NDLI: A genome-wide scan for signatures of directional selection in domesticated pigs

Content Provider	Springer Nature : BioMed Central
Author	Moon, Sunjin Kim, Tae-Hun Lee, Kyung-Tai Kwak, Woori Lee, Taeheon Lee, Si-Woo Kim, Myung-Jick Cho, Kyuho Kim, Namshin Chung, Won-Hyong Sung, Samsun Park, Taesung Cho, Seoae Groenen, Martien AM Nielsen, Rasmus Kim, Yuseob Kim, Heebal
Abstract	Background Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-015-1330-x.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-015-1330-x
Journal	BMC Genomics
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-02-25
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Pig Domestication Selective sweep Directional selection Quantitative traits
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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

Detection of selective sweeps in cattle using genome-wide SNP data

Multivariate genome-wide associations for immune traits in two maternal pig lines

Genome-wide associations for immune traits in two maternal pig lines

Genome-wide scan for runs of homozygosity in South American Camelids

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Artificial selection footprints in indigenous and commercial chicken genomes

Genomic consequences of selection and genome-wide association mapping in soybean

A genome-wide scan for signatures of directional selection in domesticated pigs

Similar Documents

Detection of selective sweeps in cattle using genome-wide SNP data

Multivariate genome-wide associations for immune traits in two maternal pig lines

Genome-wide associations for immune traits in two maternal pig lines

Genome-wide scan for runs of homozygosity in South American Camelids

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Artificial selection footprints in indigenous and commercial chicken genomes

Genomic consequences of selection and genome-wide association mapping in soybean

A genome-wide scan for signatures of directional selection in domesticated pigs