Dataset Information

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs.

ABSTRACT: The teat number is a pivotal reproductive trait that significantly influences the survival rate of piglets. A meta-analysis is a robust instrument, enhancing the universality of research findings and improving statistical power by increasing the sample size. This study aimed to identify universal candidate genes associated with teat number traits using a genome-wide association study (GWAS) meta-analysis with three breeds. We identified 21 chromosome threshold significant single-nucleotide polymorphisms (SNPs) associated with five teat number traits in single-breed and cross-breed meta-GWAS analyses. Using a co-localization analysis of expression quantitative trait loci and GWAS loci, we detected four unique genes that were co-localized with cross-breed GWAS loci associated with teat number traits. Through a meta-analysis and integrative analysis, we identified more reliable candidate genes associated with multiple-breed teat number traits. Our research provides new information for exploring the genetic mechanism affecting pig teat number for breeding selection and improvement.

SUBMITTER: Li T

PROVIDER: S-EPMC10779318 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs.

Li Tingting T Wan Pengchong P Lin Qing Q Wei Chen C Guo Kaixuan K Li Xiaojing X Lu Yujin Y Zhang Zhe Z Li Jiaqi J

International journal of molecular sciences 20231229 1

The teat number is a pivotal reproductive trait that significantly influences the survival rate of piglets. A meta-analysis is a robust instrument, enhancing the universality of research findings and improving statistical power by increasing the sample size. This study aimed to identify universal candidate genes associated with teat number traits using a genome-wide association study (GWAS) meta-analysis with three breeds. We identified 21 chromosome threshold significant single-nucleotide polym ...[more]

PMID: 38203622

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Project description:Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96-15.02 Mb, SSC7: 97.18-98.18 Mb, SSC14: 128.29-131.15 Mb, SSC17: 15.39-17.27 Mb, and SSC17: 22.04-24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

Dataset Information

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs.

Publications

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs.

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