Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies

Chen, Jianmei; Wu, Ziyi; Chen, Ruxue; Huang, Zhi‐Zhen; Han, Xuelei; Qiao, Ruimin; Wang, Kejun; Yang, Feng; Li, Xinjian; Li, Xiuling

doi:10.3390/ani12121584

Animals

2022

DOI: 10.3390/ani12121584

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Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies

Jianmei Chen

Ziyi Wu

Ruxue Chen

et al.

Abstract: 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 … Show more

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Cited by 3 publications

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Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Shi

Wang²,

Fang³

et al. 2022

Front. Genet.

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Growth and fat deposition are complex traits, which can affect economical income in the pig industry. Due to the intensive artificial selection, a significant genetic improvement has been observed for growth and fat deposition in pigs. Here, we first investigated genomic-wide association studies (GWAS) and population genomics (e.g., selection signature) to explore the genetic basis of such complex traits in two Large White pig lines (n = 3,727) with the GeneSeek GGP Porcine HD array (n = 50,915 SNPs). Ten genetic variants were identified to be associated with growth and fatness traits in two Large White pig lines from different genetic backgrounds by performing both within-population GWAS and cross-population GWAS analyses. These ten significant loci represented eight candidate genes, i.e., NRG4, BATF3, IRS2, ANO1, ANO9, RNF152, KCNQ5, and EYA2. One of them, ANO1 gene was simultaneously identified for both two lines in BF100 trait. Compared to single-population GWAS, cross-population GWAS was less effective for identifying SNPs with population-specific effect, but more powerful for detecting SNPs with population-shared effects. We further detected genomic regions specifically selected in each of two populations, but did not observe a significant enrichment for the heritability of growth and backfat traits in such regions. In summary, the candidate genes will provide an insight into the understanding of the genetic architecture of growth-related traits and backfat thickness, and may have a potential use in the genomic breeding programs in pigs.

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Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Shi

Wang²,

Fang³

et al. 2022

Front. Genet.

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Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data

Hu,

Do,

Manafiazar

et al. 2024

Front. Genet.

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Aleutian disease (AD) brings tremendous financial losses to the mink industry. Selecting AD-resilient mink has been conducted to control AD. Such selections could have altered the patterns of genetic variation responding to selection pressures. This study aimed to identify selection signatures for immune response (IRE) and resilience to AD. A total of 1,411 mink from an AD-positive facility were used. For IRE, 264 animals were categorized according to the combined results of enzyme-linked immunosorbent assay (ELISA) and counterimmunoelectrophoresis (CIEP). For resilience, two grouping methods were used: 1) general resilience performance (GRP, n = 30) was evaluated based on the feed conversion ratio, Kleiber ratio, and pelt quality; and 2) female reproductive performance (FRP, n = 36) was measured based on the number of kits alive 24 h after birth. Detection methods were the pairwise fixation index, nucleotide diversity, and cross-population extended haplotype homozygosity. A total of 619, 569, and 526 SNPs were identified as candidates for IRE, GRP, and FRP, respectively. The annotated genes were involved in immune system process, growth, reproduction, and pigmentation. Two olfactory-related Gene Ontology (GO) terms were significant (q < 0.05) for all traits, suggesting the impact of AD on the sense of smell of infected mink. Differences in detected genes and GO terms among different color types for IRE indicated variations in immune response to AD among color types. The mitogen-activated protein kinase (MAPK) signaling pathway was significant (q < 0.05) for FRP, suggesting that AD may disrupt MAPK signaling and affect FRP. The findings of this research contribute to our knowledge of the genomic architecture and biological mechanisms underlying AD resilience in mink.

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Genome-Wide Association Study of Reproductive Traits in Large White Pigs

Hong,

Tan,

et al. 2024

Animals

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(1) Background: Reproductive performance is crucial for the pork industry’s success. The Large White pig is central to this, yet the genetic factors influencing its reproductive traits are not well understood, highlighting the need for further research. (2) Methods: This study utilized Genome-Wide Association Studies to explore the genetic basis of reproductive traits in the Large White pig. We collected data from 2237 Large White sows across four breeding herds in southern China, focusing on eight reproductive traits. Statistical analyses included principal component analysis, linkage disequilibrium analysis, and univariate linear mixed models to identify significant single-nucleotide polymorphisms and candidate genes. (3) Results: Forty-five significantly related SNPs and 17 potential candidate genes associated with litter traits were identified. Individuals with the TT genotype at SNP rs341909772 showed an increase of 1.24 in the number of piglets born alive (NBA) and 1.25 in the number of healthy births (NHBs) compared with those with the CC genotype. (4) Conclusions: The SNPs and genes identified in this study offer insights into the genetics of reproductive traits in the Large White pig, potentially guiding the development of breeding strategies to improve litter size.

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Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies

Cited by 3 publications

References 45 publications

Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data

Genome-Wide Association Study of Reproductive Traits in Large White Pigs

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