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

• Published in: Animals (Basel) Vol. 15; no. 1; p. 36
• Main Authors: Wang, Xu, Zhou, Zhenqi, Chai, Xinrui, Li, Jie, Wang, Wannian, Pang, Zhixu, Cheng, Lifen, Cheng, Caihong, Qiao, Liying, Pan, Yangyang, Yang, Kaijie, Liu, Wenzhong, Liu, Jianhua
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.01.2025; MDPI
• Subjects: Analysis; Biological diversity; Blood; Ethylenediaminetetraacetic acid; Fertility; Gene loci; Generalized linear models; Genetic aspects; Genetic diversity; Genetic testing; Genomes; Genomics; Goats; kidding numbers; Livestock; Lüliang black goat; Mass spectrometry; Multiple births; Phenols; Principal components analysis; Quality control; reproductive traits; Scientific imaging; signal selection; Software; Massachusetts; China; Beijing China; genetic diversity; kidding numbers; Lüliang black goat; signal selection; reproductive traits
• ISSN: 2076-2615; 2076-2615
• DOI: 10.3390/ani15010036

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.