Jennifer Wilker

Common bean cultivars developed through interspecific crosses with five different Phaseolus species ( P. vulgaris , P. coccineus , P. acutifolius , P. dumosus , and P. parvifolius ) to combine desirable nutritional characteristics in their seeds are important for improving nutritional value and food security in the Global South. In this study, we evaluated the nutritional composition (ash, crude protein, fat, fiber, hemicellulose, cellulose and lignin) and mineral status (Fe, Zn, K, Mg and other minerals) of 112 common bean genotypes including bred lines that were developed from interspecific crosses and were grown under acidic soil and high-temperature stress conditions in Colombia’s Amazon region. Genotypes tested for nutritional composition and mineral status were grouped into three different typologies: high Fe and Zn content (HFZ); high dietary fiber and cellulose (HDFC); and low dietary fiber and cellulose (LDFC). Based on genotypic differences found and grouping of genotypes according to fiber content and mineral status, we developed nutritional composition index (NCI) as a selection criterion to assess nutritional value of common bean. The NCI was created by considering variables that have both positive and negative impacts on nutritional quality. Among the genotypes evaluated, bean materials with HFZ typology exhibited a mean NCI value of 0.53, including four genotypes (SEF 49, SEF 10, NCB 280, VAP 15) developed from interspecific crosses. Four genotypes of P. acutifolius exhibited HDFC typology with a mean NCI value higher than 0.3 compared to other genotypes. Among the genotypes of LDFC typology, P. acutifolius accession G 40001 exhibited the lowest NCI value. Regarding fiber content, HDFC typology included mainly genotypes of P. acutifolius species (G 40250, G 40253, G 40254) with NCI values higher than 0.3. NCI showed higher values of correlation coefficients with crude protein, K, Fe and Zn. Combining NCI and NQI values—which include bioactive compounds and antioxidant activity—helped identify common bean lines with superior nutritional quality. Results from this study highlight the superior nutritional value of SEF 49 and SEF 10 based on NCI values and these two genotypes could serve as valuable parents in future bean breeding programs aimed at improving the nutritional value of common bean.

Phenotyping plant traits using UAV-based multispectral imaging offers a robust and unbiased approach to assessing crop status. With approximately 70% of smallholder farmers in East and Southern Africa cultivating common beans as a key source of food and income, there is a critical need for accurate and timely measurements of crop health and yield to support data-driven management decisions and disease mitigation. Traditional phenotyping methods are labor-intensive, and existing remote sensing and machine learning approaches remain limited. This study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery. Data collected over three growing seasons (2022–2024) were used to extract canopy variables and vegetation indices (VIs) across phenological stages. For yield prediction, traditional machine learning models achieved a root mean squared error (RMSE) of 242.33 kg ha⁻¹ and an R² of 0.66 using an Extra Trees Regressor. A novel BY-GRU architecture improved performance, achieving an RMSE of 242.40 kg ha⁻¹ and an R² of 0.79. The analysis also identified 45–60 days after sowing as the optimal window for prediction. To address limitations in conventional plant health assessments, this study introduces a novel Health Index. Comparative analysis demonstrated its robustness across genotypes and stronger correlation with yield. Machine learning and deep learning models, including MaxViT, were applied to estimate the Health Index, achieving improved predictive performance. Overall, this work integrates UAV sensing and modelling to provide scalable tools for phenomics, crop management, and breeding.

Comprehensive profiling of Phaseolus species revealed key biochemical differences relevant to nutrition and crop improvement. Genotyping confirmed species-level separation and two gene pools in P. vulgaris, with evidence of introgression. Proteomic analysis identified over 11100 proteins, with P. vulgaris showing the highest diversity. Functional proteins, storage proteins, digestive enzymes, and protease inhibitors were linked to amino acid composition and digestibility. All 20 standard and nine essential amino acids were detected, with P. lunatus displaying a distinct essentials profile. Metabolomics identified 6717 compounds, 57% shared across species, dominated by flavonoids, polyphenols, and terpenoids. P. lunatus had 592 unique metabolites, while P. acutifolius had 98, suggesting a conserved, drought-adapted metabolome. Although the total fat was low, P. vulgaris accessions had higher omega-3 content and favorable omega-6/omega-3. Ionomic profiling revealed a variation in Ca, Fe, and Zn, with one P. vulgaris line accumulating unsafe Pb and Cd. Multiomics enables identification of nutrient-rich, climate-resilient, food-safe accessions.

The consumption of plant proteins is increasing worldwide as a viable alternative to animal‐derived proteins in the marketplace. The projected increase in global population to at least 10 billion by 2050 is placing greater pressure on the food supply, particularly due to the rising demand for large‐scale protein production. This protein transition is caused by macro‐drivers such as changing consumer demographics, environmental sustainability, animal ethics, regulatory influences, and changing dietary patterns. Research efforts worldwide have explored various food applications for plant protein ingredients, including meat analogs, dairy alternatives, beverages, bakery products, and hybrid products. We provide here a review of the potential for legume breeding programs to incorporate traits that target the emerging plant‐based protein market and aim to promote discussion among (but not limited to) plant breeders and geneticists, plant physiologists, agricultural economists, food scientists and chemists, and agricultural engineers. The prospects, progress, and tools developed when breeding for protein content, quality, structure, and functionality of several food legumes (common bean—Phaseolus vulgaris, pea—Pisum sativum, lentil—Lens culinaris, chickpea—Cicer arietinum, faba bean—Vicia faba, and mung bean—Vigna radiata) are presented. We also present some of the physiological processes that affect the accumulation of nitrogen and protein metabolism in tropical legume crop species, providing some insight into potential breeding targets for improving protein concentration, quality, and structural and functional properties. Finally, a perspective of industrial processing technologies for extracting and transforming plant proteins is discussed.

Maize ( Zea mays ) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during both the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an important first step in developing maize varieties that can reduce fertilizer needs in maize production across different environmental conditions.

Plant breeding and genetics play a major role in the adaptation of plants to meet human needs. The current requirement to make agriculture more sustainable can be partly met by a greater reliance on biological nitrogen fixation by symbiotic diazotrophic microorganisms that provide crop plants with ammonium. Select accessions of the cereal crop sorghum (Sorghum bicolor (L.) Moench) form mucilage-producing aerial roots that harbor nitrogen-fixing bacteria. Breeding programs aimed at developing sorghum varieties that support diazotrophs will benefit from a detailed understanding of the genetic and environmental factors contributing to aerial root formation. A genome-wide association study of the sorghum minicore, a collection of 242 landraces, and 30 accessions from the sorghum association panel was conducted in Florida and Wisconsin and under 2 fertilizer treatments to identify loci associated with the number of nodes with aerial roots and aerial root diameter. Sequence variation in genes encoding transcription factors that control phytohormone signaling and root system architecture showed significant associations with these traits. In addition, the location had a significant effect on the phenotypes. Concurrently, we developed F₂ populations from crosses between bioenergy sorghums and a landrace that produced extensive aerial roots to evaluate the mode of inheritance of the loci identified by the genome-wide association study. Furthermore, the mucilage collected from aerial roots contained polysaccharides rich in galactose, arabinose, and fucose, whose composition displayed minimal variation among 10 genotypes and 2 fertilizer treatments. These combined results support the development of sorghums with the ability to acquire nitrogen via biological nitrogen fixation.

Sorghum ( Sorghum bicolor ) is a significant crop globally, serving as an important source of food, feed, and fodder, and is increasingly recognized as an energy crop due to its high potential for biomass production. Certain sorghum accessions exhibit prolific aerial root development and produce abundant carbohydrate-rich mucilage after precipitation. This aerial root mucilage bears resemblance to that found in landraces of maize ( Zea mays ) from southern Mexico, which have previously been found to harbor diazotrophs. In this study, we examined the aerial root development of specific sorghum accessions and investigated the influence of humidity on this trait. Our microbiome analysis of the aerial root mucilage of maize and sorghum revealed the presence of numerous diazotrophs in sorghum mucilage, with Pseudomonadota , Bacillota , and Bacteriodota being the predominant phyla observed. However, the community composition varied significantly depending on the host plant and location. Through acetylene reduction, ¹⁵ N ₂ gas feeding, and ¹⁵ N isotope dilution assays, we determined that these sorghum accessions can acquire approximately 40% of their nitrogen from the atmosphere through these symbiotic associations on aerial roots. The nitrogen fixation occurring in sorghum aerial root mucilage presents a promising opportunity to reduce reliance on synthetic fertilizers and advance sustainable agricultural practices for food, feed, fodder, and bioenergy production.

Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.

Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation of SNF. High-yielding, conventionally bred bean varieties are developed using conventional production practices and selection criteria, typically not including SNF efficiency, and may have lost this trait over decades of modern breeding. In contrast, heirloom bean genotypes were developed before the advent of modern production practices and may represent an underutilized pool of genetics which could be used to improve SNF. This study compared the SNF capacity under low-N field conditions, of collections of heirloom varieties with and conventionally bred dry bean varieties. The heirloom-conventional panel (HCP) consisted of 42 genotypes from various online seed retailers or from the University of Guelph Bean Breeding program seedbank. The HCP was genotyped using a single nucleotide polymorphism (SNP) array to investigate genetic relatedness within the panel. Field trials were conducted at three locations in ON, Canada from 2014 to 2015 and various agronomic and seed composition traits were measured, including capacity for nitrogen fixation (using the natural abundance method to measure seed N isotope ratios). Significant variation for SNF was found in the panel. However, on average, heirloom genotypes did not fix significantly more nitrogen than conventionally bred varieties. However, five heirloom genotypes fixed >60% of their nitrogen from the atmosphere. Yield (kg ha^-1) was not significantly different between heirloom and conventional genotypes, suggesting that incorporating heirloom genotypes into a modern breeding program would not negatively impact yield. Nitrogen fixation was significantly higher among Middle American genotypes than among Andean genotypes, confirming previous findings. The best nitrogen fixing line was Coco Sophie, a European heirloom white bean whose genetic makeup is admixed between the Andean and Middle American genepools. Heirloom genotypes represent a useful source of genetics to improve SNF in modern bean breeding.