Early-Stage Phenotyping of Sweet Potato Virus Disease Caused by Sweet Potato Chlorotic Stunt Virus and Sweet Potato Virus C to Support Breeding.

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 enzyme-linked immunosorbent assay 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 prebreeding 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 8 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; that is, 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 to 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.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato.

BACKGROUND: Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. RESULTS: Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10- 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. CONCLUSION: Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated ß-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.].

KEY MESSAGE: ß-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, ß-carotene and starch content are negatively correlated. In populations depending on sweetpotato for food security, starch is an important source of calories, while ß-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 F1 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, ß-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 ß-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 ß-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and ß-carotene content in sweetpotato.

Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and ß-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and ß-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root ß-carotene content was negatively correlated with dry matter (r = -0.59, P < 0.001) and starch (r = -0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and ß-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.

Gender mainstreaming in sweetpotato breeding in Uganda: a case study.

Purpose: In Uganda, sweetpotato [Ipomoea batatas (L.) Lam] is typically a "woman's crop," grown, processed, stored and also mainly consumed by smallholder farmers for food and income. Farmers value sweetpotato for its early maturity, resilience to stresses, and minimal input requirements. However, productivity remains low despite the effort of breeding programs to introduce new varieties. Low uptake of new varieties is partly attributed to previous focus by breeders on agronomic traits and much less on quality traits and the diverse preferences of men and women in sweetpotato value chains. Method: To address this gap, breeders, food scientists, and social scientists (including gender specialists) systematically mainstreamed gender into the breeding program. This multidisciplinary approach, grounded in examining gender roles and their relationship with varietal and trait preferences, integrated important traits into product profiles. Results: Building on earlier efforts of participatory plant breeding and participatory varietal selection, new interventions showed subtle but important gender differences in preferences. For instance, in a study for the RTBFoods project, women prioritized mealiness, sweetness, firmness and non-fibrous boiled roots. These were further subjected to a rigorous gender analysis using the G+ product profile query tool. The breeding pipelines then incorporated these gender-responsive priority quality traits, prompting the development of standard operating procedures to phenotype these traits. Conclusion: Following an all-inclusive approach coupled with training of multidisciplinary teams involving food scientists, breeders, biochemists, gender specialists and social scientists, integration into participatory variety selection in Uganda enabled accentuation of women and men's trait preferences, contributing to clearer breeding targets. The research has positioned sweetpotato breeding to better respond to the varying needs and preferences of the users.

Market Intelligence and Incentive-Based Trait Ranking for Plant Breeding: A Sweetpotato Pilot in Uganda.

Crop breeding programs must accelerate crop improvement, spur widespread adoption of new varieties and increase variety turnover they are to meet the diverse needs of their clients. More comprehensive quantitative approaches are needed to better inform breeding programs about the preferred traits among farmers and other actors. However, the ability of current breeding programs to meet the demands of their clients is limited by the lack of insights about value chain actor preference for individual or packages of traits. Ranking traits based on monetary incentives, rather than subjective values, represents a more comprehensive, consistent, and quantitative approach to inform breeding programs. We conducted a large pilot in Uganda to assess the implementation of a novel approach to trait ranking, using a uniquely large sample of diverse sweetpotato value chain actors. We found meaningful differences in trait ranking and heterogeneity among different actors using this approach. We also show our approach's effectiveness at uncovering unmet demand for root quality traits and at characterizing the substantial trait demand heterogeneity among value chain players. Implementing this approach more broadly for sweetpotato and other crops would increase the effectiveness of breeding programs to improve food security in developing countries.

Analysis of ß-amylase gene (Amyß) variation reveals allele association with low enzyme activity and increased firmness in cooked sweetpotato (Ipomoea batatas) from East Africa.

ß-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 (Amyß) is not well studied. Amyß 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 Amyß 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.

A review of varietal change in roots, tubers and bananas: consumer preferences and other drivers of adoption and implications for breeding.

This review of the literature on varietal change in sub-Saharan Africa looks in detail at adoption of new varieties of bananas in Uganda, cassava in Nigeria, potato in Kenya, sweetpotato in Uganda and yams in Côte d'Ivoire. The review explored three hypotheses about drivers of varietal change. There was a strong confirmation for the hypothesis that insufficient priority given to consumer-preferred traits by breeding programmes contributes to the limited uptake of modern varieties (MVs) and low varietal turnover. Lack of evidence meant the second hypothesis of insufficient attention to understanding and responding to gender differences in consumer preferences for quality and post-harvest traits was unresolved. The evidence on the third hypothesis about the informal seed system contributing to slow uptake of MVs was mixed. In some cases, the informal system has contributed to rapid uptake of MVs, but often it appears to be a barrier with inconsistent varietal naming a major challenge.

Development of a food product profile for boiled and steamed sweetpotato in Uganda for effective breeding.

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.

Toxicity of seven Bacillus thuringiensis Cry proteins against Cylas puncticollis and Cylas brunneus (Coleoptera: Brentidae) using a novel artificial diet.

"Sweetpotato weevils" Cylas puncticollis (Boheman) and Cylas brunneus F. (Coleoptera: Brentidae) are the most important biological threat to sweetpotato, Ipomoea batatas L. (Lam), productivity in sub-Saharan Africa. Sweetpotato weevil control is difficult due to their cryptic feeding behavior. Expression of Cylas-active Bacillus thuringiensis (Bt) Cry proteins in sweetpotato could provide an effective control strategy. Unfortunately, Bt Cry proteins with relatively high toxicity against Cylas spp. have not been identified, partly because no published methodology for screening Bt Cry proteins against Cylas spp. in artificial diet exists. Therefore, the initial aim of this study was to develop an artificial diet for conducting bioassays with Cylas spp. and then to determine Bt Cry protein efficacy against C. puncticollis and C. brunneus by using this artificial diet. Five diets varying in their composition were evaluated. The highest survival rates for sweetpotato weevil larvae were observed for diet E that contained the highest amount of sweetpotato powder and supported weevil development from first instar to adulthood, similar to sweetpotato storage roots. Seven coleopteran-active Bt Cry proteins were incorporated into diet E and toxicity data were generated against neonate C. puncticollis and second-instar C. brunneus. All Bt Cry proteins tested had toxicity greater than the untreated control. Cry7Aa1, ET33/34, and Cry3Ca1 had LC50 values below 1 microg/g diet against both species. This study demonstrates the feasibility of using an artificial diet bioassay for screening Bt Cry proteins against sweetpotato weevil larvae and identifies candidate Bt Cry proteins for use in transforming sweetpotato varieties potentially conferring field resistance against these pests.

Efficiency of the Polycross and Controlled Hybridization Methods in Sweetpotato Breeding in Uganda.

Sweetpotato is an important crop in many parts of the world especially in developing countries. It is used for both human consumption as well as livestock feed. It is an important source of carbohydrates, vitamin C, fibre, iron, potassium, protein and ß-carotene. Its production is, however, constrained by several biotic and abiotic factors, including pests and diseases, low soil fertility, drought, cold and salinity. Breeding is one of the ways to overcome some of these constraints and in sweetpotato the polycross or controlled cross methods can be used. To determine which of the two methods was more efficient, genotypes generated by both methods were evaluated over two seasons at Namulonge and Kachwekano. The type of cross (polycross or controlled) was significantly (P ≤ 0.05) different for storage root yield, response to sweetpotato virus disease, Alternaria blight, and harvest index (HI). The controlled cross families had a significantly higher mean HI of 43.2% than the polycross families with a mean HI of 31.8%. Therefore, controlled crosses could be deployed to systematically increase the HI in sweetpotato breeding populations. Significant (P ≤ 0.05) differences were observed among families for all traits. This stresses that the parents used in a cross are very important in generating genotypes with desired attributes. It was apparent that both the polycross and controlled crosses are good methods for generating new sweetpotato genotypes in a sweetpotato breeding program. Where aggregate performance was considered (selection index) the controlled crosses method produced more (75% of the top 20 desirable genotypes) than the polycross method across the two sites. However, the best three genotypes over the two sites were from the polycross family of Ejumula. Therefore, sweetpotato controlled crosses could be very useful for population improvement using recurrent selection while polycrosses could be suitable for variety development. Both hybridization methods require cautious selection of parents to match the breeding objectives.

Gene Pool Subdivision of East African Sweetpotato Parental Material.

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.

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes.

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.

Tackling vitamin A deficiency with biofortified sweetpotato in sub-Saharan Africa.

Orange-fleshed sweetpotato (OFSP) is a rich plant-based source of beta-carotene, which the body converts into vitamin A. In sub-Saharan Africa, sweetpotato is known as a food security crop but most varieties grown are high dry matter white-fleshed types, lacking beta-carotene. In 1995, researchers recognized the potential of OFSP varieties to address widespread vitamin A deficiency in SSA using an integrated agriculture-nutrition approach. With their partners, they confronted conventional wisdom concerning food-based approaches and institutional barriers, to build the evidence base and breed 42 OFSP varieties adapted to farmer needs and consumer preferences. Subsequently, a multi-partner, multi-donor initiative, launched in 2009, has already reached 2.8 million households. This review summarizes that effort describing how the changing policy environment influenced the process.

Segregation of Hydroxycinnamic Acid Esters Mediating Sweetpotato Weevil Resistance in Storage Roots of Sweetpotato.

Resistance to sweetpotato weevils (Cylas spp.) has been identified in several sweetpotato (Ipomoea batatas) landraces from East Africa and shown to be conferred by hydroxycinnamic acids that occur on the surface of storage roots. The segregation of resistance in this crop is unknown and could be monitored using these chemical traits as markers for resistance in F1 offspring from breeding programs. For the first time in a segregating population, we quantified the plant chemicals that confer resistance and evaluated levels of insect colonization of the same progeny in field and laboratory studies. We used a bi-parental mapping population of 287 progenies from a cross between I. batatas 'New Kawogo,' a weevil resistant Ugandan landrace and I. batatas 'Beauregard' a North American orange-fleshed and weevil susceptible cultivar. The progenies were evaluated for resistance to sweetpotato weevil, Cylas puncticollis at three field locations that varied climatically and across two seasons to determine how environment and location influenced resistance. To augment our field open-choice resistance screening, each clone was also evaluated in a no choice experiment with weevils reared in the laboratory. Chemical analysis was used to determine whether differences in resistance to weevils were associated with plant compounds previously identified as conferring resistance. We established linkage between field and laboratory resistance to Cylas spp. and sweetpotato root chemistry. The data also showed that resistance in sweetpotato was mediated by root chemicals in most but not all cases. Multi-location trials especially from Serere data provided evidence that the hydroxycinnamic acid esters are produced constitutively within the plants in different clonal genotypes and that the ecological interaction of these chemicals in sweetpotato with weevils confers resistance. Our data suggest that these chemical traits are controlled quantitatively and that ultimately a knowledge of the genetics of resistance will facilitate management of these traits, enhance our understanding of the mechanistic basis of resistance and speed the development of new sweetpotato varieties with resistance to sweetpotato weevil.

Resistance to the weevils Cylas puncticollis and Cylas brunneus conferred by sweetpotato root surface compounds.

Seven resistant varieties of sweetpotato were compared with three susceptible varieties in field trials and laboratory bioassays and showed that resistance was an active process rather than an escape mechanism, as field resistant varieties also had reduced root damage and oviposition compared with susceptible varieties in the laboratory. Liquid chromatography-mass spectrometry (LC-MS) of root surface and epidermal extracts showed significant variation in the concentration of hexadecyl, heptadecyl, octadecyl, and quinic acid esters of caffeic and coumaric acid, with higher concentrations correlated with resistance. All compounds were synthesized to enable their positive identification. Octadecyl coumarate and octadecyl caffeate applied to the surface of susceptible varieties in laboratory bioassays reduced feeding and oviposition, as observed on roots of resistant varieties, and therefore are implicated in weevil resistance. Segregating populations from breeding programs can use these compounds to identify trait loci for resistance and enable the development of resistant varieties.