Summary: This study sought to understand user preferences of raw, boiled and steamed sweetpotato, a staple food in Uganda. A sequential methodology involving state of knowledge review, gendered food mapping, processing diagnosis and consumer testing was used in Lira and Kamwenge districts. Preferred raw sweetpotato characteristics were large roots (≥ 3 cm diameter) with a sweet taste, smooth skin and hard texture, while mealiness, sweet taste and good sweetpotato smell were important attributes for boiled sweetpotato. Processors, mostly women, highlighted ease of peeling and sappiness of raw roots. There were gender differences in quality characteristic preferences and perceived importance. The released variety, NASPOT 8, had the highest overall liking in Kamwenge and was well liked in Lira. Penalty analysis of consumer data showed that sweetness and firmness were key drivers of overall liking. The results will support breeding programmes in meeting specific end‐user product profiles, selection criteria and uptake of new varieties.

β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea batatas) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene (Amyβ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R = −0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding.

Pangenomics has been promoted to accelerate breeding of orphan crops, but smallholder farmers in developing nations have seen little benefit so far. To address this gap, we built a global pangenomic breeding network, integrating African breeding programs, U.S. land grant universities, and international nonprofit research organizations. Here we demonstrate that pangenomics, when integrated with local crop improvement knowledge and global scientific partnerships, can facilitate breeding of drought and pest resilient varieties for smallholders. To breed trait-enhanced sorghum varieties with lgs1-1 resistance to witchweed (Striga hermonthica) for smallholders in Niger, one of the world's least developed nations, we used population genomics across local and global scales to develop lgs1-1 Striga resistance markers, and deployed them for rapid introgression of resistance into locally-preferred varieties. Genomic characterization, along with controlled experiments in laboratory, pot, field stations, and smallholder farms, confirmed lgs1-1 resistance was introgressed without loss of essential local-preference traits. New pangenomic resources, including global resequencing and graph pangenomes, further accelerated design of broadly-applicable markers. Unlocking the potential of pangenomics for stress-resilience breeding depended on stakeholder input, strong inference, South-led decision support software, and a dense collaborative network. The experience of the network provides a scalable roadmap for collaborative pangenomic breeding of trait-enhanced varieties for the world's lowest-resourced farmers.

Enhancing grain carotenoid concentration to increase yellowness and provitamin A content in sorghum ( Sorghum bicolor [L.] Moench) is a major breeding objective across sub-Saharan Africa. Carotenoid breeding is constrained by costly post-harvest phenotyping and can be accelerated through genetic markers that capture functional variation in key carotenoid biosynthesis genes. Zeaxanthin epoxidase ( ZEP ) is a major gene controlling sorghum grain carotenoid accumulation, and SNP-based KASP markers facilitate selection of high-carotenoid grain, although quantitative variation remains among lines carrying the favorable allele. We hypothesized that additional functional variation within ZEP and other carotenoid biosynthesis pathway genes contributes to this variation and can be revealed by a pangenome-informed analysis. Using a 33-member pangenome reference, we characterized sequence and structural variation at ZEP and other key carotenoid biosynthesis genes and applied pangenome-derived genotyping to study marker diversity associated with carotenoid accumulation. Evaluation of ZEP in the pangenome reference revealed previously uncharacterized structural variation that is absent from the BTx623 primary reference genome. A pangenome-based association analysis identified genetic markers associated with the accumulation of carotenoids which were specific to particular pangenome reference members, including in RTx430 and SRN39, both yellow endosperm lines. Machine learning identified markers in ZEP , β -OH , ZDS , and Z-ISO as the most predictive for all carotenoid traits, suggesting a multi-locus genetic architecture underlies the accumulation of carotenoids in sorghum grain. By integrating sorghum pangenomic resources with machine learning, this study establishes a framework for pangenome-accelerated trait discovery and identifies new genetic targets for carotenoid biofortification in sorghum.