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Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
Genome-wide association and selective sweep analyses reveal genetic loci for teat number trait in pigs
Lumeng Liu1, Tiantian Yan2, Pengcheng Lv3
1Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; College of Animal Science and Technology, Shandong Engineering Research Center for Protection of Livestock and Poultry Genetic Resources and Biological Breeding, Qingdao Agricultural University, Qingdao 266109, China.
Abstract:
Teat number is a key reproductive trait for the commercial pig industry, as an optimum number enhances weaned piglet survival rate. This study aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with teat number in the Large White sow. A total of 1000 French Large White sows were used in an analysis of total, left/right, and maximum unilateral teat number. Environmental factor, Spearman correlation, genome-wide association study (GWAS), linkage disequilibrium, and selective sweep analyses were conducted, with validation performed in a population of 1145 Landrace pigs. Genetic statistics showed that this population's teat number had moderate-low genomic heritability (h2 = 0.17-0.21) and weak negative correlation with weaned piglet litter weight. Parity and season affected teat development. GWAS identified 17 candidate SNPs on SSC 4, 7, and 17. Combined with selective sweep analysis, two key regions on SSC 7 were found, with four teat number-related SNPs, annotated to VRTN, DIO2, NRXN3. These candidate genes are associated with thoracic vertebrae development, hormone regulation during the early stage of teat formation, and nervous system development. These five SNPs showed similar results in the Landrace pig validation population; non-mutant homozygotes had 0.25-1.15 more teats than mutant ones in both populations. This study contributes to the identification of key variant loci associated with teat number-related traits in sows, thereby providing reliable molecular markers and a theoretical basis for marker-assisted selection of sow reproductive performance.
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