Genetic Diversity and Selection Signatures of Lvliang Black Goat Using Genome-Wide SNP Data

Lvliang black goat (LBG) is an excellent local breed resource in China that is known for its black fur, excellent meat quality, and strong adaptability. Studying the genetic mechanism and germplasm characteristics of LBG can provide theoretical and practical basis for the protection of the genetic resources of this breed and help implement conservation and breeding. In this study, the genetic diversity of the LBG population was evaluated using whole-genome SNP data. It was found that the LBG population had a high genetic diversity and a low degree of inbreeding. According to the clustering results of male goats and the relationship between individuals, the LBG population was divided into 13 families. Then, through population structure analysis, it was found that LBG had a close genetic relationship with the Nanjiang goat and Qinggoda goat populations, and they may have the same ancestors. The LBG population has retained some ancient genetic characteristics and is a special population that integrates local genetic characteristics and foreign gene flow. Through four selection signal analyses, we detected multiple candidate genes related to economic traits (<i>CFL2</i>, <i>SCD</i>, <i>NLRP14</i>, etc.) and adaptability (<i>C4BPA</i>, <i>FUT8</i>, <i>PRNP</i>, etc.) in the LBG population. In addition, in a comparative analysis with three commercial breeds (Saanen goat, Boer goat and Angora goat) we also found multiple genes related to physical characteristics (<i>ERG</i>, <i>NRG3</i>, <i>EDN3</i>, etc.). Finally, we performed functional enrichment analysis on these genes and explored their genetic mechanisms. This study provides important data support for the protection and breeding of LBG and provides a new perspective for enriching the genetic diversity of goat populations.