ArticleBMC genetics2015
Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.
Article in BMC genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 46 citations in OpenAlex.
- Genomic Signatures Underlying Environmental Adaptation and Reproductive Traits in the Tibetan Pig.Animals : an open access journal from MDPI · 2026Article
- Genes and Gene Functions Associated with Morphological, Productive, Reproductive, and Carcass Quality Traits in Pigs: A Functional Bioinformatics Approach.Current issues in molecular biology · 2026Article
- Population structure, regions of homozygosity (ROH) and selection signal of two domesitic goat breeds revealed by whole-genome resequencing.BMC genomics · 2026Article
- Identification of genomic regions associated with fatty acid metabolism across blood, liver, backfat and muscle in pigs.Genetics, selection, evolution : GSE · 2024Article
- Genome-Wide Analysis Reveals Copy Number Variant GeneAnimals : an open access journal from MDPI · 2024Article
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison).Scientific reports · 2024Article
- Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis.Animals : an open access journal from MDPI · 2022Article
- Carcass Quality Profiles and Associated Genomic Regions of South African Goat Populations Investigated Using Goat SNP50K Genotypes.Animals : an open access journal from MDPI · 2022Article
- Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification.Genes · 2022Article
- Detection of whole genome selection signatures of Pakistani Teddy goat.Molecular biology reports · 2021Article
- Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea.Animal cells and systems · 2021Article
- Akirin proteins in development and disease: critical roles and mechanisms of action.Cellular and molecular life sciences : CMLS · 2020Review
- Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.Asian-Australasian journal of animal sciences · 2020Article
- A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs.Frontiers in genetics · 2020Article
- Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding.Genetics · 2018Article
- Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds.Scientific reports · 2018Article
- In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome.Asian-Australasian journal of animal sciences · 2018Article
- Comparison of growth performance of Berkshire purebreds and crossbreds sired by Hereford and Tamworth breeds raised in alternative production system.Asian-Australasian journal of animal sciences · 2017Article
- Convergent and divergent genetic changes in the genome of Chinese and European pigs.Scientific reports · 2017Article
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Authors and funding
12 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNatural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data.
resultsWe generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism.
conclusionsResults revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.
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