Makerere University Regional Centre for Crop Improvement (MaRCCI), College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda.
Tanzania Agricultural Research Institute, Kibaha, Tanzania.
J Appl Genet. 2024 Dec;65(4):683-691. doi: 10.1007/s13353-024-00892-x. Epub 2024 Jul 16.
Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.
木薯（Manihot esculenta Crantz）在全球范围内具有重要的经济意义。基于分子特征评估广泛的种质资源不仅可以增强其保存，还可以支持其在育种计划中的利用。在这项研究中，我们使用 5247 个单核苷酸多态性（SNP）标记评估了来自乌干达的 155 个木薯基因型的遗传多样性和群体结构。通过测序（GBS）进行基因分型，用于 SNP 发现，并使用 ADMIXTURE 软件评估遗传多样性和群体结构。这些木薯材料包括两个群体：49 个来自乌干达系的材料和 106 个来自南美和乌干达系杂交的材料。平均 96%的调用率用于评估标记多态性。标记的多态信息含量值范围从 0.1 到 0.5，平均值为 0.4，属于中度高。主成分分析（PCA）表明，前两个成分捕获了约 24.2%的遗传变异。平均遗传多样性为 0.3。基于 AMOVA 的分析表明，66.02%和 33.98%的总遗传变异分别发生在材料内和亚群间。基于 ADMIXTURE 结构分析，确定了五个亚群（K=5）。基于 Neighbor-Joining 树和层次聚类树，发现了三个不同的组，这些组主要基于基因型的来源。结果表明，这些木薯基因型之间存在相当大的遗传变异，这对木薯的改良和保护工作非常有用。
