Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat.

Simple Summary: Lüliang black goat (LBG) is a unique livestock genetic resource that has strong adaptability and excellent meat quality, and it occupies an important position in agricultural production in Shanxi, China. However, the low litter size and number of LBG has led to a small population. To promote the reproductive performance and economic benefits of LBG, this study used whole-genome resequencing to perform a genetic diversity analysis and found that LBG has high genetic diversity and a certain basis for genetic improvement. We also explored the selection characteristics of LBG in terms of reproductive traits using selection signal analysis. These results provide important genetic information and a theoretical basis for improving LBG reproductive traits, which will aid in the breeding and protection of goats. Lüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this breed. Therefore, improving the kidding characteristics of LBG is crucial for increasing its economic benefits. In this study, 20 LBG does were selected for whole-genome resequencing and divided into two groups: 10 in the T group (does with three consecutive kiddings of twin kids) and 10 in the S group (does with three consecutive kiddings of single kids). Based on whole-genome resequencing data, this study comprehensively assessed the population structure and genetic diversity of LBG and explored the related genes that affect reproductive performance. Three selection signal analysis methods—Fst (Fixation Index), π (nucleotide diversity), and XP-CLR (Cross Population Composite Likelihood Ratio)—were applied to screen a total of 838 genes, and enrichment analysis was performed to identify genes closely related to the reproductive performance of LBG, including ENPP3, APC, and GLI2. A generalized linear model was used to conduct a correlation analysis between non-synonymous mutations in the three genes and the number of kids produced. Two loci that were significantly correlated with kidding number were identified (p < 0.05): GLI2 g.63400363 C>T and GLI2 g.63417538 C>T. In general, the LBG population has high genetic diversity and good prospects for genetic improvement. The findings revealed that mining high-fecundity selection characteristics provides a basis for research on goat reproductive mechanisms. [ABSTRACT FROM AUTHOR]