Peas are essential for human nutrition and played a crucial role in the discovery of Mendelian laws of inheritance. In this study, we assembled the genome of the elite vegetable pea cultivar ‘Zhewan No. 1’ at the chromosome level and analyzed resequencing data from 314 accessions, creating a comprehensive map of genetic variation in peas. We identified 235 candidate loci associated with 57 important agronomic traits through genome-wide association studies. Notably, we pinpointed the causal gene haplotypes responsible for four Mendelian traits: stem length (Le/le), flower color (A/a), cotyledon color (I/i) and seed shape (R/r). Additionally, we discovered the genes controlling pod form (Mendelian P/p) and hilum color. Our study also involved constructing a gene expression atlas across 22 tissues, highlighting key gene modules related to pod and seed development. These findings provide valuable pea genomic information and will facilitate the future genome-informed improvement of pea crops.

豌豆对人类营养至关重要，在孟德尔遗传定律的发现中发挥了至关重要的作用。在这项研究中，我们在染色体水平上组装了优良蔬菜豌豆品种“浙万1号”的基因组，并分析了314份材料的重测序数据，创建了豌豆遗传变异的综合图谱。我们通过全基因组关联研究确定了与 57 个重要农艺性状相关的 235 个候选基因座。值得注意的是，我们确定了负责四个孟德尔性状的因果基因单倍型：茎长度（ Le / le ）、花颜色（ A / a ）、子叶颜色（ I / i ）和种子形状（ R / r ）。此外，我们还发现了控制豆荚形状（孟德尔P / p ）和种脐颜色的基因。我们的研究还涉及构建跨 22 个组织的基因表达图谱，突出显示与豆荚和种子发育相关的关键基因模块。这些发现提供了宝贵的豌豆基因组信息，并将促进未来豌豆作物的基因组改良。