Reducing foreign genetic contributions to the YDH pig population by segment-based advanced optimum contribution...

Area of Science:

• Animal Genetics
• Conservation Biology
• Livestock Breeding

Background:

• The Yuedonghei (YDH) pig is a unique local breed in Guangdong, China, prized for its black hair and premium market value.
• Significant genetic introgression (GI) from other breeds threatens YDH's genetic integrity due to recent crossbreeding initiatives.
• Understanding GI and evaluating conservation strategies are crucial for preserving this valuable local livestock resource.

Purpose of the Study:

• To assess the extent of genetic introgression and current conservation status in the Yuedonghei pig population.
• To test the efficacy of advanced optimum contribution selection (aOCS) in mitigating genetic introgression within the YDH breed.
• To provide strategic insights for the sustainable conservation of YDH and other local livestock genetic resources.

Main Methods:

• Analysis of genetic diversity, ancestral structure, population structure, and phylogeny using SNP chip data from 360 YDH pigs and 782 reference pigs.
• Admixture analysis to quantify foreign ancestry and identify individuals with significant genetic introgression.
• Stochastic simulation of a 10-generation conservation program using haplotype segment-based aOCS to control kinship and maintain effective population size (Ne).

Main Results:

• The YDH population exhibited heterozygosity of 0.336-0.344 and a recent effective population size (Ne) of 32.89.
• Admixture analysis revealed considerable genetic introgression, with 32.9% foreign ancestry detected in some individuals.
• Simulated aOCS increased native genomic contribution from 50.4% to 71.4% while maintaining Ne at 100, effectively reducing GI.

Conclusions:

• Advanced optimum contribution selection (aOCS), utilizing only genomic data, is a feasible and effective strategy to alleviate genetic introgression in the Yuedonghei pig population.
• aOCS can simultaneously increase the effective population size (Ne), enhancing the long-term viability of the YDH breed.
• The study offers valuable strategic insights for the sustainable conservation and management of local livestock genetic resources facing similar challenges.