.60 2.61 3.00.E-04 -2.29 0.45 0.28 year MAP3K5 9 75.55 - 75.60 147.37 2.09 3.00.E-03 -0.23 0.15 0.09 RFI PARK2 9 99.13 - 99.18 132.40 2.34 2.36.E-03 -0.27 0.30 0.17 IMF ZNF410 10 85.68 - 85.73 165.86 2.18 1.94.E-03 -0.67 0.28 0.15 year AHSA1 10 89.70 - 89.75 - 2.23 2.00.E-03 -1.47 0.31 0.17 IMF MAP4K4 11 6.65 - 6.70 - 1.85 9.00.E-03 0.72 0.08 0.05 Juicy loss NFATC2 13 80.00 - 80.05 - 2.01 4.24.E-03 2.53 0.25 0.14 year WWP1 14 78.63 - 78.68 133.90 - - 1.03 0.18 0.10 year OR2D2 , OR10A4, OR2D3 15 46.40 - 46.45 - 2.07 3.45.E-03 2.61 0.18 0.12 Food intake MAP2K3 19 35.85 - 35.90 - 1.93 4.00.E-03 -0.20 0.16 0.11 IMF PLCD3 19 45.40 - 45.45 - 1.89 5.00.E-03 -0.18 0.03 0.01 IMF TIMP2 19 54.10 - 54.15 - 1.88 7.46.E-03 -0.73 0.18 0.10 RFI PLCD1 22 11.45 - 11.50 195.30 2.12 3.00.E-03 -1.43 0.14 0.08 IMF ROCK1 24 35.48 - 35.53 130.40 2.22 1.61.E-03 0.93 0.29 0.19 year; IMF PRKG1 26 7.43 - 7.48 166.61 - - -1.27 0.13 0.07 year; IMF; RFI

Negative Tajima's D values were obtained for candidate gene sites that showed the presence of an excess of rare alleles in the population. Since the allelic gene with a low frequency (rare allelic gene) has less effect on the difference between alleles compared to the allelic gene with an appropriate frequency, the excess of rare alleles inflates the latter value disproportionately to the electronic value . Similarly, population differentiation analysis supported positive selection of candidate genes (Table 1 and Figure 4); The candidate gene region showed high Fst value. Fst was widely used to identify sites of choice in other animal species.

The GO Biological Process (GO BP) and KEGG pathway in DAVID were used to create a biological module composed of clusters of functional terms. For analysis, a total of 354 genes were included except for duplicates among the genes obtained from XP-EHH and XP-CLR statistics. Functional tinnitus clustering (p <0.05) was associated with the 44 INRICID GP BP category (Fig. 2), and KEGG-pathway analysis revealed 3 pathways (p <0.05, Table 2).

Classification count P-value gene Fold in richiment Peripheral migration of white blood cells 7 0.019 ROCK1 , PIK3CB , CLDN10 , TXK , RAPGEF4 , RAPGEF3, CTNNA3 3.24 MAPK signaling pathway 11 0.021 MAP4K4 , ACVR1B , FGF18 , MAP3K5 , MAP2K3 , MRAS, PDGFRA , PLA2G2A , NR4A1 , MAPKAPK2 , NFATC2 2.25 Melanoma 5 0.038 FGF18, PIK3CB, MITF, PDGFRA, MDM2 3.85

Biological processes and pathways associated with meat quality

Meat quality is a multi-faceted and complex feature that is influenced by other factors, from molecular to mechanical. Molecularly, genes associated with many cellular mechanisms such as muscle growth, glycation, muscle contraction, stress response, cell cycle, protein hydrolysis, protein ubiquitination and apoptosis have been reported to be associated with meat quality characteristics.

Compared with indigenous cattle, commercial cattle have found to produce better beef with lower shear forces, shorter myofibril lengths, larger rib fat thickness, better water soluble collagen and higher juice loss rates. In addition, the marsupial populations have better feeding efficiency, fertility and tick resistance in the tropics.

( Including 9 genes of FMNL1 , FMNL3 , DOCK2 , LIMA1 , ROCK1 , MRAS , PRKG1 , CAPZB and ADD1 ) and actin filament-based processes (additionally including MYO7A ) Is related to the year of meat. Cellular component tissue, ie assembly and arrangement of components or cell-level processes that degrade cell components, is important in the meat year. Five genes ( WWP1 , MDM2 , CAND1 , PARK2 and LNX1 ) are involved in protein ubiquitination, an important step in protein degradation. The ubiquitination pathway affects muscle properties related to post-mortem quality. Negative control of GO term and protein complex degradation of negative control of actin filament depolymerization is associated with regulation of adipocytes.

The KEEG MAPK pathway (p = 0.0215; Table 2), which includes 11 genes ( MAP4K4 , ACVR1B , FGF18 , MAP3K5 , MAP2K3 , MRAS , PDGFRA , PLA2G2A , NR4A1 , MAPKAPK2 and NFATC3 ), plays a role in cell proliferation. (Fig. 3). The assembly of the network actin filament bundle and the positive regulation of protein hydrolysis are in the network of the associated ridicules associated with meat quality.

Genes that influence the meat quality of anancholic cells

The genes related to meat quality and feeding efficiency were selected as positive in the anolocal species (Table 1).

 Meat-year related genes

The year of meat is an important characteristic of meat quality. This is mainly influenced by the amount and solubility of connective tissue, the constitution and contraction of muscle fibers, and the degree of protein hydrolysis in the rigor muscles. Soft meat has a high level of soluble collagen, more fat and less moisture content. The degree of myofibrillar segmentation is also positively correlated with the age of the small buttocks. Adult carcass strains have a low percentage of white muscle fibers and a degree of segmentation of high myofibers, and thus have low shear forces and high flats compared to indigenous cattle. In this study, we identified genes ( CAPZB , LIMA1 , ROCK1 , WWP1 , PARK2 , NFATC2 , COL9A2 , PDGFRA , MAP3K5 and ZNF410 ) that might affect muscle structure and development, You can give.

The CAPZB (XP-CLR = 142.50) gene codes for a beta subunit of the barbed-end actin binding protein belonging to the F-actin capping protein family. This is related to skeletal muscle development and growth, and actin regulation and signaling of muscle filament contractility. CAPZB contributes to the metabolic, structural and protein hydrolysis processes of muscles that provide connections between functional networks important for muscle maturation.

LIMA1 ( EPLIN ) encodes a cytoskeleton-related protein that inhibits depolymerization of actin filaments in the bundle and cross-links the filaments. This is related to the function of the pigs in terms of muscle development and metabolism. ZNF410 , also known as APA - 1 , was found in the previous muscle transcript analysis, indicating that ZNF410 is highly expressed in the root canal of Basque pigs, known to produce meat with high intramuscular fat and tenderness compared to large white Respectively. COL9A2 , a fibrous collagen, is the largest component of the extracellular matrix, and the amount, shape, and solubility of the extracellular matrix present in the muscle tissue has a significant effect on the age of the meat. ROCK1, a gene that regulates actin cytoskeleton and cell polarity, is associated with chicken body weight, conductance, pellet length, potential and other conductance characteristics.

The genes associated with MAPK signaling ( MAP3K5 , MAP2K3 , MAP4K4 , MAPKAPK2 ) were also identified. MAPK signaling is one of the major intracellular signaling pathways that affect muscle development.

E3 ubiquitin ligase genes ( WWP1 , PARK2 ) play an important role in the regulation of various cellular functions such as proteolysis, transcription and RNA splicing. The gene catalyzes the ubiquitination of proteins by targeting proteins to various cell endpoints. The ubiquitin-proteasome system is one of the protein hydrolysis systems responsible for most of intramuscular proteolysis associated with post-mortem quality.

NFATC2 is a calcineurin substrate expressed in skeletal muscle, which is responsible for activation of new root canal. Calcineurin is important in the determination of myocyte differentiation and slow oxidative fiber phenotype.

 Genes related to intramuscular fat in meat

Intra Mucsular Fat (IMF) is a genetic meat quality characteristic that affects meat flavors, juices, visual characteristics, and years. It has a positive correlation with body fat and red muscle fiber. Storks of the angolic bellies were reported to be more juicy than the Angkor-Boran hybrids, and the Strydom researchers reported a high level of fat thickness of the ribs of the elderly species compared to the native species.

The inventors of the present invention have identified several genes ( PLA2G2A , PRKG1 , MAP4K4 , APOL6, PARK2 , ZNF410 , MAP2K3 , PLCD3 , PLCD1 , ROCK1 and AHSA1 ) which affect the fat content of the angola beef. PLA2G2A (XP-CLR = 117.48) is a member of the phospholipase A2 family and is involved in phospholipid metabolism and hydrolysis of phospholipids to fatty acids and phosphatidylinositol. In addition, as also referred to as adipose-specific phospholipase A2 ( AdPLA ), it is associated with the metabolism of adipocytes, and the effective release of free fatty acids and lysophospholipids from phosphatidylcholine release.

ROCK1 is associated with pathways associated with the function of muscle / adipose tissue of pigs with other phenotypes for high fat characteristics. E3 ubiquitin ligase enzyme has been found to be involved in the regulation of lipid metabolism. PARK2 is a strong candidate for chicken obesity and a positive regulator of lipid metabolism. PRKG1 is associated with gap junctions in pigs and is a candidate gene for basal fat. MAP2K3 is associated with the spermatozoa and lipid characteristics of pigs. MAP4K4 is involved in lipid production, triglyceride storage, fatty acid release, fatty acid oxidation and oxidative phosphorylation of mitochondria. APOL6 is one of the most important genes associated with the metabolism of lipid proteins. The phospholipase C family genes ( PLCD1 and PLCD3 ) are involved in the production of diacylglycerol and the phosphatidylinositol catabolism and phospholipid synthesis.

 Genes related to meat color, juice loss and diet efficiency

The water holding capacity is a quality parameter used as an indicator of freshness and wholesomeness. This feature may be related to changes in glucose degradation rate and meat temperature decrease. Myoglobin, MB (XP-CLR = 129.86; XP-EHH = 1.9640; p = 5.00.E-30), a spherical single chain protein present in the sarcplasm, is responsible for the red color of the meat. Myoglobin contributes to the preliminary supply of oxygen and allows the movement of oxygen within the muscle. The Solute Carrier Family 48 (Heme Transporter), member 1 ( SLC48A1 ) will be responsible for the movement of heme from the endosome to the cytosol and will function in color. Generally, the saturation of beef varieties is higher than indigenous cattle.

The loss of reddish fluid, mainly composed of meat and protein, called juice loss, is an important meat quality feature influenced by some pre- and post-factors. Juicy loss has been reported as a small but important difference between faunal and indigenous stocks; Meat of the marsupial bovine shows high juicy loss. High expression of MAP4K4 reduces pH by inhibiting the content of intracellular glucose, which facilitates the initiation of anaerobic production of post lactate.

Food intake and efficiency, as measured by Residual Feed Intake (RFI), is an economically important feature that affects the cost of meat production. The diversity of RFIs (more efficient animals with lower RFI) has a genetic component that regulates heritability. The present inventors identified positive selected genes ( TIMP2 , PRKG1 , MAP3K5 and ATP8A1 ) reported to be associated with RFI and diet efficiency. The differential expression between RFI and high samples showed that TIMP2 gene expression was increased in low RFI samples. PRKG1 is related to the gap junction. MAP3K5 is also known as apoptosis signal-regulating kinase 1 ( ASK1 ). Olfactory receptor genes ( OR2D2 , OR10A4 and OR2D3 ) affect taste and olfactory awareness and may be associated with food intake and eating behavior. The PIK3CB and MRAS genes, respectively associated with the Akt / PI3K and MAPK signaling pathways, are important for the high-diet efficiency of the chicken. The expression of these genes will provide the clues as to why they can tolerate angk closure, survive with poor quality food, and withstand severe drought.

The effect of the results of this study on the angel species

The Angol species are one of the three families of the marsh subspecies representing the subdivisions of East Africa and Central Africa. Anchor species are widely used as valuable genetic resources due to their excellent adaptability in the region. However, pedigree improvement programs for the Angol species and other ducks of East Africa were not well planned. Selective pedigree for other South African duckbill lines (eg, Mashona, Tuli and Africander) resulted in local cattle exhibiting high meat productivity. Given the reduced genetic resources of the animal and the importance of this essential genetic resource, it is important to design a breeding plan that will help to improve and preserve the angol species. The genes identified in this study will help to use MAS (Maker Assisted Selection) to improve the quality and productivity of the lineage, because it preserves genetic resources in local and other similar environments. Identification of genotypes for desired traits and potentials is important in designing breeding programs.

conclusion

The results of whole genome scans showed several positive selection genes related to other biological and cellular functions, including affecting the quality of meat quality. These results confirmed the hypothesis that commercial beef can produce high quality meat. The genes detected in this study will be helpful in the pedigree breeding program using MAS. Merchant seeds have adaptability, disease resistance and general strengths, and thus have potential to be used as beef cattle producing high quality meat in the tropics.

While the present invention has been particularly shown and described with reference to exemplary embodiments thereof, it is to be understood that the same is by way of illustration and example only and is not to be construed as limiting the scope of the present invention. It is therefore intended that the scope of the invention be defined by the claims appended hereto and their equivalents.

Claims (10)

How to provide the information necessary for predicting meat quality of the African marsupial bred ( Bos taurus africanus ), including the following steps:
(a) separating a nucleic acid molecule of a biological sample separated from an African phylogenetic tree; And
(b) the nucleic acid PIK3CB (NCBI Gene ID 517948) in the molecule, MRAS (NCBI Gene ID 540803) , PLA2G2A (NCBI Gene ID 507201), CAPZB (NCBI Gene ID 338052), COL9A2 (NCBI Gene ID 505942), LIMA1 (NCBI Gene ID 540637), SLC48A1 (NCBI Gene ID 784685), MB (NCBI Gene ID 280695), APOL6 (NCBI Gene ID 616957), ATP8A1 (NCBI Gene ID 317692), PDGFRA (NCBI Gene ID 282301), MAP3K5 (NCBI Gene ID 537380), PARK2 (NCBI Gene ID 530858), ZNF410 (NCBI Gene ID 507530), AHSA1 (NCBI Gene ID 539220), MAP4K4 (NCBI Gene ID 509109), NFATC2 (NCBI Gene ID 530401), WWP1 (NCBI Gene ID 513789) , OR2D2 (NCBI Gene ID 504498) , OR10A4 (NCBI Gene ID 617571), OR2D3 (NCBI Gene ID 513635), MAP2K3 (NCBI Gene ID 516039), PLCD3 (NCBI Gene ID 513057), TIMP2 (NCBI Gene ID 282093), PLCD1 (NCBI Gene ID 281986) , ROCK1 (NCBI Gene ID 785911) And And PRKG1 (NCBI Gene ID 282004).
2. The method of claim 1, wherein the african amphibian species is an anoole.
The method according to claim 1, further comprising the step (c) of comparing the expression level of the gene with African indigenous ( Bos Taurus indicus ) after the step (b).
2. The method of claim 1, wherein the CAPZB , LIMA1 , ROCK1 , WWP1 , PARK2 , NFATC2 , COL9A2 , PDGFRA , MAP3K5 And ZNF410 are associated with meat quality tenderness.
2. The method of claim 1, wherein the PLA2G2A , PRKG1 , MAP4K4 , APOL6 , PARK2 , ZNF410 , MAP2K3 , PLCD3 , PLCD1 , ROCK1 and AHSA1 are associated with intramuscular fat.
2. The method of claim 1, wherein the MB and SLC48A1 are associated with meat color.
2. The method of claim 1, wherein the MAP4K4 is associated with drip loss.
2. The method of claim 1, wherein said TIMP2 , PRKG1 , MAP3K5 and ATP8A1 are related to food intake and efficiency of an individual.
The method of claim 1, wherein the PIK3CB , MRAS , PLA2G2A , CAPZB , COL9A2 , LIMA1 , SLC48A1 , MB (Myoglobin), APOL6 , ATP8A1 , PDGFRA , MAP3K5 , PARK2 , ZNF410 , AHSA1 , MAP4K4 , NFATC2 , WWP1 , OR2D2 , OR10A4, OR2D3 , MAP2K3 , PLCD3 , TIMP2 , PLCD1 , ROCK1 And Wherein the at least one gene selected from the group consisting of PRKG1 is a positive selection in comparison to the African tortoise indicus (African taurus indicus ).
PIC3CB (NCBI Gene ID 517948) , MRAS (NCBI Gene ID 540803) , PLA2G2A (NCBI Gene ID 507201) , CAPZB (NCBI Gene ID 338052) , COL9A2 (NCBI Gene ID 505942) , LIMA1 (NCBI Gene ID 540637) , SLC48A1 NCBI Gene ID 784685), MB ( NCBI Gene ID 280695), APOL6 (NCBI Gene ID 616957), ATP8A1 (NCBI Gene ID 317692), PDGFRA (NCBI Gene ID 282301), MAP3K5 (NCBI Gene ID 537380), PARK2 (NCBI Gene ID 530858), ZNF410 (NCBI Gene ID 507530), AHSA1 (NCBI Gene ID 539220), MAP4K4 (NCBI Gene ID 509109), NFATC2 (NCBI Gene ID 530401), WWP1 (NCBI Gene ID 513789), OR2D2 (NCBI Gene ID 504498 ), OR10A4 (NCBI Gene ID 617571 ), OR2D3 (NCBI Gene ID 513635), MAP2K3 (NCBI Gene ID 516039), PLCD3 (NCBI Gene ID 513057), TIMP2 (NCBI Gene ID 282093), PLCD1 (NCBI Gene ID 281986), ROCK1 (NCBI Gene ID 785911) And PRKG1 (NCBI Gene ID 282004) that a nucleotide sequence, said nucleotide sequence encoding at least one gene selected from the group comprising the complementary sequence or probe specifically binding to fragments of said nucleotide African commercial species consisting of cattle (Bos taurus africanus ).

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