Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds’ genomic characteristics

Lee, Young-Sup; Son, Seung‐Woo; Lee, Hak-Kyo; Lee, Ra Ham; Shin, Donghyun

doi:10.1080/19768354.2022.2141316

Cited by 3 publications

(2 citation statements)

References 39 publications

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“…In the present study, most variations were in the intergenic and intronic regions of the genomes of all five pig breeds, which is consistent with previous reports. Breed-specific SNPs can elucidate the genomic landscape related to the unique characteristics of a breed compared with other breeds, which implies that they may be excellent genetic markers [13].…”

Section: Discussionmentioning

confidence: 99%

Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

Wu,

Xiang,

Zhang

et al. 2024

Genes

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Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which have difficulty adapting to the modern swine industry. However, the genome-wide mutational differences between these pig breeds are yet to be evaluated. Therefore, this study aimed to evaluate genomic variation and identify breed-specific SNPs in Danish LW pigs. Here, 43 LW, 15 Diqing Tibetan (DQZ), and 15 Diannan small-ear (DN) pigs whose genomes were re-sequenced with 5× depth were selected. This was followed by a conjoined analysis of our previous resequencing data of 24 Anqing six-end white (AQ) and six Asian wild (SS) pigs. In total, 39,158,378 SNPs and 13,143,989 insertion–deletions were obtained in all breeds. The variation number of LW pigs was the lowest, with 287,194 breed-specific and 1289 non-synonymous SNPs compared with Chinese breeds. Functional analysis of the breed-specific non-synonymous SNPs indicated that these mutations were mainly associated with the reproductive performance, feed intake, and feed conversion ratio of LW pigs. These findings provide a theoretical basis for genetic improvements in the Chinese swine industry.

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Section: Discussionmentioning

confidence: 99%

Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

Wu,

Xiang,

Zhang

et al. 2024

Genes

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“…Genome-wide association studies (GWAS) aim to detect variants of genomic loci associated with complex traits in the population, and common single nucleotide polymorphisms (SNPs) are the main source of these variants. SNPs are used to describe genetic variability and identify candidate genes, and GWAS examine significant SNPs (Lee et al 2021 ; Lee et al 2022 ). Attempts to use linkage analysis for mapping genomic loci that affect complex traits are ubiquitous.…”

Section: Introductionmentioning

confidence: 99%

A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction

Lee,

Oh,

Lee

et al. 2023

Animal Cells and Systems

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Traditionally, the p -value is the criterion for the cutoff threshold to determine significant markers in genome-wide association studies (GWASs). Choosing the best subset of markers for the best linear unbiased prediction (BLUP) for improved prediction ability (PA) has become an interesting issue. However, when dealing with many traits having the same marker information, the p -values’ themselves cannot be used as an obvious solution for having a confidence in GWAS and BLUP. We thus suggest a genomic estimated breeding value-assisted reduction method of the single nucleotide polymorphism (SNP) set (GARS) to address these difficulties. GARS is a BLUP-based SNP set decision presentation. The samples were Landrace pigs and the traits used were back fat thickness (BF) and daily weight gain (DWG). The prediction abilities (PAs) for BF and DWG for the entire SNP set were 0.8 and 0.8, respectively. By using the correlation between genomic estimated breeding values (GEBVs) and phenotypic values, selecting the cutoff threshold in GWAS and the best SNP subsets in BLUP was plausible as defined by GARS method. 6,000 SNPs in BF and 4,000 SNPs in DWG were considered as adequate thresholds. Gene Ontology (GO) analysis using the GARS results of the BF indicated neuron projection development as the notable GO term, whereas for the DWG, the main GO terms were nervous system development and cell adhesion.

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SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds

Chernukha,

Kotenkova,

Fedulova

2024

Foods and Raw Materials

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Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc breed than from Landrace and the Large White breeds, which participated in the Livni breed creation. The aim of the study was to determine the SNP-based genetic signatures in fat-type Livni breed shared with commercial Landrace and the Large White breeds, and ones that are affected by putative selection. The genome-wide SNP genotyping was carried out using the Porcine GGP HD BeadChip, which contains ~ 80 000 SNPs. Obtained breed relationship and admixture results indicated the insignificant participation of the Landrace and the Large White breeds in the formation of the modern allelofund of Livni pigs. 238 candidate genes were found in the genomic regions with selection signatures, 182 genes with described functions were identified. In the Livni and Landrace breeds, 35 common genes were detected which formed one cluster with enrichment coefficient = 4.94 and predominant HOXD genes. In the Livni and Large White breeds, the largest amounts of common genes were detected (62 in average), which formed two clusters. Cluster 1, with enrichment coefficient = 2.11, was characterized with genes involved in glucose metabolism. Cluster 2, with enrichment coefficient = 1.60, demonstrated helicase genes. Annotated clusters were not determined for the Livni breed. However, 50 candidate genes were specific to Livni pigs and associated with various growth, carcass and reproductive traits, essential for thermoregulation. Results revealed common SNP-based genetic signatures and breeding effects in indigenous Livni compared with Landrace and Large White breeds.

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Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds’ genomic characteristics

Cited by 3 publications

References 39 publications

Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction

SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds

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