Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits.

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.

Genome and Transcriptome Analysis of Ascochyta pisi Provides Insights into the Pathogenesis of Ascochyta Blight of Pea.

Ascochyta blight caused by Ascochyta pisi is a major constraint to pea (Pisum sativum L.) production worldwide. Deciphering the pathogenic mechanism of A. pisi on peas will help in breeding resistant pea varieties and developing effective approaches for disease management. However, little is known about the genomic features and pathogenic factors of A. pisi. In this study, we first report that A. pisi is one of the causal agents of ascochyta blight disease of pea in China. The genome of the representative isolate A. pisi HNA23 was sequenced using PacBio and Illumina sequencing technologies. The HNA23 genome assembly is almost 41.5 Mb in size and harbors 10,796 putative protein-encoding genes. We predicted 555 carbohydrate-active enzymes (CAZymes), 1,008 secreted proteins, 74 small secreted cysteine-rich proteins (SSCPs), and 26 secondary metabolite biosynthetic gene clusters (SMGCs). A comparison of A. pisi genome features with the features of 6 other available genomes of Ascochyta species showed that CAZymes, the secretome, and SMGCs of this genus are considerably conserved. Importantly, the transcriptomes of HNA23 during infection of peas at three stages were further analyzed. We found that 245 CAZymes and 29 SSCPs were upregulated at all three tested infection stages. SMGCs were also trigged, but most of them were induced at only one stage of infection. Together, our results provide important genomic information on Ascochyta spp. and offer insights into the pathogenesis of A. pisi. IMPORTANCE Ascochyta blight is a major disease of legumes worldwide. Ascochyta pisi and other Ascochyta species have been identified as pathogens of ascochyta blight. Here, we first report that A. pisi causes ascochyta blight of pea in China, and we report the high-quality, fully annotated genome of A. pisi. Comparative genome analysis was performed to elucidate the differences and similarities among 7 Ascochyta species. We predict abundant CAZymes (569 per species), secreted proteins (851 per species), and prolific secondary metabolite gene clusters (29 per species) in these species. We identified a set of genes that may be responsible for fungal virulence based on transcriptomes in planta, including CAZymes, SSCPs, and secondary metabolites. The findings from the comparative genome analysis highlight the genetic diversity and help in understanding the evolutionary relationship of Ascochyta species. In planta transcriptome analysis provides reliable information for further investigation of the mechanism of the interaction between Ascochyta spp. and legumes.