Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population

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 studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp)

The identification of loci related to seed and yield component traits in cowpea constitutes a key step for improvement through marker-assisted selection (MAS). Furthermore, seed morphology has an impact on industrial processing and influences consumer and farmer preferences. In this study, we performed genome-wide association studies (GWAS) on a mini-core collection of cowpea to dissect the genetic architecture and detect genomic regions associated with seed morphological traits and yield components. Phenotypic data were measured both manually and by high-throughput image-based approaches to test associations with 41,533 single nucleotide polymorphism markers using the FarmCPU model. From genome-associated regions, we also investigated putative candidate genes involved in the variation of the phenotypic traits. We detected 42 marker-trait associations for pod length and 100-seed weight, length, width, perimeter, and area of the seed. Candidate genes encoding leucine-rich repeat-containing (LRR) and F-box proteins, known to be associated with seed size, were identified; in addition, we identified candidate genes encoding PPR (pentatricopeptide repeat) proteins, recognized to have an important role in seed development in several crops. Our findings provide insights into natural variation in cowpea for yield-related traits and valuable information for MAS breeding strategies in this and other closely related crops.

Salt-Resilient Cowpeas: Early Identification Through Growth Parameters and Gene Expression at Germination Stage

Soil salinity is one of the most severe impacts of climate change, negatively affecting plant growth and development. Seed germination and seedling emergence are among the most critical stages susceptible to salt stress, making it important to explore them to identify the most resilient accessions for crop yield improvement. Cowpea (Vigna unguiculata L. Walp.) is an important crop due to its ability to fix atmospheric nitrogen, improving soil health, and its high protein content. The main objectives of this study were to screen salt-resilient cowpea accessions from a worldwide collection and to evaluate cowpea responses to salt stress at germination stage through gene expression analysis. A total of 40 cowpea accessions from sixteen different countries were subjected to two treatments: control (water) and salt stress (150 mM NaCl solution). The seeds germinated, and the seedlings grew for ten days. The germination and growth parameters and lipid peroxidation quantification were determined. The results revealed significant differences in all parameters among accessions and treatments. A high variation in salt responses was detected among accessions, allowing the selection of five accessions (Co_2, Co_4, Co_21, Co_30, Co_31) as resilient to salt stress at germination stage. Subsequently, two salt stress-related genes (DREB2 and VuEXO) were evaluated through qPCR, revealing genotype-dependent regulation. These results provide valuable insights for the early selection of salt-resilient cowpea accessions, which may be considered for the development of improved and new varieties in the future.

Genome-Wide Association Study for Seed Yield of Tepary Bean Using Whole-Genome Resequencing

Tepary bean (Phaseolus acutifolius A. Gray) is a diploid legume species (2n = 2x = 22). It is the most drought- and heat-tolerant crop of the genus Phaseolus. Tepary bean is native to the northern part of Mexico and the south-western part of the U.S. The lack of molecular markers associated with agronomic traits such as 100-seed weight and seed yield limit the development of elite tepary bean cultivars. Therefore, the objectives of this study were to evaluate tepary bean for 100-seed weight and yield, and identify single-nucleotide polymorphism (SNP) markers associated with these traits. A total of 230,000 high-quality SNPs obtained from the whole-genome resequencing of 153 tepary bean accessions were used for this study. For 100-seed weight, a total of 5 and 20 SNPs were found using a mixed linear model (MLM) and compressed mixed linear model (cMLM), respectively. A candidate gene, Phacu.CVR.002G320800.13, encoding the squamosa promoter-binding protein-like (SBP domain) transcription factor family protein was found to be associated with 100-seed weight. For seed yield, a total of one and eight SNPs were identified using an MLM and cMLM, respectively. Phacu.CVR.009G294200.1, encoding for peroxidase family protein, was identified as a candidate gene for seed yield. Both Phacu.CVR.002G320800.13 and Phacu.CVR.009G294200.1 are likely to be involved in seed development of tepary bean. This is one of the few studies investigating the genetics of 100-seed weight and seed yield in tepary bean.

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach

This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Cowpea Constraints and Breeding in Europe

Cowpea (Vigna unguiculata (L.) Walp.) is a legume with a constant rate of cultivation in Southern European countries. Consumer demand for cowpea worldwide is rising due to its nutritional content, while Europe is constantly attempting to reduce the deficit in the production of pulses and invest in new, healthy food market products. Although the climatic conditions that prevail in Europe are not so harsh in terms of heat and drought as in the tropical climates where cowpea is mainly cultivated, cowpea confronts with a plethora of abiotic and biotic stresses and yield-limiting factors in Southern European countries. In this paper, we summarize the main constraints for cowpea cultivation in Europe and the breeding methods that have been or can be used. A special mention is made of the availability plant genetic resources (PGRs) and their potential for breeding purposes, aiming to promote more sustainable cropping systems as climatic shifts become more frequent and fiercer, and environmental degradation expands worldwide.