Data Sheet 2_The risk status, signatures of adaptation, and environmental suitability of village-based indigenous chickens from certain regions of Limpopo and KwaZulu-Natal provinces of South Africa.pdf

Indigenous chickens are an important Farm Animal Genetic Resource (FAnGR) in South Africa as they alleviate poverty and are a source of protein. Climate change and market demand for high-performing exotic breeds threaten and undermine locally adapted village chickens. The current study explored the risk status and signatures of adaptation of village-based indigenous chickens from two provinces and mapped their environmental suitability across the country. A total of 244 village chickens from rural areas of the Capricorn (n = 85) and Sekhukhune (n = 113) districts of Limpopo province; the Harry Gwala (n = 21) and uMzinyathi (n = 25) districts of KwaZulu-Natal province were genotyped using the Illumina 60K BeadChip. The conservation flock comprised Ovambo (OV; n = 10), Potchefstroom KoeKoek (PK; n = 20), and Venda (VD; n = 20). Naked Neck (NN; n = 20), New Hampshire (NH; n = 10), White Leghorn (WL; n = 10), and White Plymouth Rock (WR; n = 10) from the Agricultural Research Council Poultry Breeding Unit were used as reference populations and representative of flocks under conservation. The effective population size (Ne) in village chickens and conserved flocks ranged from 18 to 53 and 26 to 38 at 12 generations ago, respectively. PC1 and PC2 explained 5.64% of the total variation, which resulted in five clusters with the Venda, Naked Neck, and White Leghorn being separated from village chickens. The first three redundancy analysis (RDA) axes capture 46.8% of the total genetic variation used to detect significant outlier SNPs. A total of 386 outlier SNPs associated with all 10 environmental variables were detected. Using ecological niche modeling, chickens from Dipakakeng, Mgababa, and Podu villages, Limpopo, had a localized predicted suitability probability, while chickens originating from Nhlonga village, KwaZulu-Natal, had a broader distribution of predicted suitability habitats with elevation and BIO6 being important variables. The results of this study provide insight into the risk status, geographic suitability, and contributing environmental factors of indigenous chickens that can be used to influence conservation and improvement decisions.

本土家鸡是南非重要的农场动物遗传资源（Farm Animal Genetic Resource, FAnGR），其不仅可缓解贫困，亦是优质蛋白质来源。气候变化与市场对高性能外来品种的需求，正威胁并损害当地适应性乡村家鸡种群。本研究针对来自南非两个省份的乡村本土家鸡，探究其生存风险现状与适应性遗传特征，并绘制了其在全国范围内的环境适宜性分布。本研究共采集林波波省摩羯座区（Capricorn，n=85）、塞库胡内区（Sekhukhune，n=113）以及夸祖鲁-纳塔尔省哈里·瓜拉区（Harry Gwala，n=21）、乌姆津亚蒂区（uMzinyathi，n=25）乡村地区的244只乡村家鸡，采用Illumina 60K基因芯片（Illumina 60K BeadChip）进行基因分型。保护种群包含奥万博鸡（Ovambo, OV；n=10）、波切夫斯特鲁姆考科鸡（Potchefstroom KoeKoek, PK；n=20）以及文达鸡（Venda, VD；n=20）。来自农业研究委员会家禽育种部门的裸颈鸡（Naked Neck, NN；n=20）、新罕布什尔鸡（New Hampshire, NH；n=10）、白来航鸡（White Leghorn, WL；n=10）与白普利茅斯岩鸡（White Plymouth Rock, WR；n=10）被用作参考种群，代表当前受保护的鸡群。12个世代之前，乡村家鸡与保护种群的有效种群大小（effective population size, Ne）分别为18~53与26~38。主成分1（PC1）与主成分2（PC2）解释了总变异的5.64%，最终得到5个聚类群，其中文达鸡、裸颈鸡与白来航鸡与乡村家鸡相互分离。前三个冗余分析（Redundancy Analysis, RDA）轴解释了总遗传变异的46.8%，该分析被用于检测显著的异常单核苷酸多态性位点（SNP），最终共检测到与全部10个环境变量相关的386个异常SNP位点。借助生态位建模分析发现，来自林波波省迪帕卡肯（Dipakakeng）、姆加巴巴（Mgababa）与波杜（Podu）村的家鸡，其环境适宜性预测概率呈局部分布；而来自夸祖鲁-纳塔尔省恩隆加（Nhlonga）村的家鸡，其适宜生境的预测分布范围更广，其中海拔与BIO6为关键影响变量。本研究结果阐明了本土家鸡的生存风险现状、地理适宜性分布及其关键环境影响因子，可为本土家鸡的保护与改良决策提供科学依据。