Accurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels. Genotyping-by-sequencing (GBS) was used in a case study as an alternative method to track released varieties in farmers’ fields, using cassava, a clonally propagated root crop widely grown in the tropics, and often disseminated through extension services and informal seed systems. A total of 917 accessions collected from 495 farming households across Ghana were genotyped at 56,489 SNP loci along with a “reference library” of 64 accessions of released varieties and popular landraces. Accurate cultivar identification and ancestry estimation was accomplished through two complementary clustering methods: (i) distance-based hierarchical clustering; and (ii) model-based maximum likelihood admixture analysis. Subsequently, 30 % of the identified accessions from farmers’ fields were matched to specific released varieties represented in the reference library. ADMIXTURE analysis revealed that the optimum number of major varieties was 11 and matched the hierarchical clustering results. The majority of the accessions (69 %) belonged purely to one of the 11 groups, while the remaining accessions showed two or more ancestries. Further analysis using subsets of SNP markers reproduced results obtained from the full-set of markers, suggesting that GBS can be done at higher DNA multiplexing, thereby reducing the costs of variety fingerprinting. A large proportion of discrepancy between genetically unique cultivars as identified by markers and variety names as elicited from farmers were observed. Clustering results from ADMIXTURE analysis was validated using the assumption-free Discriminant Analysis of Principal Components (DAPC) method. We show that genome-wide SNP markers from increasingly affordable GBS methods coupled with complementary cluster analysis is a powerful tool for fine-scale population structure analysis and variety identification. Moreover, the ancestry estimation provides a framework for quantifying the contribution of exotic germplasm or older improved varieties to the genetic background of contemporary improved cultivars.

This study identified gender-based constraints affecting the production, processing and marketing of biofortified cassava in two states in Nigeria, using a mixed methods approach. The study identified major differences between the two study sites (Benue and Oyo). The scale of production of biofortified cassava is higher in Oyo state among adult men because of their active involvement and collaboration with research institutes within the state and the ease of transporting products to Lagos State for designated diverse markets. However, in Benue state more adult and young women are engaged in cultivation, processing and marketing business to meet up with the increased demand due to higher consumer acceptance in this region. Gender analysis revealed that lack of access to hired-labour restricted the scale of production among women in especially Oyo state. Low product price and high price of processing equipment, poor market infrastructure and middle men exploitation were constraints significantly more mentioned by women in general. Majorly, the men identified limited processing facilities/equipment as the most important constraint affecting the demand of biofortified cassava roots, while generally women were more constrained by the shortage of basic amenities and trainings that hindered their processing efficiency. The study proposes integration of gender-responsive strategies to further enhance the delivery of biofortified cassava products in Nigeria.

Biofortified yellow-fleshed cassava is important in countries with high cassava consumption, to improve the vitamin A status of their populations. Yellow- and white-fleshed cassava were evaluated over three locations for proximate composition and cyanide content as well as retention of carotenoids after boiling. There was significant variation in the crude fiber, fat, protein and ash content of the genotypes. All but one of the yellow-fleshed cassava genotypes recorded higher protein values than the white-fleshed local genotypes across locations. The cyanide content of the genotypes varied between locations but was within the range of sweet cassava genotypes, but above the maximum acceptable recommended limit. Micronutrient retention is important in biofortified crops because a loss of micronutrients during processing and cooking reduces the nutritional value of biofortified foods. Total carotenoid content (TCC) ranged from 1.18–18.81 μg.g⁻¹ and 1.01–13.36 μg.g⁻¹ (fresh weight basis) for fresh and boiled cassava, respectively. All the yellow-fleshed cassava genotypes recorded higher TCC values in both the fresh and boiled state than the white-fleshed genotypes used as checks.

Cassava mosaic disease (CMD) is a major viral disease adversely affecting cassava production in Africa and Asia. Genomic regions conferring resistance to the disease have been mapped in African cassava germplasm through biparental quantitative trait loci (QTL) mapping and genome-wide association studies. To facilitate the utilization of these markers in breeding pipelines to support selections, proof-of-concept technical and biological validation research was carried out using independent pre-breeding and breeding populations. Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) assays were designed from three single nucleotide polymorphism (SNP) markers linked to a major resistance locus on chromosome 12 (S12_7926132, S12_7926163) and a minor locus on chromosome 14 (S14_4626854). The designed assays were robust and easy to score with >99% genotype call rate. The overall predictive accuracy (proportion of true positives and true negatives) of the markers (S12_7926132 and S14_4626854) was 0.80 and 0.78 in the pre-breeding and breeding population, respectively. On average, genotypes that carried at least one copy of the resistant allele at the major CMD2 locus had a significantly higher yield advantage. Nevertheless, variation was observed in prediction accuracies for the major locus (S12_7926132) among sub-families from the two populations, suggesting the need for context-specific utilization, for example, by screening for co-segregation of favorable SNP alleles with resistance in the parents being used for crosses. Availability of these validated SNP markers on the uniplex KASP genotyping platform represents an important step in translational genetics toward marker-assisted selection to accelerate introgression of favorable resistant alleles in breeding populations.

A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future.

Cassava is an important root crop in sub-Saharan Africa, largely cultivated for its starchy edible roots. Biofortified cassava varieties with enhanced provitamin A carotenoid content (PVAC) developed through conventional breeding provide a solution for vitamin A deficiency among vulnerable communities. The aim of this study was to use diallel analysis of six provitamin A cassava genotypes to determine the combining ability, genetic components, heritability, and heterosis of the most important yield characteristics and total carotenoids. Genetic variability for measured characteristics were evident. Fresh root yield was mainly determined by non-additive genetic effects, while dry matter content and total carotenoids were determined by additive effects. Total carotenoids were negatively correlated with fresh root yield, indicating that selection for higher provitamin A content could reduce yield. Mid and higher parent heterosis was seen in some of the crosses for fresh root yield, dry matter content, and total carotenoids. Narrow sense heritability was moderate for fresh root yield and dry matter content, and was high for total carotenoids. This study indicated that yield and dry matter content can be improved in provitamin A cassava but that increased provitamin A content may carry a yield penalty.