Abstract
Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.
Highlights
The mammalian Y chromosome stands out from the rest of the genome because it is male specific, constitutively haploid, and exhibits unique structural and functional features (Skaletsky et al, 2003)
The copy numbers (CNs) of eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), UBE1Y, sex determining region Y (SRY), and YIR2 were estimated for test samples using the following three equations described in Hamilton et al (2009): Copy numbercalibrator
The results demonstrated that every primer pair for the target genes, EIF1AY, ETSTY1, ETSTY4, ETSTY5, ETY4, UBE1Y, SRY, and YIR2, amplified a malespecific band with the expected fragment size
Summary
The mammalian Y chromosome stands out from the rest of the genome because it is male specific, constitutively haploid, and exhibits unique structural and functional features (Skaletsky et al, 2003). This has led to a correspondingly unusual genomic landscape, rich in segmental duplications, which provide ample substrate for the generation of copy number variations (CNVs). In order to estimate the copy numbers of Y-linked genes in horses and compare the CNVs between different Chinese horse breeds, three X-degenerate genes, eukaryotic translation initiation factor 1A Y (EIF1AY), sex determining region Y (SRY), and ubiquitin activating enzyme Y (UBE1Y), were chosen to have their copy numbers determined in this study. Our results will provide fundamental information regarding the copy numbers for horse Y chromosome genes, which will benefit future functional studies
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