Novel Y‐chromosome polymorphisms in Chinese domestic yak

Abstract

Y-chromosome-specific haplotypes (Y-haplotypes) constructed using single nucleotide polymorphisms (Y-SNPs) in the MSY (male-specific region of the Y-chromosome) are valuable in population genetic studies. But sequence variants in the yak MSY region have been poorly characterized so far. In this study, we screened a total of 16 Y-chromosome-specific gene segments from the ZFY, SRY, UTY, USP9Y, AMELY and OFD1Y genes to identify Y-SNPs in domestic yaks. Six novel Y-SNPs distributed in the USP9Y (g.223C>T), UTY19 (g.158A>C and g.169C>T), AMELY2 (g.261C>T), OFD1Y9 (g.165A>G) and SRY4 (g.104G>A) loci, which can define three Y-haplotypes (YH1, YH2 and YH3) in yaks, were discovered. YH1 was the dominant and presumably most ancient haplotype based on the comparison of UTY19 locus with other bovid species. Interestingly, we found informative UTY19 markers (g.158A>C and g.169C>T) that can effectively distinguish the three yak Y-haplotypes. The nucleotide diversity was 1.7 × 10(-4) ± 0.3 × 10(-4) , indicating rich Y-chromosome diversity in yaks. We identified two highly divergent lineages (YH1 and YH2 vs. YH3) that share similar frequencies (YH1 + YH2: 0.82-0.89, YH3: 0.11-0.18) among all three populations. In agreement with previous mtDNA studies, we supported the hypothesis that the two highly divergent lineages (YH1 and YH2 vs. YH3) derived from a single gene pool, which can be explained by the reunion of at least two paternal populations with the divergent lineages already accumulated before domestication. We estimated a divergence time of 408 110 years between the two divergent lineages, which is consistent with the data from mitochondrial DNA in yaks.

Y-STR INRA189 polymorphisms in Chinese yak breeds

“…In Qinghai province, there are three yak breeds, including two indigenous breeds (Gaoyuan and Huanhu) and one improved breed (Datong). Currently, there have been few studies on Y-chromosome markers in the yak (Li et al, 2014). Previous genetic analyses indicated that INRA189 is a yak Y-chromosome-specific microsatellite (Y-STR), which has 2-3 alleles in partial Chinese yak populations and in the Swiss yak population (Han et al, 2000;Nguyen et al, 2005).…”

Identification and diversity of Y‐chromosome haplotypes in Qinghai yak populations

“…SRY4 , USP9Y , UTY19 , AMELY3 and OFD1Y10 markers; Li et al . ), we found four new Y‐SNPs mapped near the reverse primer region in the OFD1Y10 marker (g.569A>C, g.578A>C, g.608G>T and g.653G>C). All newly annotated sequences in this study were deposited in GenBank (accession nos.…”

“…Based on six Y‐chromosome single nucleotide polymorphisms (Y‐SNPs), our previous study identified three Y‐haplotypes and two highly divergent lineages in 65 male yaks (Li et al . ). However, to the best of our knowledge, besides these reports, no information is available on the genetic diversity and phylogeographical distribution of yak Y‐chromosome haplotypes.…”

“…Five fragments of the SRY4 , USP9Y , UTY19 , AMELY3 and OFD1Y10 loci carrying the six previously reported Y‐SNPs were amplified using previously described PCR primers and conditions (Table ; Li et al . ). PCR products of all male yaks were sequenced in two directions with the original PCR primers on an ABI 3730 DNA sequencer (Applied Biosystems, Inc.).…”

“…Notably, the UTY19 fragment carrying two SNPs was confirmed to discriminate the three yak Y‐haplotypes previously identified by Li et al . (). However, in the present study, the Y‐SNP combinations in UTY19 and OFD1Y10 fragments can define the seven Y‐haplotypes, which allowed us to characterize the Y‐haplotype composition in different yak populations/breeds at a relatively high resolution.…”