背景:内蒙古绒山羊(IMCG),以其卓越的羊绒品质而闻名,是中国本土山羊品种,经过长时间的自然和人工选择而发展起来。然而,最近,由于引入世界性山羊品种和缺乏适当的品种保护系统,IMCG的遗传资源受到了重大威胁。
结果:为了评估IMCG的保护效果并有效保存和利用纯种种质资源,这项研究分析了遗传多样性,亲属关系,家庭结构,并利用来自225个随机选择的个体的重新测序数据对IMCG进行近亲繁殖,这些个体使用Plink(v.1.90)进行分析,GCTA(v.1.94.1),和R(v.4.2.1)软件。通过质量控制,从225名个体获得的34,248,064个SNP位点中总共筛选出12,700,178个高质量SNP。平均次要等位基因频率(MAF),多态信息含量(PIC),香农信息指数(SHI)分别为0.253、0.284和0.530。平均观察杂合度(Ho)和平均期望杂合度(He)分别为0.355和0.351。通过状态距离矩阵和基因组关系矩阵对身份的分析表明,大多数个体的遗传距离和遗传关系都很远,近交系数低。家庭结构分析确定了23只公羊中的10个家庭。在225个个体中总共鉴定了14,109个纯合性(ROH),平均ROH长度为1014.547kb。平均近亲繁殖系数,根据ROH计算,总人口为0.026,特别是23只公羊中的0.027,表明保守人口中近亲繁殖的水平较低。
结论:IMCG表现出中等多态性和低水平的近亲繁殖发生在有限数量的个体中。同时,有必要防止血统的流失,以保证IMCGs种质资源的永存。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.