DataSheet2_Genetic diversity assessment of the indigenous goat population of Benin using microsatellite markers.docx

Improved knowledge of the diversity within and among local animal populations is increasingly necessary for their sustainable management. Accordingly, this study assessed the genetic diversity and structure of the indigenous goat population of Benin. Nine hundred and fifty-four goats were sampled across the three vegetation zones of Benin [i.e., Guineo-Congolese zone (GCZ), Guineo-Sudanian zone (GSZ), and Sudanian zone (SZ)] and genotyped with 12 multiplexed microsatellite markers. The genetic diversity and structure of the indigenous goat population of Benin were examined using the usual genetic indices (number of alleles Na, expected and observed heterozygosities He and Ho, Fixation index FST, coefficient of genetic differentiation GST), and three different methods of structure assessment [Bayesian admixture model in STRUCTURE, self-organizing map (SOM), and discriminant analysis of principal components (DAPC)]. The mean values of Na (11.25), He (0.69), Ho (0.66), FST (0.012), and GST (0.012) estimated in the indigenous Beninese goat population highlighted great genetic diversity. STRUCTURE and SOM results showed the existence of two distinct goat groups (Djallonké and Sahelian) with high crossbreeding effects. Furthermore, DAPC distinguished four clusters within the goat population descending from the two ancestry groups. Clusters 1 and 3 (most individuals from GCZ) respectively showed a mean Djallonké ancestry proportion of 73.79% and 71.18%, whereas cluster 4 (mainly of goats from SZ and some goats of GSZ) showed a mean Sahelian ancestry proportion of 78.65%. Cluster 2, which grouped almost all animals from the three zones, was also of Sahelian ancestry but with a high level of interbreeding, as shown by the mean membership proportion of only 62.73%. It is therefore urgent to develop community management programs and selection schemes for the main goat types to ensure the sustainability of goat production in Benin.

对贝宁本地动物种群多样性的深入了解对于其可持续管理日益成为必要。鉴于此，本研究评估了贝宁本土山羊群体的遗传多样性和结构。在贝宁的三个植被区（即，几内亚-刚果区域（GCZ）、几内亚-苏丹区域（GSZ）和苏丹区域（SZ））对954只山羊进行了采样，并使用12个多重微卫星标记进行了基因分型。采用常规遗传指数（等位基因数Na、期望和观察杂合度He和Ho、固定指数FST、遗传分化系数GST）以及三种不同的结构评估方法（STRUCTURE中的贝叶斯混合模型、自组织映射（SOM）和主成分判别分析（DAPC））对贝宁本土山羊群体的遗传多样性和结构进行了考察。在贝宁本土山羊群体中估算出的Na（11.25）、He（0.69）、Ho（0.66）、FST（0.012）和GST（0.012）的平均值凸显了巨大的遗传多样性。STRUCTURE和SOM的结果表明，存在两个不同的山羊群体（Djallonké和Sahelian），具有高杂交效应。此外，DAPC将源自两个祖先群体的山羊群体区分出四个聚类。聚类1和3（多数个体来自GCZ）分别显示出73.79%和71.18%的平均Djallonké血统比例，而聚类4（主要由SZ和GSZ的一些山羊组成）显示出78.65%的平均Sahelian血统比例。聚类2，将三个区域几乎所有的动物分组在一起，虽然也属于Sahelian血统，但杂交程度较高，平均成员比例仅为62.73%。因此，迫切需要制定社区管理计划和针对主要山羊类型的选育方案，以确保贝宁山羊生产的可持续性。