Instituto de Agrobiotecnología y Biología Molecular-IABiMo-INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina.
Programa Académico para la Investigación e Innovación en Biotecnología, Universidad Nacional de Moreno-UNM, Moreno 1744, Argentina.
Genes (Basel). 2020 Mar 6;11(3):283. doi: 10.3390/genes11030283.
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America-Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.
向日葵种质资源是拓宽商业杂交种遗传基础和降低气候事件风险的宝贵资源。如今，全球研究最多的向日葵预繁种资源属于 INTA（阿根廷）、INRA（法国）和 USDA-UBC（美国-加拿大）。在这项工作中，我们评估了这些收集品内部和之间遗传多样性（GD）的数量和分布，以估计全球多样性的分布模式。通过结合专有基因分型测序数据和公共全基因组测序数据，实施了混合基因分型策略，生成了一个包含三个育种收集品的综合 11834 个常见单核苷酸多态性矩阵。总的来说，获得的 GD 估计值适中。分子方差分析提供了育种收集品之间种群结构的证据。然而，最佳亚群数量（通过主成分判别分析研究（K=12）、贝叶斯 STRUCTURE 算法（K=6）和基于距离的方法（K=9））仍然不清楚，因为任何推断出的群体都没有明显的单一统一特征。跨染色体观察到不同的连锁不平衡（LD）总体模式，Chr10、Chr17、Chr5 和 Chr2 显示出最高的 LD。这项工作代表了迄今为止对栽培向日葵进行的最大和最全面的杂种间基因组多样性分析。
