Study On Markers Of IRX3 Gene Of Growth Trait Selection In Chinese Native Cattle And Their Application

Iroquois homeobox 3 is the most representative one in Iroquois homeobox family(IRXs), according to the latest report, mutation in non-coding region of FTO(fat mass and obesity associated) which is recognized obesity gene can lead to over-expression of bovine IRX3 for inducing obesity and bovine IRX3 gene can effectively control the formation of brown fat. The interaction between the two genes in humans, mice and zebrafish exists widely. Thus we presumed IRX3 gene is likely to affect fat metabolism for affecting cattle production.While IRX3 gene has not been reported in cattle currently, the analysis in IRX3 gene marker technology and its application can improve the economic efficiency of beef cattle industry which has important theoretical and practical significance.The goal of this study was to identify SNPs of bovine IRX3 gene in 724 cattle individuals(JN,n=205, QC,n=519)and to assess their associations with groth traits by DNA pool,DNA sequencing and PCR-RFLP technique,aiming to finding important molecular markers which contributs to the development of the beef cattle industry, and to propose specific applications of the technology in cattle breeding.Test results were as follows:1. Genetic variation of bovine IRX3 geneTreating equal mixture of DNA pool as template which was mixed with 30 Jinnan and Qinchuan cattle individual DNA,five pairs of primers were designed to amplify the whole of bovine gene and its promoter region.Three mutations were identified:g.-1941G>A and g.-991G> C were located in the promoter region, g.1941T>G was located in the second intron. Using typing method of Msp1-RFLP, KpnI-RFLP and Hinf1-RFLP tested genetic mutation in Jinnan cattle and Qinchuan cattle.Genetic analysis, linkage disequilibrium analysis, association analysis and haplotype analysis were carried out in the three SNPs of the bovine IRX3 gene. Genetics diversity analysis shows that there were large differences between the two cattle breeds,wild allelic frequencies(0.647 and 0.601) of SNP1 were significantly higher than the mutant allele(0.353 and 0.399), wild allelic frequencies(0.916 and 0.849) of SNP3 were significantly higher than the mutant allele(0.154 and 0.256),and mutant allelic frequency of SNP2 was higher(0.850 and 0.823); and SNP3 in Jinnan cattle was detected only two genotypes GG and GT,and there were no mutant individuals.Genetic polymorphism analysis showed that three SNPs contended rich polymorphism information and large breeding potential.In addition SNP3 in Jinnan cattle possessed low genetic diversity(PIC<0.25), while other SNPs possessed middle genetic diversity. Furthermore the χ2 –test showed that the genotype distribution within both cattle are in Hardy-Weinberg equilibrium(P>0.05) except SNP2 in Qinchuan cattle.Haplotype analysis showed that there are haplotypes frequency differences among the same speciesc and there are differences in different varieties about the same haplotype.Eight haplotypes were revealed and haplotype AGG was predominant and can be detected in Qinchuan, but only six haplotypes were detected in Jinnan cattle. Linkage analysis showed that there was a strong linkage in SNP1 and SNP3 of Jinnan cattle.2. Association of three novel SNPs of the bovine IRX3 gene with growth traitsAssociation analysis with growth traits showed that SNP1 was significantly associated with chest of Jinnan cattle(P<0.05), the individuals with genetype AA had greater chest depth than those with genotype AG; SNP2 was significantly associated with body height, chest deep, body height terms and length of Jinnan cattle(P<0.05), the individuals with genetype CC had greater body height, chest deep, body height terms and length than those with genotype CG and GG. But there was not significant impact on growth traits of Qinchuan(P>0.05); SNP3 was significantly associated with chest circunference of Qinchuan cattle(P<0.05), the individuals with genetype GG had greater chest circunferenc than those with genotype GT; But there was not significant impact on growth traits of Jinnan(P>0.05).The above analysis shows that three SNPs of IRX3 gene could raise cattle growth traits and were important molecular genetic markers using for cattle breeding.3. Applications on cattle IRX3 gene markersWe can combine IRX3 marker technology and multi-stage selection for cattle breeding effectively by the way of capacity measurement.1) Identify SNPs which have significantly association with cattle growth traits.Theoretical basis: association analysis with growth traits showed that SNP1 was significantly associated with chest deapth of Jinnan cattle(P<0.05), the individuals with genetype AA had greater chest depth than those with genotype AG; SNP2 was significantly associated with body height, chest deep, body height terms and length of Jinnan cattle(P<0.05), the individuals with genetype CC had greater body height, chest deep, body height terms and length than those with genotype CG and GG. But there was not significant impact on growth traits of Qinchuan(P>0.05); SNP3 was significantly associated with chest circunference of Qinchuan cattle(P<0.05), the individuals with genetype GG had greater chest circunferenc than those with genotype GT; But there was not significant impact on growth traits of Jinnan(P>0.05).2) Before weaning: First we should calf number and record time of birth, information of parents, and body weight for breeding work.Due to various traits in the period of weaning can not be showed, we can select early by identifying genotypes which is relevant with molecular marker and we can also choose to breed taking the advantage of parents with better genetype.Such as AA genotype corresponded with SNP1, CC genotype corresponded with SNP2 and GG genotype corresponded with SNP3.3) 6-month-old:major growth traits of cattle has showed, the period should be treated to select as the main stage.We could use molecular determination and measure their superior traits such as chest deep, body height, body length and chest circumstance.