Ongom, P. O. | Search bioRxiv

bioRxiv2026

Genetic mapping and genomic prediction for agronomic, grain compositional, and sensing-enabled traits in a cowpea MAGIC population along an environmental gradient

Cowpea (Vigna unguiculata [L.] Walp.) is a resilient grain legume and an important global source of dietary protein, yet the genetic and environmental basis of phenological and canopy development, as well as grain composition, remains incompletely characterized across production environments. In this study, we evaluated a cowpea multi-parent advanced generation intercross (MAGIC) population along an environmental gradient in California (with contrasting daylengths, temperatures, and soil types) using agronomic, grain compositional, and uncrewed aerial vehicle (UAV) and rover-enabled phenotyping. Near-infrared spectroscopy (NIRS) enabled assessment of grain compositional traits, while sensing-enabled time-series imaging captured canopy and reproductive dynamics. Quantitative trait locus (QTL) mapping identified 267 QTL, and genome-wide association studies (GWAS) detected 1,973 marker-trait associations. Integrating QTL mapping and GWAS results identified two major genomic hotspots affecting multiple traits. A chromosome 9 hotspot (5.8-6.0 Mb) was associated with flowering time and co-localized with sensing-enabled measures of flower and pod counts, plant height, and vegetation fraction, indicating broad effects on phenological and canopy development. A chromosome 8 hotspot (37.3-37.9 Mb) contained co-localized signals for seed weight, protein, starch, phytate, and moisture. A total of 22 prioritized candidate genes were identified within these and other loci with multi-environment QTL and GWAS support. Genomic predictive abilities were moderate to high for most traits and scenarios, with multi-trait MegaLMM outperforming RR-BLUP. Together, these results define major genomic regions controlling cowpea phenology, canopy development, and grain composition, and provide targets and strategies for breeding cowpea cultivars with favorable and environmentally resilient productivity and grain composition. Significance StatementTo dissect the genetic basis of cowpea productivity, adaptation, and grain composition, and how performance for these traits varies and can be predicted across environments, we combined multi-environment phenotyping, including sensing of canopy and reproductive traits, with quantitative genetic analyses in a multi-parental population. We identified genomic hotspots for seed size/composition and reproductive phenology and an across-environment predictive advantage for multi-trait vs. single-trait genomic prediction. Overall, these findings support the comprehensive improvement of cowpea.

genetics↗

bioRxiv2025

Discovery and development of single-nucleotide polymorphism markers for resistance to Striga gesnerioides in cowpea (Vigna unguiculata)

The parasitic weed [Striga gesnerioides (Willd.) Vatke] is a principal biotic constraint to cowpea [Vigna unguiculata (L.) Walp.] production in West and Central Africa, causing severe yield reductions. Multiple races of S. gesnerioides exist across the cowpea-growing areas of the sub- region. Past efforts identified some resistant sources and race-specific genes underpinning Striga resistance, but deployment of associated markers in breeding is limited. Here, we utilized a 51K cowpea iSelect single-nucleotide polymorphisms (SNPs) to decipher genomic regions underlying Striga resistance and explore marker conversion and validation for easy deployment. The study used two-year phenotypic data on a minicore panel of 368 cowpea genotypes screened at two sites in Northern Nigeria. SNPs performances were verified and validated using two independent sets of 60 and 20 diverse genotypes respectively. The minicore displayed apparent differences in response to the S. gesnerioides attack. A genome-wide scan uncovered a primary gene effect signal on chromosome Vu11 and minor regions on chromosomes Vu02, Vu03, Vu07, Vu09 and Vu10. The major effect region on Vu11 harbored a coil-coil nucleotide-binding site leucine-rich repeat (CC- NBS-LRR) protein, encoded by the RSG3-301 gene, previously implicated in race-specific resistance to S. gesnerioides in cowpea. The associated SNPs were successfully converted into Kompetitive Allele-Specific PCR (KASP) assays and validated using 20 independent diverse cowpea genotypes. Five KASP markers, snpVU00075, snpVU00076, snpVU00077, snpVU00078, and snpVU00079, depicted consistent and significant associations with the phenotype in the validation set. The markers provide valuable tools for efficient marker-assisted selection (MAS) in breeding programs focused on developing Striga-resistant cowpea varieties.

genomics↗