Potato and sweetpotato breeding at the international potato center: approaches, outcomes and the way forward.

Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.

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.

Targeting market segment needs with public-good crop breeding investments: A case study with potato and sweetpotato focused on poverty alleviation, nutrition and gender.

Crop breeding programs have often focused on the release of new varieties that target yield improvement to achieve food security and reduce poverty. While continued investments in this objective are justified, there is a need for breeding programs to be increasingly more demand-driven and responsive to the changing customer preferences and population dynamics. This paper analyses the responsiveness of global potato and sweetpotato breeding programs pursued by the International Potato Center (CIP) and its partners to three major development indicators: poverty, malnutrition and gender. The study followed a seed product market segmentation blueprint developed by the Excellence in Breeding platform (EiB) to identify, describe, and estimate the sizes of the market segments at subregional levels. We then estimated the potential poverty and nutrition impacts of investments in the respective market segments. Further, we employed the G+ tools involving multidisciplinary workshops to evaluate the gender-responsiveness of the breeding programs. Our analysis reveals that future investments in breeding programs will achieve greater impacts by developing varieties for market segments and pipelines that have more poor rural people, high stunting rates among children, anemia prevalence among women of reproductive age, and where there is high vitamin A deficiency. In addition, breeding strategies that reduce gender inequality and enhance appropriate change of gender roles (hence gender transformative) are also required.

Heterosis and Responses to Selection in Orange-Fleshed Sweetpotato (Ipomoea batatas L.) Improved Using Reciprocal Recurrent Selection.

Sweetpotato is a highly heterozygous hybrid, and populations of orange-fleshed sweetpotato (OFSP) have a considerable importance for food security and health. The objectives were to estimate heterosis increments and response to selection in three OFSP hybrid populations (H1) developed in Peru for different product profiles after one reciprocal recurrent selection cycle, namely, H1 for wide adaptation and earliness (O-WAE), H1 for no sweetness after cooking (O-NSSP), and H1 for high iron (O-HIFE). The H1 populations were evaluated at two contrasting locations together with parents, foundation (parents in H0), and two widely adapted checks. Additionally, O-WAE was tested under two environmental conditions of 90-day and a normal 120-day harvest. In each H1, the yield and selected quality traits were recorded. The data were analyzed using linear mixed models. The storage root yield traits exhibited population average heterosis increments of up to 43.5%. The quality traits examined have exhibited no heterosis increments that are worth exploiting. The storage root yield genetic gain relative to the foundation was remarkable: 118.8% for H1-O-WAE for early harvest time, 81.5% for H1-O-WAE for normal harvest time, 132.4% for H1-O-NSSP, and 97.1% for H1-O-HIFE. Population hybrid breeding is a tool to achieve large genetic gains in sweetpotato yield via more efficient population improvement and allows a rapid dissemination of globally true seed that is generated from reproducible elite crosses, thus, avoiding costly and time-consuming virus cleaning of elite clones typically transferred as vegetative plantlets. The population hybrid breeding approach is probably applicable to other clonally propagated crops, where potential for true seed production exists.

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.

Variance component estimations and mega-environments for sweetpotato breeding in West Africa.

The current study was aimed at identifying mega-environments in Ghana and evaluating adaptability of superior sweetpotato [Ipomoea batatas (L.) Lam.] genotypes from a targeted breeding effort. Three sets of genotypes were evaluated in multi-environment trials (MET). Twelve sweetpotato varieties were evaluated across nine environments representing the main agro-ecological zones in Ghana. MET analysis was conducted using a stage-wise approach with the genotype × environment (G × E) table of means used as a starting point to model the G × E interaction for sweetpotato yield. Emphasis was given to the genetic correlation matrix used in a second-order factor analytic model that accommodates heterogeneity of genetic variances across environments. A genotype main effect and G × E interaction of storage root yield explained 82% of the variation in the first principal component, and visualized the genetic variances and discriminating power of each environment and the genetic correlation between the environments. Two mega-environments, corresponding to northern and southern trial sites, were delineated. Six breeding lines selected from the south and eight breeding lines selected from the north were tested and compared to two common check clones at five locations in Ghana. A Finlay-Wilkinson stability analysis resulted in stable performances within the target mega-environment from which the genotypes were selected, but predominantly without adaptation to the other region. Our results provide a strong rationale for running separate programs to allow for faster genetic progress in each of these two major West African mega-environments by selecting for specific and broad adaptation.

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations.

Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.

Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.

In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. [Formula: see text], is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population ('Beauregard' × 'Tanzania') with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs.

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.

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.

Continuous Storage Root Formation and Bulking in Sweetpotato.

This study investigated the phenotypic variation of continuous storage root formation and bulking (CSRFAB) growth patterns underlying the development of sweetpotato genotypes for identification of potential varieties adapted to piecemeal harvesting for small scale farmers. The research was conducted between September 2016 and August 2017 in Uganda. Genotypes from two distinct sweetpotato genepool populations (Population Uganda A and Population Uganda B) comprising 130 genotypes, previously separated using 31 simple sequence repeat (SSR) markers were used. Measurements (4 harvest times with 4 plants each) were repeated on genotypes in a randomized complete block design with 2 replications in 2 locations for 2 seasons. We developed a scoring scale of 1 to 9 and used it to compare growth changes between consecutive harvests. Data analysis was done using residual or restricted maximum likelihood (REML). Data showed a non-linear growth pattern within and between locations, seasons, and genotypes for most traits. Some genotypes displayed early initiation and increase of bulking, while others showed late initiation. Broad sense heritability of CSRFAB was low due to large GxE interactions but higher in other traits  probably due to high genetic influence and the effectiveness of the methodology. A high level of reproducibility (89%) was observed comparing 2016B and 2017A seasons (A and B are first and second season, respectively) at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda. Choosing CSRFAB genotypes can more than double the sweetpotato production (average maximum yield of 13.1 t/ha for discontinuous storage root formation and bulking (DSRFAB) versus 28.6 t/ha for CSRFAB, demonstrating the importance of this underresearched component of storage root yield.

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.

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.

Evaluation of Performance of Introduced Yam Bean (Pachyrhizus spp.) in Three Agro-Ecological Zones of Rwanda.

The yam bean (Pachyrizhus spp) was recently introduced as a root crop with high-yield potential, considerable protein and micro-nutrient concentration to investigate its potential for food production in Rwanda. Except for Chuin types (Pachyrizhus tuberosus) which have high storage root dry matter (RDM) (26 to 36%), most accessions are consumed raw and are reported to have low RDM. The present study aimed to evaluate and identify adapted high yielding yam bean accessions in major agro-ecological zones of Rwanda. Field experiments with 22 accessions were conducted in 2012 at three research sites representing the major agro-ecologies of Rwanda. Strict reproductive pruning was followed to enhance fresh storage root yields. Across locations, ANOVA indicated highly significant differences (p < 0.01) for genotypes (G), locations (L), seasons (S) and G x L effects for storage root yield, vine yield and harvest index and accounted for 21.88%, 43.41%, 1.43% and 13.25% of the treatment sum of squares, respectively. The GGE bi-plot revealed that EC209018 is high yielding but unstable. However, genotypes, AC209034, AC209035 and EC209046, were outstanding in terms of adaptation and relative stability across the 3 locations, suggesting consistent root yields irrespective of location and environmental conditions. The GGE scatter plot showed that all genotypes formed one mega-environment for storage root yield (Karama, Musanze and Rubona) and two mega-environments for biomass yield (Karama and Rubona as one mega-environment and Musanze the second one). This study revealed that Karama is the most suitable environment for evaluation and selection of yam bean for yield components in Rwanda.