Biotechnology Platform, Agricultural Research Council, 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.
Heredity (Edinb). 2018 Apr;120(4):369-378. doi: 10.1038/s41437-017-0044-z. Epub 2018 Feb 9.
In Africa, extensively raised livestock populations in most smallholder farming communities are exposed to harsh and heterogeneous climatic conditions and disease pathogens that they adapt to in order to survive. Majority of these livestock species, including goats, are of non-descript and uncharacterized breeds and their response to natural selection presented by heterogeneous environments is still unresolved. This study investigated genetic diversity and its association with environmental and geographic conditions in 194 South African indigenous goats from different geographic locations genotyped on the Illumina goat SNP50K panel. Population structure analysis revealed a homogeneous genetic cluster of the Tankwa goats, restricted to the Northern Cape province. Overall, the Boer, Kalahari Red, and Savanna showed a wide geographic spread of shared genetic components, whereas the village ecotypes revealed a longitudinal distribution. The relative importance of environmental factors on genetic variation of goat populations was assessed using redundancy analysis (RDA). Climatic and geographic variables explained 22% of the total variation while climatic variables alone accounted for 17% of the diversity. Geographic variables solitarily explained 1% of the total variation. The first axis (Model I) of the RDA analysis revealed 329 outlier SNPs. Landscape genomic approaches of spatial analysis method (SAM) identified a total of 843 (1.75%) SNPs, while latent factor mixed models (LFMM) identified 714 (1.48%) SNPs significantly associated with environmental variables. Significant markers were within genes involved in biological functions potentially important for environmental adaptation. Overall, the study suggested environmental factors to have some effect in shaping the genetic variation of South African indigenous goat populations. Loci observed to be significant and under selection may be responsible for the adaption of the goat populations to local production systems.
在非洲，大多数小农社区中广泛饲养的牲畜种群面临着恶劣和多样的气候条件和疾病病原体的威胁，它们需要适应这些条件才能生存。这些牲畜物种中，包括山羊，大多属于无特征和无特色的品种，它们对异质环境带来的自然选择的反应仍未得到解决。本研究调查了遗传多样性及其与环境和地理条件的关系，对来自不同地理位置的 194 只南非本土山羊进行了 Illumina 山羊 SNP50K 面板基因分型。种群结构分析显示，坦卡瓦山羊形成了一个同质的遗传群体，仅限于北开普省。总体而言，布尔、卡拉哈里红和萨凡纳山羊表现出广泛的地理分布和共同的遗传成分，而乡村生态型则呈现出纵向分布。使用冗余分析（RDA）评估环境因素对山羊种群遗传变异的相对重要性。气候和地理变量解释了总变异的 22%，而气候变量单独解释了 17%的多样性。地理变量单独解释了总变异的 1%。RDA 分析的第一轴（模型 I）揭示了 329 个异常 SNP。空间分析方法（SAM）的景观基因组方法共鉴定出 843 个（1.75%）SNP，而潜在因子混合模型（LFMM）鉴定出 714 个（1.48%）与环境变量显著相关的 SNP。显著标记位于涉及生物学功能的基因内，这些功能可能对环境适应很重要。总的来说，该研究表明环境因素对塑造南非本土山羊种群的遗传变异有一定的影响。观察到的与环境因素显著相关且受选择影响的基因座可能是山羊种群适应当地生产系统的原因。
