Data from: Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs

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.