Faculty of Agroforestry, University of Guantánamo, Guantánamo, Cuba.
Earth and Life Institute, Université catholique de Louvain, Louvain-la-neuve, Belgium.
PLoS One. 2024 May 31;19(5):e0304753. doi: 10.1371/journal.pone.0304753. eCollection 2024.
Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.
可可（Theobroma cacao L.）植物的正确基因型鉴定对于保护和利用该物种的遗传资源是强制性的。一组 15 个国际标准 SSR 标记被假定为通用可可基因型鉴定系统。最近，不同的 SNP 和 SNP 基因分型技术已在可可中得到利用。然而，对于应该使用哪种技术还没有达成共识，这促使人们寻找新的方法。为了验证一种新的 ddRADseq 可可基因分型协议，我们比较了使用 ddRADseq 获得的 7880 个 SNP 数据集和上述 SSR 数据集的基因型数据进行群体分析的性能，使用了来自生产性农场和基因库的 158 株可可植物。使用 STRUCTURE 和 ADMIXTURE 软件，分别使用 SSR 和 SNP 数据鉴定了四个遗传群体。这些群体之间的可可祖先相似性允许鉴定类似的个体群体对，称为：G1SSR/G1SNP、G2SSR/G2SNP、G3SSR/G3SNP、G4SSR/G4SNP，无论使用 SSR 还是 SNP。两种标记系统都鉴定出 Amelonado 和 Criollo 是所有样本中最丰富的可可祖先。根据 Mantel 检验（p<0.0001），两种数据类型的遗传距离矩阵非常相似。PCoA 和 UPGMA 聚类主要证实了所鉴定的遗传群体。AMOVA 和 FST 成对比较显示，SSR 和 SNP 数据中鉴定的群体之间存在中度至非常大的遗传分化。SSR 的遗传多样性参数（Hobs=0.616、Hexp=0.524 和 PIC=0.544）高于 SNP 数据（0.288、0.264 和 0.230）。在这两种情况下，携带最高比例 Amelonado 的遗传群体（G1SSR 和 G1SNP）在鉴定的群体中具有最低的遗传多样性参数。两种系统的群体分析结果高度一致，验证了用于可可 SNP 基因分型的 ddRADseq 协议。这些结果可以为开发非常需要的可可遗传研究的通用 SNP 基因分型系统提供新的途径。
