A Gene Catalogue of the Euchromatic Male-Specific Region of the Horse Y Chromosome: Comparison with Human and Other Mammals

Abstract

Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY) contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY gene catalogue was developed for the horse – an odd-toed ungulate. Using direct cDNA selection from horse testis, and sequence analysis of Y-specific BAC clones, 37 horse MSY genes/transcripts were identified. The genes were mapped to the MSY BAC contig map, characterized for copy number, analyzed for transcriptional profiles by RT-PCR, examined for the presence of ORFs, and compared to other mammalian orthologs. We demonstrate that the horse MSY harbors 20 X-degenerate genes with known orthologs in other eutherian species. The remaining 17 genes are acquired or novel and have so far been identified only in the horse or donkey Y chromosomes. Notably, 3 transcripts were found in the heterochromatic part of the Y. We show that despite substantial differences between the sequence, gene content and organization of horse and other mammalian Y chromosomes, the functions of MSY genes are predominantly related to testis and spermatogenesis. Altogether, 10 multicopy genes with testis-specific expression were identified in the horse MSY, and considered likely candidate genes for stallion fertility. The findings establish an important foundation for the study of Y-linked genetic factors governing fertility in stallions, and improve our knowledge about the evolutionary processes that have shaped Y chromosomes in different mammalian lineages.

Relative Quantification of Expression of Y-Specific Genes and its Association with Semen Production Traits in Crossbred Jersey Bulls

“…Hence, the TSPY gene expression is more during early spermatogenesis process and as the spermatogenesis continued for several years after sexual maturity; its gene expression is reduced in subsequent ages. The decreased expression of USP9Y gene was in general, negatively correlated with semen volume, sperm concentration, initial sperm motility and post-thaw motility, which was not in agreement with earlier reports of Paria et al, (2011) and Mukherjee et al, (2013), who postulated that USP9Y gene was a single copy gene in cattle. In human, Vineeth and Malini (2011) observed that USP9Y gene could not be considered as a major gene involved in spermatogenesis.…”

“…However, in the present study DDX3Y gene has been used as a reference gene. This gene has been reported to be a single copy gene in the genome of mammals (Paria et al, 2011). Its utility has also been established in relative quantification in bulls and its expression level has been reported to remain unchanged irrespective of seasons and age (Yue et al, 2014).…”

Copy number variations of five Y chromosome genes in donkeys

“…The male-specific primers of five Y chromosome genes -CUL4BY, ETSTY1, ETSTY4, ETSTY5, and SRYwere acquired from Paria et al (2011). Details of primers are shown in Table 2.…”

“…Thus, it is crucial to make clear of its CNV for a better understanding of SRY gene in donkeys. The testisspecific transcript Y (ETSTY) family is identified to consist of equine-specific genes (Paria et al, 2011); three of them (ETSTY1, ETSTY4, and ETSTY5) were chosen to analyze the CNVs in this study. The copy number of the cullin 4 B Y (CUL4BY) gene has been detected in other species, such as cats and dogs (Murphy et al, 2006;Pearks Wilkerson et al, 2008).…”

Genetics in Domestic Animal Reproduction

“…In the horse this region was very helpful in mapping of the euchromatic region of the equine Y-chromosome. These investigations were very helpful for the prediction of male fertility in horses and are therefore considered in horse breeding [4,5].…”