Copy number variations of five Y chromosome genes in donkeys

Haoyuan Han,Ruihua Dang,Chuzhao Lei,Xiaoting Xia,Hong Chen,Xiaocheng Zhao

doi:10.5194/aab-60-391-2017

Haoyuan Han, Ruihua Dang + Show 4 more

Open Access

https://doi.org/10.5194/aab-60-391-2017

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Abstract

Abstract. In mammals, the Y chromosome plays a pivotal role in male sex determination and is essential for normal sperm production. A number of studies were conducted on Y chromosome genes of various species and identified single-copy and multi-copy genes. However, limited studies about donkey Y chromosome genes have been done. In this study, 263 male samples from 13 Chinese donkey breeds were collected to analyze the copy number variations (CNVs) of five Y chromosome genes using the quantitative PCR (qPCR) method. These five genes (cullin 4 B Y (CUL4BY), equus testis-specific transcript y1 (ETSTY1), equus testis-specific transcript y4 (ETSTY4), equus testis-specific transcript Y 5 (ETSTY5), and sex-determining region Y (SRY) were identified as multi-copy, whose median copy numbers (MCNs) were 5, 45, 2, and 2, and 13 with CNV ranges of 1–57, 1–227, 1–37, 1–86 and 1–152, respectively. The CNVs of these five genes were shared in different breeds. Compared to previous studies, the copy numbers of five genes showed some distinct consequences in this study. In particular, the well-known single-copy SRY gene showed CNVs in donkeys. Our results provided genetic variations of donkey Y chromosome genes.

Highlights

As a consequence of 230–300 million years of independent and non-recombining evolution, the majority (95 %) of the present-day Y chromosome is a male-specific region (MSY) that does not recombine with the X chromosome during meiosis to undergo homologous recombination (Graves, 1998; Quintana-Murci and Fellous, 2011)
The cycle threshold (CT) values generated from DNA of graded concentrations for reference ( ACTB) and targeted genes (CUL4BY, ETSTY1, ETSTY4, ETSTY5, and sex-determining region Y (SRY)) were used to calculate the standard curves and their linear regression equations, the slopes of which were applied to measure primer efficiencies according to the equation E = 10(−1/slope)
In order to minimize technical error and to obtain an accurate copy number (CN) estimation, raw quantitative PCR (qPCR) data showing a coefficient of variation (CV) > 1 % between the duplicates were excluded from further analysis

Summary

Introduction

As a consequence of 230–300 million years of independent and non-recombining evolution, the majority (95 %) of the present-day Y chromosome is a male-specific region (MSY) that does not recombine with the X chromosome during meiosis to undergo homologous recombination (Graves, 1998; Quintana-Murci and Fellous, 2011). Studies on CNV do not include an analysis of variation on the Y chromosome generally and only focus on a few Y-linked genes (Skaletsky et al, 2003). The CUL4BY gene was involved in this study in order to determine its copy numbers in donkeys. Copy numbers reveal the basic genetic and structural information of Y chromosome genes. The previous study determining copy numbers on donkey Y chromosome genes was limited. The quantitative PCR (qPCR) method was performed to determine the copy number variations of five Y chromosome genes (CUL4BY, ETSTY1, ETSTY4, ETSTY5, and SRY) in 263 males from 13 Chinese donkey breeds, which would provide novel genetic variations of donkey genome

Sampling

Primer design

Statistical analysis

Male specificity of primers

The CNVs of five Y chromosome genes in donkeys

Conclusions