A Global Analysis of Y-STR INRA189 Polymorphism in Chinese Domestic Yak Breeds/Populations.

Zhijie Ma,Jianlin Han,Ma Bai,Chuzhao Lei,Xiaoting Xia,Shengmei Chen

doi:10.3390/ani10030393

Abstract

Simple SummaryY chromosome-specific markers have been widely used in studying the origin, migration, diversity, and population relationship in several mammalian species. So far, the investigations on yak paternal genetics were mostly based on Y-SNPs information, but very few on Y-STR markers. In this study, we comprehensively investigated the polymorphism of Y-STR INRA189 locus, identified the geographical distribution pattern of its alleles in 15 Chinese domestic yak breeds/populations, and provided basic data for yak paternal genetic analysis. Our results showed that INRA189 is an intermediate polymorphic Y-STR marker with six alleles present among 15 Chinese domestic yak breeds/populations and that the variation among six alleles was due to different numbers of repetitions of a TG dinucleotide motif.The objective of this study was to probe into the polymorphism of Y-STR INRA189 and identify the geographical distribution pattern of its alleles in the Chinese domestic yak gene pool. We examined the variation at INRA189 locus in 682 male yaks representing 15 breeds/populations in China. The results showed that six alleles, including five reported previously (149, 155, 157, 159, and 161 bp) and a new one identified in this study (139 bp), were detected at INRA189 locus based on genotyping analysis. The frequencies of six alleles varied among the 15 yak breeds/populations with a clear phylogeographical pattern, which revealed the paternal genetic difference among Chinese yak breeds/populations. The average polymorphism information content (PIC) among the 15 yak breeds/populations was 0.32, indicating INRA189 to be an intermediate polymorphic Y-STR marker (0.25 < PIC < 0.5) in yak. Sequence alignment revealed that the variations among six alleles at INRA189 were defined by a TG dinucleotide repeat motif, which repeated for 12, 17, 20, 21, 22, and 23 times, corresponding to the alleles of 139, 149, 155, 157, 159, and 161 bp, respectively. Therefore, we believe that the polymorphic yak Y-STR INRA189 can be used to characterize male-mediated genetic events, including paternal genetic origin, diversity, and evolution.

Highlights

In accordance with previous reports [9,10,11], our current results showed that INRA189 was only present in male yaks, which further confirmed it to be a yak Y-chromosome specific microsatellite marker
We comprehensively examined the polymorphism of INRA189 marker in 15 Chinese yak breeds/populations
The results showed that the average polymorphism information content (PIC) for INRA189 marker in three Chinese yak breeds (Gaoyuan, Huanhu, and Datong) was 0.2379, which indicated that this marker was a minimally informative STR

Summary

Introduction

They provide products (milk, meat, hair, hides, and manure for fuel) and services (draught, packing, and riding) to pastoralists and agro-pastoralists living in these. China owns rich yak genetic resources with more than 15 million animals represented by fuel) and services (draught, packing and riding) to pastoralists and agro-pastoralists living in these. 15 million animals represented by (such as single nucleotide polymorphisms (SNPs), 12 Y-chromosome-specific officially recognized breedspolymorphisms and several local populations [2]. Y-chromosome-specific (such as single polymorphisms (SNPs), insertion-deletion (Indels), with short tandem repeats (STRs) andinferred copy from number variations mutations (CNVs)) can add microsatellites significant genetic information to what can be numberand variations (CNVs)) can add [3,4].

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