Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of Chinese Jiangquhai pigs in a global perspective1

Abstract

Jiangquhai pigs are one of the 42 representative local breeds listed in the national livestock genetic resources conservation project of China. This breed is known for its prolificacy, desirable meat quality, and excellent adaptability to crude feed and local environments. In this study, we genotyped 105 Jiangquhai pigs from the state conservation farm using GeneSeek GGP Porcine 80K SNP chip, and explored the SNP data to unravel genetic diversity, evolutionary phylogeny, signatures of selection, and population structure of Jiangquhai pigs in a context of 33 global breeds. Five indices of observed heterozygosity, expected heterozygosity, effective population size, runs of homozygosity, and linkage disequilibrium extent indicate that the Jiangquhai breed are still rich in genetic diversity in comparison with other breeds also from East China despite the recent decline of its population size. Phylogenetic, principal component, TreeMix, and admixture analyses show that Jiangquhai pigs represent an authentic genetic resource and have close genetic relationships with East Chinese breeds, their geographical neighbors. A genome scan unravels a list of reproduction-related genes potentially under selection in Jiangquhai pigs. Using the neighbor-joining clustering approach, we reconstructed the family structure of the conservation population of Jiangquhai pigs. This finding allowed us to suggest a rotational mating scheme across the reconstructed families to reduce the risk of inbreeding depression in the population.

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

“…A similar result was also found in the SZ breed ( Figure 3 and Supplementary Figure S1 ). However, our result contradicts that of Xu et al (2019) , which reported a higher LD extent greater than 0.3, at SNPs distance of 99.66 kb in the JQ breed using Porcine 80 K SNP chips. This difference might be due to the larger sample size, density, and type of SNP data used in the study (as reviewed by Qanbari, 2020 ).…”

“…Moreover, recent studies had reported ongoing selection processes in Chinese pig breeds ( Quan et al, 2020 ), which calls for the strategic management of these breeds to prevent the loss of important traits or genes. Although many studies had reported high genetic diversity in the JQ breed ( Fan et al, 2002 ; Xu et al, 2019 ), most of these reported metrics do not perfectly reflect the ability of the breed to cope with a future unexpected change in breeding preference or disease outbreak. Therefore, the lower haplotype diversity observed in the JQ breed could be an indicator of a reduction in their genetic diversity, indicating a need for proper management of the JQ population in conservation pig farming.…”

“…Recent studies had revealed high genetic diversity within the JQ pig breed ( Hua et al, 2014 ; Xiao et al, 2017b ; Xu et al, 2019 ). Genomic analysis also revealed that this breed might have undergone selection in the past, which could account for some adaptive traits in the breed ( Meng et al, 2018 ; Xu et al, 2019 ). However, there is still a dearth of information on the genetic architecture of some economically important traits in this pig breed.…”

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

“…Furthermore, approximately 65% of the single nucleotide polymorphisms (SNPs) were highly variable with a minor allele frequency (MAF) > 0. 3 Table 3). The total length of ROH in CKA sheep, in the range of < 0.5 Mb, was lowest, suggesting CKA sheep have higher genetic diversity (Fig.…”

“…Although SNP arrays have been extensively used to identify genetic variations [ 3 – 6 ], the results are limited by low probe density. High-throughput sequencing has allowed for improved characterization of genome characteristics and population structure at a genome-wide level [ 7 ].…”