Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population

• Published in: Archiv für Tierzucht Vol. 66; no. 4; pp. 357 - 368
• Main Authors: Zhang, Yu, Lai, Jinhua, Wang, Xiaoyi, Li, Mingli, Zhang, Yanlin, Ji, Chunlv, Chen, Qiang, Lu, Shaoxiong
• Format: Journal Article
• Language: English
• Published: Germany Copernicus GmbH 23-11-2023; Copernicus Publications
• Subjects: Analysis; Animal husbandry; Animal populations; Breeding; Genes; Genetic aspects; Genetic research; Genome-wide association studies; Genomes; Genomics; Hogs; Litter size; Livestock industry; Molecular modelling; Nucleotides; Original Study; Polymorphism; Pork industry; Protein-tyrosine kinase receptors; Quality control; Reproduction; Signature analysis; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Software; Swine; North Carolina; Beijing China; United States > US; China
• ISSN: 2363-9822; 0003-9438; 2363-9822
• DOI: 10.5194/aab-66-357-2023

The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and
. Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (
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