Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea (Pisum sativum)

A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects

Food legume crops, including common bean, faba bean, mungbean, cowpea, chickpea, and pea, have long served as vital sources of energy, protein, and minerals worldwide, both as grains and vegetables. Advancements in high-throughput phenotyping, next-generation sequencing, transcriptomics, proteomics, and metabolomics have significantly expanded genomic resources for food legumes, ushering research into the panomics era. Despite their nutritional and agronomic importance, food legumes still face constraints in yield potential and genetic improvement due to limited genomic resources, complex inheritance patterns, and insufficient exploration of key traits, such as quality and stress resistance. This highlights the need for continued efforts to comprehensively dissect the phenome, genome, and regulome of these crops. This review summarizes recent advances in technological innovations and multi-omics applications in food legumes research and improvement. Given the critical role of germplasm resources and the challenges in applying phenomics to food legumes-such as complex trait architecture and limited standardized methodologies-we first address these foundational areas. We then discuss recent gene discoveries associated with yield stability, seed composition, and stress tolerance and their potential as breeding targets. Considering the growing role of genetic engineering, we provide an update on gene-editing applications in legumes, particularly CRISPR-based approaches for trait enhancement. We advocate for integrating chemical and biochemical signatures of cells ('molecular phenomics') with genetic mapping to accelerate gene discovery. We anticipate that combining panomics approaches with advanced breeding technologies will accelerate genetic gains in food legumes, enhancing their productivity, resilience, and contribution to sustainable global food security.

Genome-wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance

Pea (Pisum sativum L.) is an important temperate legume crop providing plant-based proteins for food and feed worldwide. Pea yield can be limited by several biotic stresses, among which rust represents a major limiting factor in many temperate and subtropical regions. Some efforts have been made to assess the natural variation in pea resistance to rust, but its efficient exploitation in breeding is limited since the resistance loci identified so far are scarce and their responsible gene(s) unknown. To overcome this knowledge gap, a comprehensive genome-wide association study (GWAS) has been performed on pea rust, caused by Uromyces pisi, to uncover genetic loci associated with resistance. Utilizing a diverse collection of 320 pea accessions, we evaluated phenotypic responses to two rust isolates using both traditional methods and advanced image-based phenotyping. We detected 95 significant trait-marker associations using a set of 26,045 Diversity Arrays Technology-sequencing polymorphic markers. Our in silico analysis identified 62 candidate genes putatively involved in rust resistance, grouped into different functional categories such as gene expression regulation, vesicle trafficking, cell wall biosynthesis, and hormonal signaling. This research highlights the potential of GWAS to identify molecular markers associated with resistance and candidate genes against pea rust, offering new targets for precision breeding. By integrating our findings into current breeding programs, we can facilitate the development of pea varieties with improved resistance to rust, contributing to sustainable agricultural practices and food security. This study sets the stage for future functional genomic analyses and the application of genomic selection approaches to enhance disease resistance in peas.

Understanding the root of the problem for tackling pea root rot disease

Pea (Pisum sativum), a crop historically significant in the field of genetics, is regaining momentum in sustainable agriculture due to its high protein content and environmental benefits. However, its cultivation faces significant challenges from root rot, a complex disease caused by multiple soil-borne pathogens prevalent across most pea growing regions. This disease leads to substantial yield losses, further complicated by the dynamic interactions among pathogens, soil conditions, weather, and agricultural practices. Recent advancements in molecular diagnostics provide promising tools for the early and precise detection of these pathogens, which is critical for implementing effective disease management strategies. In this review, we explore how the availability of latest pea genomic resources and emerging technologies, such as CRISPR and cell-specific transcriptomics, will enable a deeper understanding of the molecular basis underlying host-pathogen interactions. We emphasize the need for a comprehensive approach that integrates genetic resistance, advanced diagnostics, cultural practices and the role of the soil microbiome in root rot. By leveraging these strategies, it is possible to develop pea varieties that can withstand root rot, ensuring the crop's resilience and its continued importance in global agriculture.

Identification of Sources of Resistance to Aphanomyces Root Rot in Pisum

Aphanomyces root rot (ARR), caused by Aphanomyces euteiches, is one of the most devastating diseases that affect the production of peas. Several control strategies such as crop rotation, biocontrol, and fungicides have been proposed, but none provides a complete solution. Therefore, the deployment of resistant cultivars is fundamental. ARR resistance breeding is hampered by the moderate levels of resistance identified so far. The available screening protocols require post-inoculation root assessment, which is destructive, time-consuming, and tedious. In an attempt to address these limitations, we developed a non-destructive screening protocol based on foliar symptoms and used it to identify new sources of resistance in a Pisum spp. germplasm collection. Accessions were root inoculated separately with two A. euteiches isolates, and leaf symptoms were assessed at 5, 10, 14, 17, and 20 days after inoculation (DAI). Although the majority of accessions exhibited high levels of susceptibility, thirty of them exhibited moderate resistance. These thirty accessions were selected for a second experiment, in which they were inoculated with both A. euteiches isolates at two inoculum doses. The objective of this second trial was to confirm the resistance of these accessions by evaluating root and biomass loss, as well as foliar symptoms, and to compare root and foliar evaluations. As a result, a high correlation (R2 = 0.75) between foliar and root evaluations was observed, validating the foliar evaluation method. Notably, accessions from P.s. subsp. humile exhibited the lowest symptomatology across all evaluation methods, representing valuable genetic resources for breeding programs aimed at developing pea varieties resistant to ARR.

Pathotype characterization of Aphanomyces euteiches isolates collected from pea breeding nurseries

Introduction

Aphanomyces euteiches Drechsler is an oomycete pathogen that affects legume crops, causing root rot, a severe disease of peas (Pisum sativum L.) worldwide. While significant research progress has been made in breeding pea-resistant varieties, there is still a need for a deeper understanding of the diversity of pathogen populations present in breeding nurseries located in various legume-growing regions around the world.

Methods

We analysed the diversity of 51 pea-infecting isolates of A. euteiches, which were recovered from four American (Athena, OR; Le Sueur, MN; Mount Vernon, WA; Pullman, WA) and three French (Riec-sur-Belon, Templeux-le-Guérard, Dijon) resistance screening nurseries. Our study focused on evaluating their aggressiveness on two sets of differential hosts, comprising six pea lines and five Medicago truncatula accessions.

Results

The isolates clustered into three groups based on their aggressiveness on the whole pea set, confirming the presence of pathotypes I and III. Pathotype I was exclusive to French isolates and American isolates from Athena and Pullman, while all isolates from Le Sueur belonged to pathotype III. Isolates from both pathotypes were found in Mount Vernon. The M. truncatula set clustered the isolates into three groups based on their aggressiveness on different genotypes within the set, revealing the presence of five pathotypes. All the isolates from the French nurseries shared the same Fr pathotype, showing higher aggressiveness on one particular genotype. In contrast, nearly all-American isolates were assigned to four other pathotypes (Us1, Us2, Us3, Us4), differing in their higher aggressiveness on two to five genotypes. Most of American isolates exhibited higher aggressiveness than French isolates within the M. truncatula set, but showed lower aggressiveness than French isolates within the P. sativum set.

Discussion

These results provide valuable insights into A. euteiches pathotypes, against which the QTL and sources of resistance identified in these nurseries displayed effectiveness. They also suggest a greater adaptation of American isolates to alfalfa, a more widely cultivated host in the United States.

Fine mapping of Ae-Ps4.5, a major locus for resistance to pathotype III of Aphanomyces euteiches in pea

KEY MESSAGE

QTL mapping and recombinant screening confirmed the major effect of QTL Ae-Ps4.5 on pea resistance to pathotype III of Aphanomyces euteiches and fine-mapped the QTL to a 3.06-Mb interval. Aphanomyces root rot, caused by Aphanomyces euteiches, is the most important disease of pea (Pisum sativum L.) worldwide. The development of pea-resistant varieties is a major challenge to control the disease. Previous linkage studies identified seven main resistance quantitative trait loci (QTL), including the QTL Ae-Ps4.5 associated with partial resistance in US nurseries infested by the pea pathotype III of A. euteiches. This study aimed to confirm the major effect of Ae-Ps4.5 on A. euteiches pathotype III, refine its interval, and identify candidate genes underlying the QTL. QTL mapping on an updated genetic map from the Puget × 90-2079 pea recombinant inbred line population identified Ae-Ps4.5 in a 0.8-cM confidence interval with a high effect (R2 = 89%) for resistance to the Ae109 reference strain of A. euteiches (pathotype III) under controlled conditions. However, the QTL mapping did not detect Ae-Ps4.5 for resistance to the RB84 reference strain of A. euteiches (pathotype I). Screening 224-pea BC5F2 plant progeny derived from three near-isogenic lines (NILs) carrying the 90-2079 allele at Ae-Ps4.5 in the Puget genetic background with 26 SNP markers identified 15 NILs showing recombination in the QTL interval. Phenotyping of the recombinant lines for resistance to the Ae109 strain of A. euteiches reduced the QTL to a physical interval of 3.06 Mb, containing 50 putative annotated genes on the Caméor pea genome V1a among which three candidate genes highlighted. This study provides closely linked SNP markers and putative candidate genes to accelerate pea breeding for resistant varieties to Aphanomyces root rot.