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. 2019 Oct 10;14(10):e0223671.
doi: 10.1371/journal.pone.0223671. eCollection 2019.

Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing

Farhad Bordbar  1 , Just Jensen  2 , Bo Zhu  1 , Zezhao Wang  1 , Lei Xu  1 , Tianpeng Chang  1 , Ling Xu  1 , Min Du  3 , Lupei Zhang  1 , Huijiang Gao  1 , Lingyang Xu  1 , Junya Li  1
Affiliations

Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing

Farhad Bordbar et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Locations of width, length, and circumference of hind leg measurements for the experimental beef carcasses.
Fig 2
Fig 2. Library construction plot.
The plot was provided by Genome Sequencing company Novogene (https://en.novogene.com).
Fig 3
Fig 3. Manhattan plot of -log10 (p) for the region associated with the width of hind leg.
The horizontal line represents the assigned threshold of significance.
Fig 4
Fig 4. Linkage disequilibrium plot.
The high LD block spans 19 kb, which harbors the most significant SNP for width of hind leg.
Fig 5
Fig 5. Linkage disequilibrium plot.
The plot reveals a high LD block spanning 3 kb around the associated SNP chr4:96893352 in Sub-section 2.
See this image and copyright information in PMC

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