NDLI: Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

Content Provider	Springer Nature : BioMed Central
Author	Jeong, Hyeonsoo Song, Ki-Duk Seo, Minseok Caetano-Anollés, Kelsey Kim, Jaemin Kwak, Woori Oh, Jae-don Kim, EuiSoo Jeong, Dong Kee Cho, Seoae Kim, Heebal Lee, Hak-Kyo
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.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-015-0265-1.pdf
Ending Page	9
Page Count	9
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-015-0265-1
Journal	BMC Genomic Data
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-08-20
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics de novo assembly Berkshire pigs Selection signature Meat quality XP-EHH XP-CLR
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits

Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

Genome-wide detection of runs of homozygosity in Ding’an pigs revealed candidate genes relating to meat quality traits

Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

Similar Documents

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits

Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

Genome-wide detection of runs of homozygosity in Ding’an pigs revealed candidate genes relating to meat quality traits

Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing