Mdladla K, Dzomba E F, Huson H J, Muchadeyi F C
Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa.
Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
Anim Genet. 2016 Aug;47(4):471-82. doi: 10.1111/age.12442. Epub 2016 Jun 15.
The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2) = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations.
南部非洲边缘地区山羊养殖的可持续性取决于适应特定农业生态条件的本地品种。未经改良的普通山羊是南非用于培育商业肉用型品种的主要遗传资源。人们对这些本土山羊种群的遗传多样性和适应性遗传学了解甚少。本研究调查了南非山羊种群的遗传多样性、种群结构和品种关系、连锁不平衡、有效种群大小以及配子相的持续性。使用Illumina山羊50K SNP芯片分析法对来自东开普省、夸祖鲁 - 纳塔尔省、林波波省和西北省四个山羊养殖省份的三个本地培育的肉用型品种布尔山羊（n = 33）、热带草原山羊（n = 31）、卡拉哈里红山羊（n = 40）、一个野生品种坦克瓦山羊（n = 25）以及未经改良的普通乡村生态型山羊（n = 110）进行了评估。次要等位基因频率>0.05的单核苷酸多态性（SNP）比例在坦克瓦山羊中为84.22%，在科萨生态型山羊中为97.58%，各群体的平均值为0.32±0.13。主成分分析、混合分析和成对FST分析确定坦克瓦山羊是一个基因独特的种群，并支持根据种群的历史起源进行聚类。全基因组FST分析确定了坦克瓦山羊中101个可能受到正选择的标记。平均连锁不平衡在坦克瓦山羊中最高（r(2) = 0.25±0.26），在乡村生态型山羊中最低（r(2)范围为0.09±0.12至0.11±0.14）。我们观察到所有种群在13代之前的有效种群大小均小于150。除了热带草原山羊和茨瓦纳山羊种群外，所有品种对在标记距离>100 kb时的估计相关性均低于0.80。本研究突出了南非本土山羊的高水平遗传多样性以及全基因组SNP标记面板在这些种群遗传研究中的实用性。
