Open AccessIdentification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing
Author(s) -
Farhad Bordbar,
Just Jensen,
Bo Zhu,
Zezhao Wang,
Xu Liu,
Tianpeng Chang,
Lei Xu,
Min Du,
Lupei Zhang,
Huijiang Gao,
Lingyang Xu,
Junya Li
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0223671
Subject(s) - candidate gene , biology , single nucleotide polymorphism , linkage disequilibrium , genetics , genome wide association study , haplotype , gene , beef cattle , genetic association , bovine genome , quantitative trait locus , genome , allele , genotype
Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was to detect potential candidate genes associated mainly with muscle development traits related to dimension of hindquarter in cattle. A next generation sequencing (NGS) dataset to imputed to 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were used to search for genes affecting hindquarter traits using a linear, mixed model approach. We also used haplotype and linkage disequilibrium blocks to further support our identifications. We identified 202 significant SNPs in the bovine BTA4 chromosome region associated with width of hind leg, based on a stringent statistical threshold (p = 0.05/ effective number of SNPs identified). After exploring the region around these SNPs, we found candidate genes that were potentially related to the associated markers. More importantly, we identified a region of approximately 280 Kb on the BTA4 chromosome that harbored several muscle specific candidate genes, genes to be in a potential region for muscle development. However, we also found candidate gene SLC13A1 on BTA4, which seems to be associated with bone disorders (such as chondrodysplasia) in Simmental beef cattle.