Key message β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. Abstract In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F 1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

Sweetpotato [Ipomoea batatas (L.) Lam] breeding is important for food security and health in East Africa (EA), and a breeding platform in Uganda provides national researchers and breeders in EA with true seed. Our objectives were to characterize genetic relationships among parental material used at the EA breeding platform. There were 135 parents and six check clones analyzed using 31 simple sequence repeat primers. An average of 7.13 alleles per primer was found, and Jaccard similarity coefficients were in the range of 0.298 to 1.00 with a mean of 0.542. Unweighted pair group cluster analysis placed most African parents in two main subclusters showing no association with morphology or geographical origin. The subclusters were also supported by principal coordinate analysis, derivative analysis of principal components, and population structure simulations. The analyzed breeding material from EA was highly genetically variable, grouped in two distinct genetic pools, and suitable to study heterosis exploiting breeding schemes.

Sweetpotato is a resilient food crop with great potential to contribute to reduced hunger in the world. Sweetpotato shows significant potential to contribute to reducing the Global Hunger Index, which reflects deficiencies in calories and micronutrients based on the components of hunger, undernourishment, under-five mortality rate, stunting and wasting. Its genetic diversity has been harnessed through breeding to increase vitamin A, iron, and zinc content, virus resistance and climate resilience for the world's food needs. Africa and India are the most food-insecure regions. The main objectives of this research were to: provide information and a knowledge base on sweetpotato breeding in Africa for biofortification of vitamin A, iron, and zinc, drought tolerance and virus resistance; recommend procedures for generating new breeding populations and varieties; and develop new tools, technologies and methods for sweetpotato improvement. The research was implemented between 2009 and 2020 in 14 collaborating African countries using introduced and local genotypes. The redesigned accelerated breeding scheme resulted in increased genetic gains for vitamin A, iron, zinc contents and virus resistance, and the release by sub-Saharan African countries of 158 varieties; 98 of them orange-fleshed; 55 varieties bred by an accelerated breeding scheme; 27 drought-tolerant and two with enhanced iron and zinc content. Our experience has demonstrated that through the use of more optimized, standardized and collaborative breeding procedures by breeding programs across Africa, it is possible to speed official sweetpotato variety release and contribute to reducing the severe micronutrient deficiencies on the continent.

Orange‐fleshed sweetpotato [Ipomoea batatas (L.) Lam.] (OFSP) breeding populations have gained importance for food security and health reasons. This study's main objectives were to determine genetic diversity in parental material of two OFSP populations developed in Peru (Jewel [PJ] and Zapallo [PZ]) relative to mega‐clones (MCs) using agronomic traits and simple sequence repeat (SSR) markers and to determine whether PJ and PZ are mutually heterotic by developing a PJ × PZ hybrid population (H0). Field trials were performed with clones for PJ (n = 49), PZ (n = 31), MC (n = 21), and H0 (n = 6,898) in Peru. Traits recorded were storage root yield (RYTHA), number of commercial roots per plant, foliage yield, biomass, harvest index, and dry matter (RDM), β‐carotene (RBC), protein, starch, sucrose, iron, zinc, and calcium content of storage roots. Sixty‐six pairs of SSR primers were used to determine molecular diversity. Statistics used were linear mixed models, principal component analysis, and standard procedures for molecular data. New genetic variation was found in PJ and PZ (e.g., RDM ≥29% with RBC ≥25 mg 100 g−1 dry weight basis). For most traits, genetic variance in PJ and PZ was as large as in MC. The SSR marker data clearly separated PJ and PZ into two gene‐pools, together covering nearly the entire MC molecular diversity. Average RYTHA in H0 was high (40.7 t ha−1) with average heterosis increment of 21.8% and range −30.6 to 139.4%. The PJ and PZ lend themselves to study of the efficiency of reciprocal recurrent selection in sweetpotato population hybrid breeding.

Highlights Transcriptome responses in sweet potato infected with SPCSV and/or SPFMV were studied. Numerous genes, miRNAs and phasiRNAs were responsive mainly to the dual infection. Salicylic acid-mediated pathways play important roles in antiviral defense responses.

Potato virus Y (PVY) and Phytophthora infestans (Mont.) de Bary that causes potato late blight (LB), pose serious constraints to cultivated potatoes due to significant yield reduction, and phenotyping for resistance remains challenging. Breeding operations for vegetatively propagated crops can lead to genotype mislabeling that, in turn, reduces genetic gains. Low-density and low-cost molecular marker assessment for phenotype prediction and quality control is a viable option for breeding programs. Here, we report on the development of kompetitive allele specific PCR (KASP) markers for LB and PVY resistance, and for routine quality control assessment of different breeding populations. Two KASP markers for LB resistance and two for PVY Ryadg were validated with an estimated assay power that ranged between 0.65 and 0.88. The developed QC KASP markers demonstrated the capability of discriminating tetraploid calls in breeding materials, including full-sibs and half-sibs. Routine implementation of the developed markers in a breeding program would assist with better allocation of resources and enable precise characterization of breeding material, thereby leading to increased genetic gains.

Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.

Sweet potato virus disease (SPVD) is a global constraint to sweetpotato (Ipomoea batatas) production, especially under intensive cultivation in the humid tropics such as East Africa. The objectives of this study were to develop a precision SPVD phenotyping protocol, to find new SPVD-resistant genotypes, and to standardize the first stages of screening for SPVD resistance. The first part of the protocol was based on ELISA results for sweet potato chlorotic stunt virus (SPCSV) and sweet potato virus C (SPVC) with adjustments to a negative control (uninfected clone ‘Tanzania’) and was performed on a pre-breeding population (VZ08) comprising 455 clones and 27 check clones graft-inoculated under screenhouse conditions. The second part included field studies with 52 selected clones for SPCSV resistance from VZ08 and eight checks. In screenhouse conditions, the resistant and susceptible check clones performed as expected, 63 clones from VZ08 exhibited lower relative absorbance values for SPCSV and SPVC than inoculated check Tanzania. Field experiments confirmed SPVD resistance of several clones selected by relative absorbance values (nine resistant clones in two locations, i.e. 17.3% of the screenhouse selection), supporting the reliability of our method for SPVD-resistance selection. Two clones were promising, exhibiting high storage root yields of 28.7–34.9 t ha−1 and SPVD resistance, based on the proposed selection procedure. This modified serological analysis for SPVD-resistance phenotyping might lead to more efficient development of resistant varieties by reducing costs and time at early stages, and provide solid data for marker assisted selection with a quantitative tool for classifying resistance.