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Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Jeong, Hyeonsoo | - |
dc.contributor.author | Song, Ki-Duk | - |
dc.contributor.author | Seo, Minseok | - |
dc.contributor.author | Caetano-Anollés, Kelsey | - |
dc.contributor.author | Kim, Jaemin | - |
dc.contributor.author | Kwak, Woori | - |
dc.contributor.author | Oh, Jae-don | - |
dc.contributor.author | Kim, EuiSoo | - |
dc.contributor.author | Jeong, Dong Kee | - |
dc.contributor.author | Cho, Seoae | - |
dc.contributor.author | Kim, Heebal | - |
dc.contributor.author | Lee, Hak-Kyo | - |
dc.date.accessioned | 2017-02-09T00:21:32Z | - |
dc.date.available | 2017-02-09T00:21:32Z | - |
dc.date.issued | 2015-08-20 | - |
dc.identifier.citation | BMC Genetics, 16(1):104 | ko_KR |
dc.identifier.uri | https://hdl.handle.net/10371/100562 | - |
dc.description | This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. | ko_KR |
dc.description.abstract | Abstract
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. | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BioMed Central | ko_KR |
dc.subject | Berkshire pigs | ko_KR |
dc.subject | Selection signature | ko_KR |
dc.subject | Meat quality | ko_KR |
dc.subject | XP-EHH | ko_KR |
dc.subject | XP-CLR | ko_KR |
dc.subject | de novo assembly | ko_KR |
dc.title | Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing | ko_KR |
dc.type | Article | ko_KR |
dc.contributor.AlternativeAuthor | 정현수 | - |
dc.contributor.AlternativeAuthor | 송기덕 | - |
dc.contributor.AlternativeAuthor | 서민석 | - |
dc.contributor.AlternativeAuthor | 김재민 | - |
dc.contributor.AlternativeAuthor | 곽우리 | - |
dc.contributor.AlternativeAuthor | 오재돈 | - |
dc.contributor.AlternativeAuthor | 김의수 | - |
dc.contributor.AlternativeAuthor | 정동기 | - |
dc.contributor.AlternativeAuthor | 조서애 | - |
dc.contributor.AlternativeAuthor | 김희발 | - |
dc.contributor.AlternativeAuthor | 이학교 | - |
dc.identifier.doi | 10.1186/s12863-015-0265-1 | - |
dc.language.rfc3066 | en | - |
dc.rights.holder | Jeong et al. | - |
dc.date.updated | 2017-01-06T10:17:30Z | - |
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