Abstract
Efficient production of high-quality semen is a crucial trait in the dairy cattle breeding due to the widespread use of artificial insemination. However, the genetic architecture (e.g., distributions of causal variants and their corresponding effects) underlying such semen quality traits remains unclear. In this study, we performed genome-wide association studies to identify genes associated with five semen quality traits in Chinese Holstein population, including ejaculate volume, progressive sperm motility, sperm concentration, number of sperm, and number of progressive motile sperm. Our dataset consisted of 2,218 Holstein bulls in China with full pedigree information, representing 12 artificial insemination centers, with 1,508 genotyped using the Illumina BovineSNP50 BeadChip. We used a weighted single-step genome-wide association method with 10 adjacent Single nucleotide polymorphisms (SNPs) as sliding windows, which can make use of individuals without genotypes. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. In total, we detected 36 window regions related to one or multiple semen traits across 19 chromosomes. Promising candidate genes of PSMB5, PRMT5, ACTB, PDE3A, NPC1, FSCN1, NR5A2, IQCG, LHX8, and DMRT1 were identified in these window regions for these five semen traits. Our findings provided a solid basis for further research into genetic mechanisms underlying semen quality traits, which may contribute to their accurate genomic prediction in Chinese Holstein population.
Highlights
The fertility of dairy cattle has decreased over recent decades due to highly intensive selection for milk production (Royal et al, 2000; Lucy, 2001; Walsh et al, 2011)
The results indicated that only 19 Single nucleotide polymorphisms (SNPs) were significantly associated with five semen traits
The proportions of genetic variance explained by each window for the five traits were obtained by WssGWAS
Summary
The fertility of dairy cattle has decreased over recent decades due to highly intensive selection for milk production (Royal et al, 2000; Lucy, 2001; Walsh et al, 2011). Unlike many male fertility traits measured based on the records of females (e.g., sire conception rate and daughter pregnancy rate), semen traits are measured directly in males Semen traits such as progressive sperm motility (SM) and ejaculate volume (VE) are complex and affected by genetic factors Many studies (Suchocki and Szyda; Hering et al, 2014a; Hering et al, 2014b; Qin et al, 2017) have focused on identifying genes and genetic markers associated with bovine semen traits, in order to understand their genetic architectures of these traits. Since few genes were shared among these studies, the genetic architecture underlying semen traits still remains elusive
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