Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes.

Xiaoming Ma,Donghai Fu,Pengjia Bao,Xian Guo,Jie Pei,Xiaoyun Wu,Min Chu,Chunnian Liang,Congjun Jia,Ping Yan,Xuezhi Ding

doi:10.3390/genes10060463

Abstract

Yak (Bos grunniens) is an important domestic animal living in high-altitude plateaus. Due to inadequate disease prevention, each year, the yak industry suffers significant economic losses. The identification of causal genes that affect blood- and immunity-related cells could provide preliminary reference guidelines for the prevention of diseases in the population of yaks. The genome-wide association studies (GWASs) utilizing a single-marker or haplotype method were employed to analyze 15 hematological traits in the genome of 315 unrelated yaks. Single-marker GWASs identified a total of 43 significant SNPs, including 35 suggestive and eight genome-wide significant SNPs, associated with nine traits. Haplotype analysis detected nine significant haplotype blocks, including two genome-wide and seven suggestive blocks, associated with seven traits. The study provides data on the genetic variability of hematological traits in the yak. Five essential genes (GPLD1, EDNRA, APOB, HIST1H1E, and HIST1H2BI) were identified, which affect the HCT, HGB, RBC, PDW, PLT, and RDWSD traits and can serve as candidate genes for regulating hematological traits. The results provide a valuable reference to be used in the analysis of blood properties and immune diseases in the yak.

Highlights

Yak (Bos grunniens) is an iconic symbol of the Qinghai–Tibet Plateau and adjacent high-altitude areas [1]
The coefficient of variation (CV) values ranged from a minimum of 2.92 to a maximum of 57.71 for mean corpuscular hemoglobin concentration (MCHC) and platelet-large cell ratio (P-LCR), respectively
A total of 42,276 SNPs failed the missingness test (GENO > 0.05), 653,185 SNPs had a minor allele frequency (MAF) of less than 0.05, and 8710 SNPs were severely departing from the Hardy Weinberg Equilibrium (HWE) (p-value less than 10−5 )

Summary

Introduction

Yak (Bos grunniens) is an iconic symbol of the Qinghai–Tibet Plateau and adjacent high-altitude areas [1]. This region is well known for its high-altitude, pristine natural environment, and extreme seasonal changes [2]. While only a few animal species can survive in the Qinghai–Tibet Plateau, yaks thrive in the extreme conditions present in this area. They provide food such as meat and milk, a mode of transportation, shelter, and fuel for the residents of this high-altitude region [5,6]. Due to relatively primitive breeding technology used by the herdsmen, and the difficulty or even lack of implementing immunizations and other measures preventing epidemics, yaks are very susceptible to parasites, which has caused significant economic losses to the yak-breeding industry

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