Li Guixin, Tang Jianhong, Huang Jinyan, Jiang Yongchuang, Fan Yin, Wang Xiaopeng, Ren Jun
Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China.
Front Genet. 2022 Apr 26;13:774196. doi: 10.3389/fgene.2022.774196. eCollection 2022.
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5-2 Mb and 0.5-1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55-50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21-132.54 Mb) containing two genes associated with embryonic development ( and ) was detected in domestic goat breeds worldwide. Tajima's D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
纯合性片段（ROH）和杂合性片段（ROHet）是了解种群人口历史和适应性进化的窗口。众多研究表明，有害突变在人类、猪、牛和鸡的ROH中富集。然而，有害变异与山羊ROH的关系以及山羊ROHet的模式在很大程度上尚未得到充分研究。在此，利用Illumina GoatSNP50 BeadChip对来自中国江西省的240只广丰山羊和赣西山羊进行基因分型，并在32个全球山羊品种的背景下进行全基因组ROH、ROHet和遗传负荷分析。ROH和ROHet比例最高的类别分别为0.5 - 2 Mb和0.5 - 至1 Mb。基于单核苷酸多态性（SNP）和ROH的近交系数以及ROHet测量结果表明，广丰山羊的遗传变异性高于大多数中国山羊，而赣西山羊存在高度近交，甚至超过了商业山羊品种。接下来，预测的有害纯合子在长ROH中更为富集，尤其是在广丰山羊中。因此，我们建议在育种和保护计划的设计中也应纳入有害等位基因的信息。在两个江西山羊品种的ROH热点区域中鉴定出了与繁殖力、生长和环境适应性相关的基因列表。一个与感官相关的ROH热点区域（12号染色体：50.55 - 50.81 Mb）在全球山羊品种中共享，并且可能在山羊驯化之前就经历了选择。此外，在全球范围内的家养山羊品种中检测到一个相同的ROHet热点区域（1号染色体：132.21 - 132.54 Mb），其中包含两个与胚胎发育相关的基因（和）。 Tajima's D和BetaScan2统计表明，该区域可能是由长期平衡选择导致的。这些发现不仅为江西山羊品种的保护策略设计提供了指导，也丰富了我们对山羊适应性进化的理解。
