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.

对本地动物种群内部及其间的多样性进行深入了解，对于其可持续管理日益显得至关重要。因此，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（GCZ）、几内亚-苏丹区（GSZ）和苏丹区（SZ））中采集了954只山羊，并使用12个多重微卫星标记进行基因分型。本研究通过常规遗传指数（等位基因数Na、预期和观察杂合度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）的平均值突显了极大的遗传多样性。STRUCTURE和SOM的结果显示存在两个不同的山羊群体（Djallonké和Sahelian）并表现出显著的杂交效应。此外，DAPC将源自两个祖先群体的山羊群体区分出四个簇。簇1和簇3（主要来自GCZ的个人）分别显示出73.79%和71.18%的平均Djallonké血统比例，而簇4（主要由SZ的山羊和一些GSZ的山羊组成）显示出78.65%的平均Sahelian血统比例。簇2，几乎将三个区域的所有动物归为一组，虽然也是Sahelian血统，但杂交程度高，如平均成员比例仅为62.73%所示。因此，迫切需要开发针对主要山羊类型的社区管理计划与选育方案，以确保贝宁山羊生产的可持续性。