The hybridization analysis of pedigree: whole-genome re-sequencing reveals genomics characterization and genetic basis of growth trait of Qinchuan black pigs

Understanding the genetic basis of hybridization trait between Chinese indigenous pig and their commercial relatives may contribute to germplasm innovation. The Qinchuan black (QCB) pig is a new composite breed under development generated from Chinese indigenous pig breeds (i.e., Guanzhong black pig, GZB) and intensive pig breeds (i.e., Yorkshire, also called Large white pig, LW). Investigated gene functions inherited from parent help us to understand the genetic basis of excellent phenotype similar with their parents, in which parents correspond to grandparents for hybrid population in our study. Here, we performed population structure and admixture analyses to elucidate the genetic position of QCB among Asian and European pig breeds. Ancestral track analysis revealed the LW contributed more genomic components in QCB genome, particularly on chromosome 7. This asymmetric inheritance may be influenced by linkage disequilibrium blocks. The offspring genome exhibited high genetic diversity, as did its maternal genome (GZB). Both genomes were characterized by a reduced number and shorter length of Run of Homozygosity (ROH). Finally, we used HKA test to investigated key gene in QCB that were inherited from its parents and that regulate important economic traits. Our results identified a significant association between an NPC1L1 haplotype inherited from the LW genome and body weight in four-month-old QCB. Our research provides a novel strategy for utilizing previously identified functional loci or genes to guide the breeding of domestic pig for improvement economic traits in crossbreeding systems.