Study On Genes Responsible For Fiber And Immune Traits In Yak

The yak is distributed in the highland alpine and subalpine areas with an average altitude above3000m and centered on the Qinghai-Tibetan Plateau. It is a unique and valuable gene pool of livestock genetic resources. China accounts for about95%of the world’s total yak population. Yak has a strong adaptability to the alpine grasslands, survives freely and reproduces normally with thin air, short grass growing season, cold weather and very harsh environmental conditions. These distinctive physiological characteristics are attributed not only to its exceptional fiber and coat structures to become accustomed to cold and to prevent strong ultraviolet radiation, but also to its cardiopulmonary and immune systems to adapt to less oxygen in the air.In this study, a few key genes including seven keratin-associated proteins (KAPs)(KAP3-1, KAP7, KAP13-1and four members of KAP1family and the highly polymorphic exon2of DRB3genes associated with fiber and immunity traits were selected as candidates critical to genetic improvement of yak grown and development. The complete coding sequences of the seven KAPs genes were generated for the first time in yak. The genetic diversity, haplotype reconstruction and probable function of these genes were investigated in yak as well as taurine cattle. The major research findings are as follows:The PCR product of KAP3-1gene was525bp in length containing the297bp long complete coding sequence (CDS). There were four SNPs determining four haplotypes and genotypes each with the major yak haplotype BOSGR-KRTAP3-1*A present in all six yak populations at frequencies more than0.81and genotype AABB to be predominant in all six yak populations. Two of the four haplotypes were closely linked to the major taurine cattle haplotype and present at relatively low frequencies in five yak populations, indicating their taurine cattle origins through genetic introgression following historical hybridization events. Three out of the four SNPs were found in the CDS region and they were all synonymous. The PCR product of KAP7gene was375bp in length carrying the264bp long complete CDS. Yak only had a single haplotype which was shared by the major taurine cattle haplotype. There was a second haplotype in taurine cattle with two SNPs between the two haplotypes, of which one was non-synonymous but the other to be synonymous. The PCR product of KAP’13-1gene was607bp in length including the495bp long complete CDS. Three SNPs were found between the yak and cattle haplotypes while there were three non-synonymous SNPs present within the CDS of yak KAP13-1gene defining four haplotypes and seven genotypes, of which TTTTGG was the predominant genotype and BOSGR-KRTAP13-1*A to be the dominant haplotype.Among the KAP1gene family, the PCR product of KAP1-1gene was617bp in length including471bp long CDS. There were14SNPs defining11genotypes and seven haplotypes with ABCD genotype to be most frequent and present in all five yak populations and BOSGR-KRTAP1-1*A and BOSGR-KRTAP1-1*B to be major haplotypes. The PCR product of KAP1-2gene was624bp in length carrying501bp long complete CDS which had three SNPs determining five genotyping and four haplotypes with AACCAA genotype to be predominant and BOSGR-KRTAP1-2*A to be major haplotype. This study successfully generated the complete CDS of yak and taurine cattle KAP1-3gene which filled the gap in the current bovine genome assembly. The PCR product of KAP1-3gene was525bp including429bp long complete CDS. Five SNPs were detected in yak sequences and they defined five genotypes and haplotypes each with AABB genotype to be predominant and BOSGR-KRTAP1-3*A to be major haplotype. The KAP1-4gene in yak had length polymorphisms of30bp In/Del in its CDS with length variations in471bp,441bp and411bp. There was no SNP in471bp and411bp long fragments but two SNPs were found in441bp long fragment. The length polymorphisms and SNPs determined nine genotypes and five haplotypes, of which ABDD genotype were present in all yak populations though it was less frequent than the AADD genotype present only in GT, DQK and AD yak populations. It is evident that the numbers of haplotypes across the four members of the KAP1gene family were all different, indicating possible recombination in this closely linked genomic region which calls for further investigation.In search for polymorphisms and determining haplotypes in yak DRB3exon2, we not only used direct and cloning sequencing protocols, but also explored an allele-specific sequencing method to ensure the PCR amplifications of specific haplotypes from this highly polymorphic genomic fragment. A total of66SNPs present in bi-, tri-or tetra-alleles as well as a single amino acid codon In/Del mutations were identified within the yak DRB3exon2, of which only three SNPs leading to amino acid replacements were predicted to have probable functional and structural significance:157G/T mutation for Val>Leu,220G/A mutation for Cys>Ser, and259G/A mutation for to Arg>Thr. Forty haplotypes were reconstructed from82samples of Tianzhu White yak and Gannan yak. Fu and Li’s D*neutrality test revealed a probable impact of artificial selection on the genetic diversity of DRB3exon2in the Tianzhu White yak.