Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

These datasets contain phenotypic and genotypic data of a MAGIC (Multiparent Advanced Generation Inter-Crosses) population of common bean (Phaseolus vulgaris L.), developed by inter-crossing of eight Mesoamerican elite breeding lines. The main goal for this population is to be used for applications in breeding and breeding tool development, which will support efforts to develop climate resilient germplasm, as well as information for basic research questions aiming to uncover the genetic basis of important agronomic traits. The raw phenotypic data come from three different trials carried out in Palmira (Colombia). Two replicated trials were laid out in the field with an alpha-lattice experimental design in 2013 and 2014, and an additional non-replicated trial in 2016. Several agronomic traits were assessed, including Days to Flowering (DF), Days to Physiological Maturity (DPM), 100 seed weight (100SdW), Yield (Yd), Pod Harvest Index (PHI), Iron and Zinc content (SdFe and SdZn). The agronomic performance of the population was modeled using linear mixed models with spatial correction. From these models, best linear unbiased estimators / predictors were obtained (BLUEs/BLUPs). The genotypic datasets include a variant call format (VCF) file of 20,615 GBS variants genotyped for 629 RILs (recombinant inbred lines) and 8 founder. From this matrix, a large and dense genetic map was obtained. This map accounts for multiple recombination events from multiple founder lines using SNP data, conferring higher accuracy due to the large population size. It makes it suitable for analyzing the linkage and segregation patterns for genetic mapping in the species Phaseolus vulgaris.

本数据集包含普通菜豆（Phaseolus vulgaris L.）多亲本高级世代互交群体（Multiparent Advanced Generation Inter-Crosses, MAGIC）的表型与基因型数据，该群体由8个中美洲优良育种系互交选育而成。该群体的核心应用目标为育种实践与育种工具开发，可为培育气候适应性种质资源的工作提供支撑，同时也可为解析重要农艺性状遗传基础的基础研究提供数据支持。原始表型数据采自哥伦比亚帕尔米拉市开展的3组不同试验：2013年与2014年的2组重复试验采用α格子试验设计进行田间布局，2016年增设1组非重复试验。本研究测定了多项农艺性状，包括开花天数（Days to Flowering, DF）、生理成熟天数（Days to Physiological Maturity, DPM）、百粒重（100 seed weight, 100SdW）、产量（Yield, Yd）、荚收获指数（Pod Harvest Index, PHI）以及籽粒铁、锌含量（Iron and Zinc content, SdFe与SdZn）。研究采用带有空间校正的线性混合模型对该群体的农艺性状表现进行建模，基于上述模型可获得最佳线性无偏估计值/最佳线性无偏预测值（BLUEs/BLUPs）。基因型数据集包含一份变异检测格式（Variant Call Format, VCF）文件，其中包含针对629个重组自交系（recombinant inbred lines, RILs）与8个创始亲本的20615个基因型测序（Genotyping-by-Sequencing, GBS）变异位点。基于该基因型矩阵可构建一张大型高密度遗传图谱，该图谱利用单核苷酸多态性（SNP）数据整合了多个创始亲本的多重重组事件，且因群体规模较大而具备更高的分析精度，适用于解析普通菜豆（Phaseolus vulgaris L.）遗传定位所需的连锁与分离模式。