Accession PRJCA016953
Title Accurate haplotype construction and detection of selection signatures enabled by 889 high quality pig genome sequences
Relevance Agricultural
Data types Whole genome sequencing
Raw sequence reads
Organisms Sus scrofa
Description High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 889 pigs, retrieve 207 resequencing data, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures amount to 1,096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1,874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genome selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.
Sample scope Multiisolate
Release date 2023-06-29
Publication
PubMed ID Article title Journal name DOI Year
37612277 Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences Nature Communications 10.1038/s41467-023-40434-3 2023
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) 31790413
Major Scientific and Technological R & D Projects of Jiangxi Provincial Department of Science and Technology 20213AAF01010
Submitter Tong    Xinkai  (xinkaitong@hotmail.com)
Organization Jiangxi Agricultural University
Submission date 2023-05-13

Project Data

Resource name Description
BioSample (1490)  show -