DOI: 10.5061/dryad.vh6t0c7
title: Data from: Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs

description: The distribution of Asian ancestry in the genome of Danish Duroc pigs was
 investigated using whole-genome sequencing data from European wild boars,
 Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes
 deriving from Meishan and Bamaxiang occur widely across the genome.
 Signatures of selection on Asian haplotypes are common in the genome, but
 few of these haplotypes have been fixed. By defining 50 kb windows with
 more than 50% Chinese ancestry, which did not exhibit extreme genetic
 differentiation between Meishan and Bamaxiang as candidate regions, the
 enrichment of quantitative trait loci in candidate regions support that
 Asian haplotypes under selection play an important role in contributing
 genetic variation underlying production, reproduction, meat and carcass,
 and exterior traits. Gene annotation of regions with the highest
 proportion of Chinese ancestry revealed genes of biological interest, such
 as NR6A1. Further haplotype clustering analysis suggested that a haplotype
 of Chinese origin around the NR6A1 gene was introduced to Europe and then
 underwent a selective sweep in European pigs. Besides, functional genes in
 candidate regions, such as AHR and PGRMC2, associated with fertility, and
 SAL1, associated with meat quality were identified. Our results
 demonstrate the contribution of Asian haplotypes to the genomes of
 European pigs. Findings herein facilitate further genomic studies such as
 genome-wide association study and genomic prediction by providing ancestry
 information of variants.
description: hap_chr5.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr10.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr11.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr12.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr16.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr17.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr18.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr15.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr14.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr8.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr9.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr7.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr6.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr4.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr3.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr13.part1.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr13.part2.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr2.part1.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr2.part2.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr1.part1.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.hap_chr1.part2.txtChromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.pos.txtSNP positions in ChromoPainter results