期刊论文详细信息
BMC Genetics
Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing
Hak-Kyo Lee5  Heebal Kim3  Seoae Cho6  Dong Kee Jeong1  EuiSoo Kim2  Jae-don Oh5  Woori Kwak6  Jaemin Kim4  Kelsey Caetano-Anollés7  Minseok Seo4  Ki-Duk Song5  Hyeonsoo Jeong4 
[1] Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Ara-1 Dong, Jeju-Do 690-756, Jeju, Republic of Korea;Department of Animal Science, Iowa State University, Ames 50011, IA, USA;Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul 151-741, Kwan-ak Gu, Republic of Korea;Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea;C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea;Department of Animal Sciences, University of Illinois, Urbana 61801, IL, USA
关键词: de novo assembly;    XP-CLR;    XP-EHH;    Meat quality;    Selection signature;    Berkshire pigs;   
Others  :  1224626
DOI  :  10.1186/s12863-015-0265-1
 received in 2015-04-19, accepted in 2015-08-13,  发布年份 2015
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【 摘 要 】

Background

Natural 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.

Results

We 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.

Conclusions

Results 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.

【 授权许可】

   
2015 Jeong et al.

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