Data from: Association mapping of agronomic and quality traits in USDA pea single-plant collection

Association mapping is an efficient approach for the identification of the molecular basis of agronomic traits in crop plants. For this purpose in pea (Pisum sativum L.), we genotyped and phenotyped individual lines of the single-plant-derived core collection of the USDA pea collection including accessions from 330 landraces and cultivars of Pisum sativum subsp. sativum var. sativum, 28 P. sativum subsp. elatius var. elatius, 16 P. sativum subsp. sativum var. arvense, four P. sativum subsp. elatius var. pumilio, three P. abyssinicum, two P. fulvum, and one P. sativum subsp. transcaucasicum. These 384 accessions were collected or donated from a total of 64 countries. The accessions were genotyped with 256 informative SNPs using a primer extension chemistry and matrix-assisted laser desorption/ionization (MALDI–TOF) mass spectrometry assay. Genetic structure analysis showed that the collection was structured into two main groups, corresponding roughly to the cultivated types/landraces and the more primitive form species and subspecies, with some intermediates. Linkage disequilibrium of pairwise loci and population structure of the collection were analyzed, and an association analysis between SNP genotypes and 25 valuable traits such as disease resistance, seed type/color, flower color, seed low molecular weight carbohydrate concentration, and seed mineral nutrient concentration was performed using a mixed linear model. A total of 71 marker–trait associations were detected as significant with 1–34 markers per trait based on the false discovery rate (FDR < 0.05). This study demonstrates the potential of using association mapping to identify markers for pea breeding. Resources in this dataset:Resource Title: Supplementary material. File Name: Web Page, url: https://link.springer.com/article/10.1007/s11032-015-0277-6#Sec16

基因关联映射是识别作物植物农艺性状分子基础的高效方法。为此，在豌豆（Pisum sativum L.）中，我们对美国农业部豌豆收集的单一植株衍生的核心收集系中的各个品系进行了基因分型和表型分析，包括来自330个地方种和栽培种、28个P. sativum subsp. elatius var. elatius、16个P. sativum subsp. sativum var. arvense、4个P. sativum subsp. elatius var. pumilio、3个P. abyssinicum、2个P. fulvum以及1个P. sativum subsp. transcaucasicum的样本。这384个样本来自全球64个国家。利用引物延伸化学法和基质辅助激光解吸/电离（MALDI–TOF）质谱法对样本进行了256个信息SNP的基因分型。遗传结构分析显示，该收集系大致分为两组，分别对应栽培类型/地方种以及更为原始的物种和亚种，其中也包含一些过渡类型。对成对位点的连锁不平衡和收集系的种群结构进行了分析，并利用混合线性模型在SNP基因型和25个重要性状（如抗病性、种子类型/颜色、花色、种子低分子量碳水化合物浓度和种子矿物质养分浓度）之间进行了关联分析。根据假发现率（FDR < 0.05），共检测到71个显著的标记-性状关联，每个性状的标记数量从1到34不等。本研究展示了利用基因关联映射识别豌豆育种标记的潜力。本数据集包含资源：资源标题：补充材料。文件名：网页，网址：https://link.springer.com/article/10.1007/s11032-015-0277-6#Sec16