Genome-Wide Association Study Reveals Candidate Genes for Growth Relevant Traits in Pigs

Abstract

Improvement of the growth rate is a challenge in the pig industry, the Average Daily Gain (ADG) and Days (AGE) to 100 kg are directly related to growth performance. We performed genome-wide association study (GWAS) and genetic parameters estimation for ADG and AGE using the genomic and phonemic from four breed (Duroc, Yorkshire, Landrace, and Pietrain) populations. All analyses were performed by a multi-loci GWAS model, FarmCPU. The GWAS results of all four breeds indicate that five genome-wide significant SNPs were associated with ADG, and the nearby genomic regions explained 4.08% of the genetic variance and 1.90% of the phenotypic variance, respectively. For AGE, six genome-wide significant SNPs were detected, and the nearby genomic regions explained 8.09% of the genetic variance and 3.52% of phenotypic variance, respectively. In total, nine candidate genes were identified to be associated with growth and metabolism. Among them, TRIB3 was reported to associate with pig growth, GRP, TTR, CNR1, GLP1R, BRD2, HCRTR2, SEC11C, and ssc-mir-122 were reported to associate with growth traits in human and mouse. The newly detected candidate genes will advance the understanding of growth related traits and the identification of the novel variants will suggest a potential use in pig genomic breeding programs.

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model

“…Evaluation of gene prioritization model. A total of nine traits from seven GWAS studies [43][44][45][46][47][48][49] were selected for testing the performance of the gene-prioritization model (Supplementary Table 9). All candidate genes were evaluated by the CNN model, represents a CNN model trained by using variation counts, expression level, QTANs/QTALs number, and WGCNA module features of the training data.…”

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

“…For instance, we detected three CNVRs affecting both traits. The computational formulas of ADG and AGE in this study show an inverse relationship, and both themselves also have relatively high genetic associations [19]. That may explain why most CNVRs were signi cant in both traits.…”

“…Growth rate and fatness are vital objectives in the process of pig breeding, which are directly related to economic advantages. The growth rate measured at different stages mainly included average daily gain (ADG) during the test period as well as age (AGE) that adjusted to a certain weight [19]. Fat deposition is also a critical biological process, generally measured by backfat thickness (BFT) or intermuscular fat content.…”

“…However, the systematic association studies for complex quantitative traits based on CNVs were rarely explored [18,23], and the full relevance of CNVs to the genetic basis involved is yet to be clari ed. Besides, the genetic architectures of these traits are usually complex and commonly controlled by multiple genes [19], considering that the majority of association studies for growth traits and fatness in pigs have only used a small sample of genotyped animals, which has limited the statistical power of the association analysis [24]. It is necessary to conduct CNVs association analysis in a population with su cient sample size.…”

“…In the Canadian Duroc pigs, we also identi ed three, and four CNVRs reached the threshold (8.20E-03; 8.20E-03) for ADG and AGE, respectively, and these CNVRs overlapped 45 protein-coding genes. It should be noted that, due to the high genetic correlation between ADG and AGE[19], six and three CNVRs in American and Canadian Duroc pigs showed signi cant in both traits separately. However, no shared CNVR was identi ed in the two experimental populations.For fatness traits, we identi ed 14 CNVRs in the BFT trait of American Duroc pigs, where threshold values were set to 1.25E-02.…”