South Africa has a diverse array of phenotypically distinct and locally adapted sheep breeds that have been developed for different production systems ranging from mutton to wool and pelt, and some dual‐purpose and nondescript breeds kept by smallholder farmers. This study investigated genetic diversity, population genetic structure and divergence between South African sheep breeds in order to gain an insight into breed history and genomic architecture aligned to breeding goals and production systems. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 14 breeds representing mutton, pelt and mutton and wool dual‐purpose breeds. Nguni sheep were included as a representative of indigenous nondescript breeds that are reared by smallholder farmers. Seeking a clearer understanding of the genetic diversity of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. These sheep breeds included six African, two Asian and eight European breeds. Across breeds, genetic diversity ranged from observed heterozygosity (H₀) = 0.26 ± 0.02 in Namaqua Afrikaner to H₀ = 0.38 ± 0.01 in Dohne Merino. The overall mean H₀ was 0.35 ± 0.04. The African and Asian populations were the most inbred populations with F_IS ranging from 0.17 ± 0.05 in Grey Swakara and Ronderib Afrikaner sheep to 0.34 ± 0.07 in the Namaqua Afrikaner. The South African Dohne Merino (F_IS = 0.03 ± 0.01), SA Merino (F_IS = 0.05 ± 0.04) and Afrino (F_IS = 0.09 ± 0.02) and other global Merino‐derived breeds were the least inbred. The first principal component explained 27.7% of the variation and separated the fat‐ and rump‐tailed sheep (i.e. Swakara, Nguni, Blackhead Persian, Ethiopian Menzi, Meatmaster) from the Merino and Merino‐derived breeds and the Dorset Horn. The second principal component separated the Merino and Merino‐derived breeds from the English breed of Dorset Horn. Overall, South African indigenous breeds clustered together with indigenous breeds from other African and Asian countries. The optimal admixture cluster (K = 20) revealed various sources of within‐ and amongst‐breed genomic variation associated with production purpose, adaptation and history of the breeds. The Blackhead Persian, Nguni and Namaqua Afrikaner breeds differed significantly from other breeds, particularly with the South African Mutton Merino and Dorset Horn. Breed‐differentiating SNPs were observed within genomic regions associated with growth, adaptation and reproduction. Genes such as RAB44, associated with growth and meat/carcass traits, differentiated the Blackhead Persian from the Dorset Horn and South African Mutton Merino. The MAP2 and HRAS genes, which are associated with immune traits involving Toll‐like receptors and Chemokine signalling pathways, differentiated the Nguni from the Dorset Horn. The current results give insight into the current status of the sheep genetic resources of South Africa relative to the global sheep population, highlighting both genetic similarities as well as divergence associated with production systems, geographical distribution and local adaptation.

中文翻译：

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相对于全球绵羊种群，南非羊肉，毛皮，两用和非描述性绵羊品种的基因组结构。

南非拥有多种在表型上不同且适应当地情况的绵羊品种，这些绵羊品种是为不同的生产系统开发的，从羊肉到羊毛和兽皮，还有一些由小农户饲养的双重用途和非描述性品种。这项研究调查了南非绵羊品种之间的遗传多样性，种群遗传结构和差异，以了解与繁殖目标和生产系统相一致的品种历史和基因组结构。Illumina OvineSNP50 BeadChip用于对400个绵羊进行基因分型，属于14个品种，分别代表羊肉，兽皮和羊肉以及羊毛两用品种。Nguni绵羊被列为由小农户饲养的土著非描述品种的代表。为了更清楚地了解南非品种相对于全球种群的遗传多样性，分析中包括了来自全球种群的623个基因型绵羊。这些绵羊品种包括六个非洲品种，两个亚洲品种和八个欧洲品种。在各个品种中，遗传多样性范围从观察到的杂合性（在Namaqua Afrikaner中，H ₀）= 0.26±0.02； 在多纳美利奴州中，H ₀ = 0.38±0.01。总体平均H ₀为0.35±0.04。非洲和亚洲种群的F _IS最近交种群，范围从Gray Swakara和Ronderib Afrikaner绵羊的0.17±0.05到Namaqua Afrikaner的0.34±0.07。南非Dohne Merino（F _IS  =  0.03±0.01），SA Merino（F _IS  = 0.05±0.04）和Afrino（F _IS = 0.09±0.02）和其他全球性的美利奴犬衍生品种。第一个主要成分解释了27.7％的变异，并从美利奴羊和美利奴羊衍生的品种和多塞特角中分离出了肥尾羊（即Swakara，Nguni，Blackhead波斯，埃塞俄比亚Menzi，Meatmaster）。第二个主要组成部分将美利奴羊和美利奴羊衍生的品种与英国多塞特霍恩品种分开。总体而言，南非土著品种与其他非洲和亚洲国家的土著品种聚在一起。最佳外加剂簇（K = 20）揭示了品种内和品种间基因组变异的各种来源，这些变异与生产目的，品种的适应性和历史有关。黑头波斯，Nguni和Namaqua Afrikaner品种与其他品种有显着差异，尤其是南非羊肉美利奴羊和多塞特角。在与生长，适应和繁殖相关的基因组区域内观察到了具有繁殖差异的SNP。与生长和肉/ car体性状相关的基因（如RAB44）使黑头波斯人与多塞特角和南非羊肉美利奴羊区别开来。该MAP2和HRASNguni基因与涉及Toll样受体和趋化因子信号传导途径的免疫性状相关，使Nguni与Dorset Horn区别开来。目前的结果使人们了解了南非绵羊遗传资源相对于全球绵羊种群的现状，突出了遗传相似性以及与生产系统，地理分布和局部适应性相关的差异。