Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

Abstract

BackgroundIn recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines.ResultsWe identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway.ConclusionsWe identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0412-z) contains supplementary material, which is available to authorized users.

Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts

“…Multiples studies have reported SPATA7 as having an important role in spermatogenesis in human, mouse, and rat [38][39][40]. This gene has also been suggested as a candidate gene for semen traits in a GWAS study using commercial Large White and Landrace [41]. Gene expression studies using mice and rats showed that TGFB3 are involved in reproductive functions, such as gonadal and secondary sex organ [42][43][44][45].…”

Gene Polymorphisms in Boar Spermatozoa and Their Associations with Post-Thaw Semen Quality

“…Several authors have reported an increasing number of markers related to reproduction traits in pigs [12][13][14]. Advances in molecular genetics have resulted in the identification of several single nucleotide polymorphisms (SNPs) that are associated with the quality parameters of boar spermatozoa (including motility and morphology), and there has been increasing interest to understand the molecular processes that affect the sperm phenotype traits [12,15]. Evidence has shown that polymorphisms in boar sperm could be used as markers for semen quality [12,15,16].…”

“…Advances in molecular genetics have resulted in the identification of several single nucleotide polymorphisms (SNPs) that are associated with the quality parameters of boar spermatozoa (including motility and morphology), and there has been increasing interest to understand the molecular processes that affect the sperm phenotype traits [12,15]. Evidence has shown that polymorphisms in boar sperm could be used as markers for semen quality [12,15,16]. However, to date, there is limited information about the associations of SNPs with post-thaw quality of boar semen.…”

Weighted Single-Step Genome-Wide Association Study for Growth Traits in Chinese Simmental Beef Cattle

“…These findings implied that these windows (BTA3: 106,574,782-106,644,015 bp; BTA21: 5,941,998-5,968,820 bp; and BTA5: 77,160,030-77,212,501 bp) need more attention when selecting candidate genes for BYADG. Table 5 shows the 21 windows associated with 18MW which were located on BTA1, 3,4,5,9,10,14,20,21,22,23,25, and 26, together with 16 genes near the most important SNP within each window. The identified genomic windows explained 1.01-3.44% of the genetic variance for 18MW.…”

“…This approach can make full use of genealogical information and phenotypes of genotyped and nongenotyped animals [9]. The weighted single-step approach has been successfully applied to domesticated animals, and has led to the detection of additional QTLs and candidate genes for growth traits in Nellore cattle [3], semen traits in Duroc boar pigs [10], and milk protein composition traits in Chinese Holstein dairy cattle [11]. However, to our knowledge, few of the studies examining growth traits in Simmental beef cattle have used wssGWAS.…”