Summary
Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the ...available diversity due to lack of efficient germplasm characterization and structure. In recent years large‐scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics‐based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on‐going genomic and phenotypic studies will enhance ’omics‐wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.
Significance Statement
A metabolite‐specific database cataloguing the biochemical diversity within and between root, tuber, and banana (RTB) crops has been compiled from profiling thousands of accessions. The database records the extent of metabolite concentrations available in screened germplasm of each RTB crop and therefore can be used to set breeding targets. This information aids in crop breeding programmes to improve the livelihoods for more than two billion people reliant on RTB crops.
Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and ...abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.
Crop wild relatives of sweetpotato Ipomoea series Batatas (Choisy) D. F. Austin are a group of species with potential for use in crop improvement programs seeking to breed for drought tolerance. ...Stress memory in this group could enhance these species' physiological response to drought, though no studies have yet been conducted in this area. In this pot experiment, drought tolerance, determined using secondary traits, was tested in 59 sweetpotato crop wild relative accessions using potential short-term memory induction. For this purpose, accessions were subjected to two treatments, i) non-priming: full irrigation (up to field capacity, 0.32 w/w) from transplanting to harvest and ii) priming: full irrigation from transplanting to flowering onset (FO) followed by a priming process from FO to harvest. The priming process consisted of three water restriction periods of increasing length (8, 11, and 14 days) followed each by a recovery period of 14 days with full irrigation. Potential stress memory induction was calculated for each accession based on ecophysiological indicators such as senescence, foliar area, leaf-minus-air temperature, and leaf 13C discrimination. Based on total biomass production, resilience and production capacity were calculated per accession to evaluate drought tolerance. Increase in foliar area, efficient leaf thermoregulation, improvement of leaf photosynthetic performance, and delayed senescence were identified in 23.7, 28.8, 50.8, and 81.4% of the total number of accessions, respectively. It was observed that under a severe drought scenario, a resilient response included more long-lived green leaf area while a productive response was related to optimized leaf thermoregulation and gas exchange. Our preliminary results suggest that I. triloba and I. trifida have the potential to improve sweetpotato resilience in dry environments and should be included in introgression breeding programs of this crop. Furthermore, I. splendor-sylvae, I. ramosissima, I. tiliacea, and wild I. batatas were the most productive species studied but given the genetic barriers to interspecific hybridization between these species and sweetpotato, we suggest that further genetic and metabolic studies be conducted on them. Finally, this study proposes a promising method for improving drought tolerance based on potential stress-memory induction, which is applicable both for wild species and crops.
The goal of yam bean improvement in Africa is to develop superior high yielding and high dry matter cultivars that are preferred for adoption. In this study, the estimates of variance components, ...heritability and response to selection were studied in F
3
yam bean families selected from interspecies crosses targeting improvement of storage root dry matter and associated traits. Breeding populations were generated using North Carolina II (NC II) mating design involving high dry matter
P. tuberosus
chuin cultivar, low dry matter
P. ahipa
and the high yielding
P. erosus
yam beans. The progenies were advanced through selfing from F
1
to F
2
population and then exposed to selection at 10% selection intensity to obtain 83 high dry matter lines. The selected lines were evaluated in an F
3
trial using a randomized complete block design (RCBD) with three replications at the National Crops Resources Research Institute (NaCRRI) Namulonge, in Central Uganda. The results revealed significant (
P
< 0.001) genetic variation for storage root dry matter (RDM), storage root fresh yield (RFY), storage root dry yield (RDY), vine yield (VNY), fresh biomass yield (FBY), harvest index (HI), starch (STA) and protein (PRO) content. High genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) were obtained for VNY, RDY, FBY, RFY, RDM and STA. Narrow sense heritability was higher than 0.5 and response to selection was 15.5 to 33.1 for RDM, RFY, RDY, VNY, FBY and STA, indicating rapid genetic progress is achievable and early generation selection would be effective to improve these traits. Significant (
P
< 0.01) positive genetic correlations were observed between RDM, RDY, RFY, VNY, FBY and STA ranging from 0.422 to 0.963 implying that simultaneous improvement of these traits is possible in the current yam bean populations.
Sweet potato (
, Lam.) is an important root vegetable in developing countries. After its domestication in Neotropical America, human migration led to the distribution of the sweet potato plant ...throughout the world. Both leaf and storage root are high in compounds of nutritional value. Yet, the storage roots are of particular value due to their significant content of provitamin A (β-carotene). The breeding effort for elite sweet potato lines led to the reduction of genetic diversity and the potential to improve other traits. The focus of the present study was to assess the metabolic diversity of 27 sweet potato cultivars including landraces and improved varieties. A metabolite profiling approach was optimised for sweet potato leaf and storage root tissue and 130 metabolites identified with three different analysis platforms. The data highlighted a lack of correlation between storage root phenotype and leaf metabolism. Furthermore, the metabolic diversity of storage roots was based on the secondary metabolism, including phenylpropanoids and carotenoids. Three cultivars of three different flesh colouration (yellow, orange and purple) showed a significant difference of the primary metabolism. This data demonstrates the value of metabolite profiling to breeding programs as a means of identifying differences in phenotypes/chemotypes and characterising parental material for future pre-breeding resources.
Biochemical characterisation of germplasm collections and crop wild relatives (CWRs) facilitates the assessment of biological potential and the selection of breeding lines for crop improvement. Data ...from the biochemical characterisation of staple root, tuber and banana (RTB) crops, i.e. banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas) and yam (Dioscorea spp.), using a metabolomics approach is presented. The data support the previously published research article “Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops” (Price et al., 2020) 1.
Diversity panels for each crop, which included a variety of species, accessions, landraces and CWRs, were characterised. The biochemical profile for potato was based on five elite lines under abiotic stress. Metabolites were extracted from the tissue of foliage and storage organs (tuber, root and banana pulp) via solvent partition. Extracts were analysed via a combination of liquid chromatography – mass spectrometry (LC-MS), gas chromatography (GC)-MS, high pressure liquid chromatography with photodiode array detector (HPLC-PDA) and ultra performance liquid chromatography (UPLC)-PDA. Metabolites were identified by mass spectral matching to in-house libraries comprised from authentic standards and comparison to databases or previously published literature.
The CGIAR Research Program (CRP) on Roots, Tubers and Bananas (RTB) includes vegetatively propagated staple crops linked by common breeding, seed, and postharvest issues, and by the frequency with ...which women are involved in their production and use. RTB crops are the backbone of food security across the humid tropics in sub-Saharan Africa (SSA) and in more localized areas of Asia and Latin America. Around 300 million poor people in developing countries currently depend on RTB value chains for food security, nutrition and income. Climate change poses challenges which could undo progress in poverty reduction and markedly increase food insecurity. This article examines planning and research for climate resilience across RTB crops, with a particular focus on the contrasting potato and sweet potato cases in SSA. A six-step framework for climatesmart breeding is proposed: (1) downscaling climate change models and crop modeling; (2) identifying and understanding key climate change responsive traits; (3) breeding and varietal selection; (4) phenotyping and genomic research to accelerate gains; (5) developing management options for climate-smart varieties; and (6) deployment (seed systems). In summary, climate-smart breeding means we need to do what we already do but faster, better, and smarter.
Pueraria montana var. lobata and P. phaseoloides originating from tropical Asia and parts of Oceania are ecologically and economically important legumes that are used as green manure, cover crop or ...forage plants. Conservation and use of plant genetic resources require an understanding of the extent and distribution of genetic diversity in any given region. In this study, genetic variation of five P. montana var. lobata and 16 P. phaseoloides accessions was analysed developing a random amplified polymorphic DNA (RAPD) marker methodology for Pueraria species and thereby creating basic data for follow-up research and the development of conservation strategies. Seeds were collected from native populations in Bac Kan Province, a mountainous region in Northeast Vietnam. P. montana var. lobata presented a high level of variation with 54.3% of the detected markers being polymorphic, whereas P. phaseoloides exhibited an intermediate to high level of variation (45.5%). The P. montana var. lobata accessions clustered in congruence with their eco-geographical origin. For P. phaseoloides no correspondence between sampling sites and genetic differentiation was found. Inter-population differentiation was measured as Jaccard's similarity coefficient (JSC). Mean JSC amounted to 0.35 in P. montana var. lobata and 0.52 in P. phaseoloides. Results are compared to other genetic studies of herbaceous legumes and conservation strategies are suggested.
Sweetpotato (Ipomoea batatas L. Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large ...genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato.
The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages.
Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.
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