Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes.

Ting Sun,Chuzhao Lei,Hong Chen,Ruihua Dang,Quratulain Hanif

doi:10.3390/ani10010031

Abstract

Simple SummaryThe amplification of the male-specific region of the Y chromosome was a unique phenomenon during mammalian sex chromosome evolution. The Y-linked copy number variations of many species have been confirmed. However, the Y-linked copy number variations (CNVs) in water buffalo are still unknown. In this study, we investigated the copy number variations of four Y-linked genes (SRY, UTY, DBY, and OFD1Y) in buffalo. Our results showed that UTY was a single-copy gene in buffalo, while DBY, OFD1Y, and SRY exhibited copy number variations in buffalo.Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.

Highlights

Copy number variation (CNV) is a significant source of genetic diversity, comprised of varying copy numbers of DNA segments within species [1]
The aim of the study was to investigate the CNVs of sex determining Region of Y-Chromosome (SRY), DBY, oral-facial-digital syndrome 1 Y-linked (OFD1Y), and UTY of two river buffaloes and 254 swamp buffaloes from 15 populations distributed in China, Vietnam, and Laos using quantitative real-time PCR (qPCR)
The results showed that each pair of primers amplified a male specific band with the expected fragment size, confirming that the designed primers were male-specific and could be used for the qPCR analysis in this study (Figure 1)

Summary

Introduction

Copy number variation (CNV) is a significant source of genetic diversity, comprised of varying copy numbers of DNA segments (at least 50 bp in size) within species [1]. CNVs are known to be associated with gene expression, phenotypic variation, adaption, and the development of various diseases [2,3]. The CNV is associated with resistance or susceptibility to gastrointestinal nematodes [4], production traits [5,6], and muscle [7]. Studies showed that the CNV plays a key role in the coat color in goat [8], pig [9], and horse [10]. Chromosome Y is rich in segmental duplications and provides a rich environment for Animals 2020, 10, 31; doi:10.3390/ani10010031 www.mdpi.com/journal/animals

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