Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.
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.
Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul, Kwan-ak Gu, 151-741, Republic of Korea. hs_jeong@snu.ac.kr.
Hyeonsoo
H
Jeong
Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea. kiduk.song@gmail.com.
Ki-Duk
KD
Song
Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul, Kwan-ak Gu, 151-741, Republic of Korea. nijorral@gmail.com.
Minseok
M
Seo
Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA. kelseyca@gmail.com.
Kelsey
K
Caetano-Anollés
Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul, Kwan-ak Gu, 151-741, Republic of Korea. jmkim85@snu.ac.kr.
Jaemin
J
Kim
Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul, Kwan-ak Gu, 151-741, Republic of Korea. asleo@cnkgenomics.com.|C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea. asleo@cnkgenomics.com.
Woori
W
Kwak
Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea. oh5ow@naver.com.
Jae-Don
JD
Oh
Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. ekim5@uwalumni.com.
EuiSoo
E
Kim
Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Ara-1 Dong, Jeju-Do, Jeju, 690-756, Republic of Korea. dkjeong@jejunu.ac.kr.
Dong Kee
DK
Jeong
C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea. seoae@cnkgenomics.com.
Seoae
S
Cho
Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Seoul, Kwan-ak Gu, 151-741, Republic of Korea. heebal@snu.ac.kr.|C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.|Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-742, South Korea. heebal@snu.ac.kr.
Heebal
H
Kim
Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea. breedlee@empas.com.
Hak-Kyo
HK
Lee
D000818:Animals; D001947:Breeding; D019295:Computational Biology; D005828:Genetics, Population; D016678:Genome; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D008460:Meat / Q000592:standards*; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D013552:Swine