Yuedonghei (YDH) is the only local pig breed with full black hair among the four well-known local pig breeds originated and distributed in Guangdong province, China, which caters to the consumers' preference of the local market of 127 million residents and thus brings a significantly above-average price. However, considerable genetic introgressions (GI) have been reported for the YDH population, i.e., gene flow into YDH from other pig breeds, which is mainly due to the recent crossbreeding with several mainstream breeds for upgrading reasons. Therefore, this study aimed to evaluate the GI as well as the conservation status in the current YDH population and test the feasibility of advanced optimum contribution selection (aOCS) in alleviating GI in YDH. We first analyzed the genetic diversity, ancestral structure, population structure, and phylogeny of 360 YDH relative to 782 publicly downloaded pigs of 42 Eurasian or American breeds and wild boars, based on single nucleotide polymorphism chip data. Then we selected 304 initial YDH and stochastically simulated a practical conservation program that spanned 10 discrete generations and implemented haplotype segment-based aOCS in every generation. The expected and observed heterozygosity of 360 YDH were 0.344 and 0.336. The linkage disequilibrium-based recent effective population size (Ne) was 32.89. Considerable GI amounting to 32.9% foreign ancestry was found in 28 lowly related YDH individuals using admixture analysis. In the simulated YDH conservation program, the average native genomic contribution was increased from 50.4% to 71.4% while maintaining a Ne of 100 by controlling classic kinship and native kinship. Our study showed that segment-based aOCS that required only genomic data can be used to alleviate GI in the current YDH population and meanwhile increase its Ne, which provided strategic insights into the sustainable conservation of local genetic resources of livestock.

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