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Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs.

ABSTRACT: OBJECTIVE:Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. METHODS:We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. RESULTS:After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. CONCLUSION:This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

SUBMITTER: Quan J

PROVIDER: S-EPMC5838319 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs.

Quan Jianping J Ding Rongrong R Wang Xingwang X Yang Ming M Yang Yang Y Zheng Enqin E Gu Ting T Cai Gengyuan G Wu Zhenfang Z Liu Dewu D Yang Jie J

Asian-Australasian journal of animal sciences 20171020 4

<h4>Objective</h4>Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population.<h4>Methods</h4>We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models.<h4>Results</h4>After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly ass ...[more]

PMID: 29059722

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Project description:Simple Summary Due to the complexity of sperm cell reproduction and maturation, the genetic structure of semen traits remains largely unknown. In our study, we used weighted single-step GWAS to detect genetic regions and further candidate genes related to semen traits in Duroc boars. This study provides in-depth understanding of the genetic structure of semen traits and the biological information provided by gene networks, and can be applied to speed up the genetic process of semen traits in boars. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. Abstract Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility—sperm progressive motility, sperm abnormality rate, and total sperm count—explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.

Dataset Information

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs.

Publications

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs.

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