Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

• Published in: BMC genomics Vol. 25; no. 1; pp. 698 - 14
• Main Authors: Wang, Ruijun, Wang, Xinle, Qi, Yunpeng, Li, Yanbo, Na, Qin, Yuan, Huiping, Rong, Youjun, Ao, Xiaofang, Guo, Furong, Zhang, Lifei, Liu, Yan, Shang, Fangzheng, Zhang, Yanjun, Wang, Yu
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16.07.2024; BioMed Central; BMC
• Subjects: Analysis; Animal breeding; Animals; Biological diversity; Breeding; Camelids; Cashmere; China; Chromosomes; Conserved sequence; DNA sequencing; Family structure; Gene Frequency; Gene sequencing; Genetic analysis; Genetic aspects; Genetic distance; Genetic diversity; Genetic relationship; Genetic resources; Genetic Variation; Genomes; Genomic analysis; Germplasm; Goats; Goats - genetics; Heterozygosity; Homozygosity; Identification and classification; Inbreeding; Inbreeding coefficient; Indigenous animals; Inner Mongolia cashmere goats; Kinship; Low level; Nucleotide sequencing; Phylogenetics; Polymorphism; Polymorphism, Single Nucleotide; Quality control; Rams; Single-nucleotide polymorphism; Software; Structural analysis; System effectiveness; Whole Genome Sequencing; China; Kinship; Inbreeding coefficient; Genetic diversity; Family structure; Inner Mongolia cashmere goats
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10485-x

Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals' genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs' germplasm resources.