Correa Abondano Miguel, Ospina Jessica Alejandra, Wenzl Peter, Carvajal-Yepes Monica
Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Palmira, Colombia.
Front Plant Sci. 2024 Jul 11;15:1338332. doi: 10.3389/fpls.2024.1338332. eCollection 2024.
Genotyping large-scale gene bank collections requires an appropriate sampling strategy to represent the diversity within and between accessions.
A panel of 44 common bean ( L.) landraces from the Alliance Bioversity and The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) gene bank was genotyped with DArTseq using three sampling strategies: a single plant per accession, 25 individual plants per accession jointly analyzed after genotyping (), and by pooling tissue from 25 individual plants per accession (). Sampling strategies were compared to assess the technical aspects of the samples, the marker information content, and the genetic composition of the panel.
The strategy resulted in more consistent DNA libraries for quality and call rate, although with fewer polymorphic markers (6,142 single-nucleotide polymorphisms) than the (14,074) or the single plant sets (6,555). Estimates of allele frequencies by and genotyping were consistent, but the results suggest that the difference between pools depends on population heterogeneity. Principal coordinate analysis, hierarchical clustering, and the estimation of admixture coefficients derived from a single plant, -, and successfully identified the well-known structure of Andean and Mesoamerican gene pools of across all datasets.
In conclusion, proved to be a viable approach for characterizing common bean germplasm compared to genotyping individual plants separately by balancing genotyping effort and costs. This study provides insights and serves as a valuable guide for gene bank researchers embarking on genotyping initiatives to characterize their collections. It aids curators in effectively managing the collections and facilitates marker-trait association studies, enabling the identification of candidate markers for key traits.
对大规模基因库中的样本进行基因分型需要一种合适的抽样策略，以体现种质内和种质间的多样性。
利用三种抽样策略，对来自生物多样性国际联盟及国际热带农业中心（CIAT）基因库的44个菜豆地方品种进行DArTseq基因分型：每个种质取单株；每个种质取25株单株，基因分型后联合分析（）；每个种质取25株单株的组织混合（）。对抽样策略进行比较，以评估样本的技术方面、标记信息含量和样本组的遗传组成。
策略在DNA文库质量和检出率方面更为一致，尽管其多态性标记（6142个单核苷酸多态性）比（14074个）或单株组（6555个）少。和基因分型的等位基因频率估计值一致，但结果表明混合样本间的差异取决于群体异质性。主坐标分析、层次聚类以及从单株、和得出的混合系数估计，在所有数据集中都成功识别出了菜豆安第斯和中美洲基因库的著名结构。
总之，与分别对单株进行基因分型相比，通过平衡基因分型工作和成本，被证明是一种可行的菜豆种质特征分析方法。本研究为基因库研究人员开展基因分型计划以描述其种质提供了见解和宝贵指导。它有助于管理者有效管理种质，并促进标记-性状关联研究，从而识别关键性状的候选标记。
