Snps Detection Of IRS-1, TNFSF11, TNFRSF11β Gene And Its Relationship With Body Measurement And Meat Quality Traits In Qjnchuan Cattle

This research studied on the polymorphisms of bovine IRS-1, TNFSF11, TNFRSF11βgene and their associations with body measurements and meat quality in Qinchuan cattle. Weemployed PCR-RFLP, PCR-SSCP and DNA sequencing to detect polymorphisms in bovineIRS-1, TNFSF11and TNFRSF11β genes.399Qinchuan heifers with18to24months old wereselected to analyze the polymorphisms with their body measurement and meat quality traits tosearch the best gene or genotype relating to these traits. Detection result revealed as thebelow showed.(1)We identified two SNPs in exons of bovine IRS-1gene: g.+2346G>A, Glu>Glu; B1site: g.+2394G>A, Leu>Leu. It showed two genotypes in each site(B1site: CC and CD；B2site：AA and AB) and homozygote DD and BB were not detected in the study. χ2test showed,B1site was in agreement with the Hardy-Weinberg equilibrium (P>0.05), B2site wassignificantly deviated from Hardy-Weinberg equilibrium (P<0.01). At B1locus, genotype CCis dominant genotype, allele C was preponderant allele, belonged to intermediate geneticdiversity; At B2locus, genotype AA is dominant genotype, allele A was preponderant allele,belonged to low genetic diversity. As association analysis demonstrated, at B1site:individuals with different genotypes had significant differences in body length, hip width,chest circumference and loin muscle area (P<0.05), at B2site: individuals with differentgenotypes had significant differences on hip width, chest depth and backfat thickness(P<0.05). Furthermore, haplotype analysis showed body measurement traits of combinedgenotype ABCD were significantly higher than those of the other kinds of combinationsexcept on backfat thickness and intramuscular fatty content. What's more, the effect sizes ofmulti-loci combinations on individuals were higher than those of single-marker loci. As theresult showed, IRS-1gene had a significant effect on body measurement and carcass traits inQinchuan cattle. Hence, it could be took as a candidate gene for selecting new breed ofQinchuan cattle and the ABCD genotype maybe the best one for the Qinchuan beef cattlebreeding.(2)We identified three SNPs in bovine TNFSF11gene:SNP34080(C�'T mutation),named as C331;SNP34096(T�'C mutation),named as C332;SNP34117(A�'G mutation), named as C333.After PCR-RFLP analyzing, the C331site had three genotypes(GG\GH\HH)with restriction enzyme-HincⅡ.And C332site also had three genotypes(MM\MN\NN) withrestriction enzyme-BseL Ⅰ. PCR-SSCP showed the C333site had three genotypes(PP\PQ\QQ). All the genotypes were coincided with the consequences of DNA sequencing.Moreover, χ2test showed the C331and C333site was in agreement with the Hardy-Weinbergequilibrium (P>0.05), C332site was significantly deviated from Hardy-Weinberg equilibrium(P<0.01), in the detected Qinchuan cattle populations. In C331site, GH genotype waspreponderant genotype, G allele was preponderant allele, and it belonged to intermediategenetic diversity. InC332site, MM genotype was preponderant genotype, M allele waspreponderant allele, and it also belonged to intermediate genetic diversity. InC333site, PPgenotype was preponderant genotype, P allele was preponderant allele, and it also belongedto intermediate genetic diversity. Association analysis in C331site showed individuals withdifferent genotypes had significant differences on hip height, hip width and chestcircumference (P<0.05), while in C332site individuals with different genotypes hadsignificant differences on body length and hip height (P<0.05). After linkage disequilibriumanalysis, it had linkage between these two sites. The results of haplotype analysis withcombining the two loci showed body measurement traits of combined genotype HHMM weresignificantly higher than those of the other kinds of combinations. And the effect size ofmulti-loci combinations markers was higher than those of single-marker loci. And the C333site associated with body measurement and meat quality traits. It maintained the QQ hadsignificant differences on body length, hip width, ischium width, loin muscle depth (P<0.05).And these entire results provided evidence thatTNFSF11gene had a significant effect on bodymeasurement traits in Qinchuan cattle populations, thus, it could be a candidate gene in thebreeding of Qinchuan beef cattle. Additionally, the combined genotype HHMM genotypeshould be selected as a molecular marker for beef cattle breeding as its superior performanceon beef cattle body measurement traits in Qinchuan cattle populations.(3) We just identified only one SNPs in the second exon of bovine TNFRSF11β gene: g.+18871C>T, Leu>Leu; After PCR-RFLP analyzing, the C43site had two genotypes (RR\RT)with restriction enzyme-BoxI. And the other homozygote was not detected. All the genotypeswere coincided with the consequences of DNA sequencing. But result of associationdisplayed there was no traits had significant differences with the detected genotypes. So, weconcluded that the SNP had little effect to body measurement and detected meat quality traits,and it couldn't be selected in Qinchuan beef cattle breeding.