Abstract South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers. Highlights The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.

中文翻译：

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使用微卫星和线粒体 DNA 标记的夸祖鲁-纳塔尔本土鸡生态型的遗传多样性、种群结构和祖先起源

摘要 南非本土鸡品种也不例外，当地家养品种的减少早已被认可并发现与家畜育种商业化有关。该研究的目的是：(i) 全面了解四个夸祖鲁-纳塔尔土著鸡种群（Jozini、Newcastle、Pietermaritzburg 和 Port Shepstone）的遗传变异，以及 (ii) 估计通过对 19 个常染色体微卫星位点的个体进行基因分型，对来自三个保守的南非本土纯种（Potchefstroom koekoek、Ovambo 和 Venda）的村庄种群进行了分析。最后，(iii) 通过线粒体 DNA 探索它们的系统发育关系和它们可能的母系起源，可以获得关于夸祖鲁-纳塔尔土著鸡种群历史的新信息。结果表明，在生态型内部和生态型之间存在明显的遗传多样性，它们之间具有清晰的亚结构。土著种群具有很高的遗传多样性（观察到的杂合度范围从彼得马里茨堡的 0.61 到 Jozini 的 0.70），而保守种群在种群近交系数内表现出相当大（从 Potchefstroom koekoek 的 0.01 到 Ovambo 的 0.18）。中值连接网络分析表明单倍群 E 占主导地位，这表明可能起源于东南亚和/或印度次大陆。单倍群 B 和 C 的存在不仅强调了多母系起源，而且还突出了具有商业基因型的当地鸡的遗传渗入。这些结果突出了当地品种作为遗传库的重要性；此外，保护当地品种可以在当地经济中发挥重要作用，为消费者提供优质产品。亮点研究了夸祖鲁-纳塔尔本土鸡群和纯南非鸡品种的遗传变异和分化。村庄种群表现出明显的遗传变异性，它们之间具有明显的亚结构。结果可用于改进可持续育种和保护计划，以控制商业基因型可能造成的遗传稀释。