Genetic Diversity and Selection Signal Analysis of Xinjiang Black Pig Based on Whole Genome Resequencing

TL;DR

This study analyzes the genetic diversity and selection signals in Xinjiang Black pigs using whole genome resequencing to understand their genetic makeup and guide future breeding.

Contribution

The study identifies 686 selection regions and 406 candidate genes linked to traits like fat deposition and reproduction in Xinjiang Black pigs.

Findings

Xinjiang Black pigs show severe inbreeding and close genetic ties to Landrace pigs.

Candidate genes like SOX5 and HMG20A are linked to fat deposition, while SPRY1 and MNS1 relate to male reproductive ability.

Genes such as ARPP19 and TLN2 are strongly associated with oestrous cycle regulation and oocyte maturation.

Abstract

Background: The Xinjiang Black pig is an excellent breed developed by the Xinjiang Production and Construction Corps in the 1990s; however, it has been endangered by the impact of commercial breeds. Methods: Whole genomes of 224 individuals from the Xinjiang Black pig conservation population were resequenced. Results: Genetic structure and diversity analyses revealed that Xinjiang Black pigs underwent severe inbreeding and were genetically closely linked to Landrace pigs. The genetic diversity of the F2 generation was well preserved in the existing breeding scheme. A total of 686 significant selection regions and 406 candidate genes were identified using FST and θπ complementary methods, with Xinjiang Black pigs, Min pigs, and Laiwu pigs as ancestral populations, and F2. Based on Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and quantitative trait loci annotations, potential germplasm candidate genes were identified. Among these, SOX5, HMG20A, and NEDD4 are associated with fat deposition; SPRY1, MNS1, DMXL2, and ALB are closely associated with male reproductive ability; ARPP19 and TLN2 are strongly associated with oestrous cycle regulation and oocyte maturation; and SLC4A4 and SLC12A1 are extremely important for osmotic regulation and foetal survival. Conclusions: These findings deepen our understanding of the genetic mechanisms of artificial selection in Xinjiang Black pigs and provide a theoretical basis for subsequent breeding and genetic research on this breed.

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