Breeding for resilience: genomic and agronomic characterization of Kenyan sorghum (Sorghum bicolor L) and common beans (Phaseolus vulgaris) potential for intercropping

Smallholder farming in East Africa is rain-fed, low-input, and increasingly exposed to climate variability. While farmers commonly use mixed cropping especially cereal–legume intercrops to reduce climate risk, most crop varieties are bred for monoculture and underperform in these systems. Despite rich cereal and legume agrobiodiversity in Kenya's fields and genebanks, there are no intercrop-optimized varieties and little guidance on which genotype pairings work best. This thesis addresses that gap by applying genomic, statistical, and participatory approaches to identify climate-ready sorghums, farmer-preferred beans, and field-validated sorghum–bean combinations. We first characterized climate-associated genomic variation in 239 Kenyan sorghum landraces. Using Single Nucleotide Polymorphism and non-collinear bioclimatic variables, we detected 13 adaptation-associated loci. Gradient-Forest modeling suggested future scenarios of sorghum adaptation in Kenya, pinpointing adaptive alleles and priority deployment zones. Next, we assembled 96 common-bean varieties and combined field data, participatory varietal selection, and GWAS. Women and men expressed distinct trait priorities, and converged on 14 jointly preferred genotypes that were earlier flowering and with higher yields. With 45,609 SNPs, GWAS identified six quantitative trait nucleotides for growth habit, plant height, and seeds per pod, providing markers to track farmer-valued traits during selection. Finally, split-plot trials of 60 sorghum genotypes and 4 bean varieties chosen on the basis of experimental work identified best intercropping combinations. Interaction metrics and trait dissection revealed an intercrop-friendly sorghum ideotype. Together, these results deliver climate-anchored sources of sorghum adaptation, bean candidates aligned with farmer preferences, and evidence-based pairs of sorghum and beans to guide intercrop-first breeding and deployment of resilient sorghum–bean varieties for Kenya’s smallholder systems