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Yunong black pig is an indigenous black pig breed being cultivated that has a pure black whole body. However, some individuals appear with a white spot on the nose. We performed case–control association studies and FST approaches in 76 animals with nose color records (26 white‐nosed pigs vs. 50 black‐nosed pigs) by Illumina Porcine SNP50 BeadChip data. In total, 76 SNPs, which included 2 genome‐wide significant SNPs and 18 chromosome‐wide suggestive SNPs, were identified by association study. The top‐ranked 0.1% windows of FST results as signals under selection and 24 windows were selected. The lymphoid enhancer binding factor 1 was identified as candidate gene with strong signal in analyses of genome‐wide association study and FST in black‐ and white‐nosed pigs. Overall, our findings provide evidence that nose color is a heritable trait influenced by many loci. The results contribute to expand our understanding of pigmentation in pigs and provide SNP markers for skin color and related traits selection in Yunong black pigs. Additional research on the genetic link between nose pigmentation is needed. [ABSTRACT FROM AUTHOR]

Simple Summary: Sow reproductive performance is crucial in the entire pig industry. However, the heritability of reproductive traits is slowthat it is difficult to make great genetic progress by traditional breeding methods. Therefore, in this study, we performed genome-wide association analyses of litter traits in French White sows to explore genes related to sow reproductive traits and we finally detected a notable region (10.72–11.06 Mb on chromosome 7) and four promising genes (JARID2, PDIA6, FLRT2 and DICER1). The results of this study provide a theoretical basis for subsequent molecular breeding. The reproductive traits of sows are one of the important economic traits in pig production, and their performance directly affects the economic benefits of the entire pig industry. In this study, a total of 895 French Large White pigs were genotyped by GeneSeek Porcine 50K SNP Beadchip and four phenotypic traits of 1407 pigs were recorded, including total number born (TNB), number born alive (NBA), number healthy piglets (NHP) and litter weight born alive (LWB). To identify genomic regions and genes for these traits, we used two approaches: a single-locus genome-wide association study (GWAS) and a single-step GWAS (ssGWAS). Overall, a total of five SNPs and 36 genomic regions were identified by single-locus GWAS and ssGWAS, respectively. Notably, fourof all five significant SNPs were located in 10.72–11.06 Mb on chromosome 7, were also identified by ssGWAS. These regions explained the highest or second highest genetic variance in the TNB, NBA and NHP traits and harbor the protein coding gene ENSSSCG00000042180. In addition, several candidate genes associated with litter traits were identified, including JARID2, PDIA6, FLRT2 and DICER1. Overall, these novel results reflect the polygenic genetic architecture of the litter traits and provide a theoretical reference for the following implementation of molecular breeding. [ABSTRACT FROM AUTHOR]

Body traits are important economic factors in the pig industry. Genome‐wide association studies (GWASs) have been widely applied using high‐density genotype data to detect QTL in pigs. The aim of the present study was to detect the genetic variants significantly associated with body traits in crossbred pigs using the Illumina Porcine SNP50 BeadChip and imputed whole‐genome sequence data. A set of seven body traits – body length, body height, chest circumference, cannon bone circumference, leg buttock circumference, back fat thickness and loin muscle depth – were measured. Moderate to high heritabilities were obtained for most traits (from 0.14 to 0.46), and significant genetic and phenotypic correlations among them were observed. GWAS identified 714 significantly associated SNPs located at 39 regions on all autosomes for body traits, and a total of seven functionally related candidate genes: PIK3CD, HOXA, PCGF2, CHST11, COL2A1, BMI1 and OSR2. Functional enrichment analysis revealed that candidate genes were enriched in the estrogen signaling pathway, embryonic skeletal system morphogenesis and embryonic skeletal system development. These results aim to uncover the genetic mechanisms underlying body development and marker‐assisted selection programs focusing on body traits in pigs. [ABSTRACT FROM AUTHOR]