Andreas W. Ebert

Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection

The present study was undertaken to examine the population structure of the Solanum pimpinellifolium collection maintained by AVRDC – The World Vegetable Center – and to construct a core set of this collection. Out of the entire collection of 322 accessions, a diverse subset of 190 accessions was chosen representing 14 countries of origin. Data on 32 qualitative and 22 quantitative phenotypic traits (IPGRI–AVRDC descriptor traits) and 48 simple sequence repeat markers evenly distributed over the genome were used to develop the core set. A total of 377 alleles were detected with 7.85 alleles per locus, on average. Of these, 52 alleles at 28 loci were extremely rare-frequency alleles. The 190 accessions clustered into two main populations and an admixture group. Population I (PopI) included 99 accessions, 93 of which originated from Peru. Population II (PopII) contained 49 accessions, the majority of which originated from Ecuador and Mexico. The remaining 42 accessions were classified as admixture group. The two main populations were further subdivided into five subgroups. Values of Fst among the five sub-populations were significant (average pairwise Fst of 0.296), suggesting a real difference between these populations. A clear differentiation was observed among and within populations based on geography. Peruvian accessions were genetically more diverse than accessions originating in Ecuador and Mexico. Within the Peruvian group, a gradual increase in genetic diversity was observed from southern to northern Peru. The constructed core collection consists of 75 accessions representing 23.4% of AVRDC’s entire S. pimpinellifolium collection and 39.5% of the subset used in this study. It is a well-balanced core with a good representation of the different populations (31 accessions from PopI, 22 from PopII and 22 from the Admixture group) and geographic origins (40 accessions from

The okra (Abelmoschus esculentus) transcriptome as a source for gene sequence information and molecular markers for diversity analysis.

A combined leaf and pod transcriptome of okra (Abelmoschus esculentus (L.) Moench) has been produced by RNA sequencing and short read assembly. More than 150,000 unigenes were obtained, comprising some 46 million base pairs of sequence information. More than 55% of the unigenes were annotated through sequence comparison with databases. The okra transcriptome sequences were mined for simple sequence repeat (SSR) markers. From 935 non-redundant SSR motifs identified in the unigene set, 199 were chosen for testing in a germplasm set, resulting in 161 polymorphic SSR markers. From this set, 19 markers were selected for a diversity analysis on 65 okra accessions comprising three different species, revealing 58 different genotypes and resulted in clustering of the accessions according to species and geographic origin. The okra gene sequence information and the marker resource are made available to the research community for functional genomics and breeding research.

Relationship between survival and yield related traits in Solanum pimpinellifolium under salt stress

A subset of the Solanum pimpinellifolium collection maintained by AVRDC—The World Vegetable Center, Taiwan was evaluated to assess effects of salt stress on physiological traits and yield-related traits with the aim of identifying potential S. pimpinellifolium accessions useful for salt tolerance breeding in tomato. We undertook a comparative analysis of yield and plant survival traits under normal and salt stress conditions to obtain a first indication of the crucial traits associated with salt tolerance in S. pimpinellifolium. Although most traits of S. pimpinellifolium accessions showed a similar percent decrease in mean under salt stress compared with the cultivated checks, the former exhibited a wide range for all traits, suggesting great genetic diversity that can be exploited for the identification of salt tolerant genotypes. Genetic variability for yield and survival traits under salt stress was quantitative with low to moderate heritability. Results of correlation and path coefficient analysis revealed no correlation between any of the physiological traits with yield-related traits indicating that the ability to survive and yield under salt stress are two independent sets of traits in S. pimpinellifolium. Results of the path analysis along with heritability and genetic advance showed that shoot dry weight and K/Na ratio are the two most critical component traits for survival, while fruit number is critical for yield per plant. The large S. pimpinellifolium panel evaluated in this study revealed five genotypes possessing better survival traits, seven genotypes with good yield traits, and two genotypes combining both superior survival and yield traits under salt stress.

The AVRDC – The World Vegetable Center mungbean (Vigna radiata) core and mini core collections

BackgroundLarge ex situ germplasm collections generally harbor a wide range of crop diversity. AVRDC – The World Vegetable Center is holding in trust the world’s second largest mungbean (Vigna radiata) germplasm collection with more than 6,700 accessions. Screening large collections for traits of interest is laborious and expensive. To enhance the access of breeders to the diversity of the crop, mungbean core and mini core collections have been established.ResultsThe core collection of 1,481 entries has been built by random selection of 20% of the accessions after geographical stratification and subsequent cluster analysis of eight phenotypic descriptors in the whole collection. Summary statistics, especially the low differences of means, equal variance of the traits in both the whole and core collection and the visual inspection of quantile-quantile plots comparing the variation of phenotypic traits present in both collections indicated that the core collection well represented the pattern of diversity of the whole collection. The core collection was genotyped with 20 simple sequence repeat markers and a mini core set of 289 accessions was selected, which depicted the allele and genotype diversity of the core collection.ConclusionsThe mungbean core and mini core collections plus their phenotypic and genotypic data are available for distribution to breeders. It is expected that these collections will enhance the access to biodiverse mungbean germplasm for breeding.

Vitamin C and reducing sugars in the world collection of Capsicum baccatum L. genotypes.

This study aimed to analyze 123 genotypes of Capsicum baccatum L. originating from 22 countries, at two stages of fruit development, for vitamin C content and its relationship with reducing sugars in fruit pericarp. Among the parametric population, vitamin C and reducing sugar concentrations ranged between 2.54 to 50.44 and 41-700mgg(-1) DW of pericarp, respectively. Overall, 14 genotypes accumulated 50-500% of the RDA of vitamin C in each 2g of fruit pericarp on a dry weight basis. Compared with ripened fruits, matured (unripened) fruits contained higher vitamin C and lower reducing sugars. About 44% variation in the vitamin C content could be ascribed to levels of reducing sugars. For the first time, this study provides comprehensive data on vitamin C in the world collection of C. baccatum genotypes that could serve as a key resource for food research in future.

Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium)

Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.

Development of best practices for ex situ conservation of radish germplasm in the context of the crop genebank knowledge base

Information about crop-specific best practices for ex situ conservation of plant genetic resources has been difficult to find until recently. The CGIAR, together with national and regional partners, started to fill that gap by publishing best practices on the crop genebank knowledge base (CGKB -http://cropgenebank.sgrp.cgiar.org/), a website specifically developed and officially launched in 2010 to provide easy access to knowledge about all aspects of ex situ conservation of specific crops to genebank managers and ex situ conservation researchers. A collaborative study, undertaken by Bioversity International with eight national and international genebanks, utilized the framework provided by the CGKB to develop and publish radish conservation best practices. This paper focuses on two aspects of this study: (1) Differences in procedures and practices in radish conservation currently applied in five key genebank activities, namely, acquisition of germplasm, viability testing and monitoring, seed drying, seed storage, and regeneration. While in a few cases genebanks agreed on a specific best practice to recommend, in others it was not desirable to identify one practice as superior to another, therefore a range of existing practices is described as a variety of equivalent options. The results highlight the importance of proactive genebank management aimed at meeting the standards within the specific context in which a genebank operates. (2) The framework and template provided by the CGKB in guiding the development of genebank best practices, and the CGKB as an excellent resource to widely and freely share best practices with the global community to support the effective management of crop genebanks.

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajimas D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajimas D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9–2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.

Ex Situ Conservation of Plant Genetic Resources of Major Vegetables

Vegetables form a large and economically important commodity group comprising a wide range of genera and species. Depending on the crop, roots, stems, leaves, flowers and fruit are consumed raw, cooked, steamed, fried or pickled. World production of vegetables and melons comprising 27 distinct commodities reached over one billion tonnes in 2009. The ten major commodities contributing to this impressive output were: fresh vegetables, not elsewhere specified; tomatoes; watermelons; dry onion; cabbages and other brassicas; cucumbers and gherkins; eggplants; carrots and turnips; green chilies and peppers, and other melons, including cantaloupes. Asia is the largest vegetable producer worldwide with China alone producing close to 52 % of world output, followed by India with 9.2 % of global production. Considering a significant overlap of crops with multiple uses, as vegetables, grains, food legumes and fibers, about one million accessions of crops used at least partially as vegetables are conserved ex situ worldwide. In a narrow sense of exclusive use of crops as vegetables, about 500,000 accessions of vegetables representing 7 % of the globally held 7.4 million accessions of plant genetic resources are maintained ex situ. Tomatoes, capsicums, melons and cantaloupe, brassicas, cucurbits, alliums, okra, and eggplant are well represented in ex situ collections at the global level, with a range between 84,000 and 22,000 accessions per vegetable group. As genetic erosion continues in situ for various reasons, complementary collecting efforts should be made with a major focus on crop wild relatives and poorly represented cultivated forms of some vegetable groups such as those described for the genera Brassica and Capsicum in this chapter. AVRDC – The World Vegetable Center plays a major role in the conservation, breeding and distribution of vegetable germplasm worldwide. The Center maintains about 58,000 accessions of vegetable germplasm, representing 170 genera and 434 species. Major vegetable crop groups, including the genera Allium, Brassica, Raphanus, Capsicum, Solanum section Lycopersicon, as well as African and Asian eggplant of the genus Solanum are briefly described in this chapter.

Nutritional composition of mungbean and soybean sprouts compared to their adult growth stage

This study determined the level of phytonutrients in mungbean and soybean sprouts compared to mature mungbean grain and vegetable soybean. The comparison included landraces and improved mungbean and soybean varieties to assess the effect of breeding on the phytonutrient content of both crops. Sprouting mungbean enhanced vitamin C content 2.7-fold compared to mature mungbean grain. Relatively old mungbean accessions were superior in protein, calcium (Ca), iron (Fe), zinc (Zn), carotenoid and vitamin C content compared to improved mungbean lines at the fully mature stage. With regard to nutritional value, the vegetable soybean stage was superior to soybean sprouts in terms of content of protein (14% increase), Zn (45%), Ca (72%), and Fe (151%). Isoflavones, reported to have beneficial effects on human health, are found at high concentrations in soybean sprouts and could easily provide the recommended anticarcinogenic dose range from 1.5 to 2.0mg/kg of body weight per day.