Mungbean (Vigna radiata (L.) Wilczek), also known as greengram, is the most widely cultivated Asian Vigna species. Improved mungbean cultivars have a narrow genetic base that limits yield potential and they are poorly adapted to varying growth conditions in different agro-ecological conditions. The genetic potential of landrace germplasm accessions in gene- banks therefore needs to be better exploited. Germplasm core collections are made of a reduced set of representative accessions from the entire diversity maintained by genebanks. This subset of accessions can be used for testing general combining ability with local germplasm in the search for yield enhancement. Core collections also help breeders in selecting parental material that could maximize potential genetic gain from derived hybrid populations. At the National Bureau of Plant Genetic Resources (NBPGR), India, genetic enhancement/pre- breeding studies in mungbean have been initiated involving diverse parents mainly from the cultivated gene pool, using the Bureau's core collection as starting material. Germplasm enhancement aims at widening the genetic base of breeding materials by transferring desired genes from unimproved germplasm into enhanced varieties. Mild and decentralized selected material was maintained in target sites across the country. A total of 102 progenies were advanced to F5 for further selection and use by the breeders in Delhi. The genetic potential of a few selected enhanced progenies with desired plant types and better yield-related traits is presented in this paper. The study clearly demonstrates the potential of germplasm accessions conserved in genebanks for use in large-scale base-broadening efforts in mungbean.

The Ethiopian core collection of the USDA-Agriculture Research Service, National Plant Germplasm System (NPGS) includes 376 accessions and a genomic characterization that revealed 151,210 single nucleotide polymorphisms. This collection, however, lacks phenotypic characterization for several important agriculture traits. A total of 330 accessions from this NPGS Ethiopian core set were evaluated for grain mould resistance response across four tropical environments. Most of the accessions in the NPGS Ethiopian collection showed susceptibility to grain mould based on the low emergence rate and high seed deterioration observed in the seeds. The population structure of the collection was not related to grain mould resistance response suggesting this germplasm originated in regions with low disease pressure. The analysis identified two accessions with high emergence (PI 457867 and PI 454221) and three (PI 455036, PI 455213 and PI 330821) with low seed degradation. Genome-wide association analysis found genomic regions in chromosome 1, 3 and 8 associated with the observed grain mould resistance variation. Candidate gene analysis within these three loci identified diseases resistance genes involved in pathogen recognition and signalling cascades of the plant immunity system. These five NPGS Ethiopian accessions are candidates for use in a pre-breeding germplasm programme to develop improved germplasm with grain mould resistance.

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the analysis of molecular variance (AMOVA), 28% of the total variation resides among accessions and 72% occurs within populations. The AMOVA computed in order to differentiate cultivars, displayed the same trends when no prior grouping of accessions was considered. The differentiation within cultivar (97%) was more than that, among cultivars (3%). Tree topologies inferred by neighbour-joining analysis reflected no clear cut off grouping.

To group accessions, we used a Bayesian clustering analysis which exhibited two clusters. Using the informativeness of the primer combinations analysed in the present study, an orientation was given for the choice of the accessions which would be used to build a core collection.

ICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

Direct sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

Development of core collection representing the diversity in the entire germplasm creates a better access and enhanced utilization of the main collection thus allowing rapid evaluation in crop improvement programs. Core collections are dynamic in nature and needs revisiting when additional germplasm and information becomes available. In the current study, an attempt was made to re-define the previously developed yam (Dioscorea spp) core collection using 56 morphological traits. Information on additional acquired germplasm and presence of duplicates or mislabelled accessions in the entire collection was also used. The re-defined core collection consisted of 843 accessions and represented about 20% of the entire collection. It included six Dioscorea species, of which accessions of Dioscorea rotundata are in the majority (73.54%) followed by Dioscorea alata (21.35%), Dioscorea bulbifera (1.66%), Dioscorea cayenensis (1.42%), Dioscorea dumetorum (1.42%) and Dioscorea esculenta (0.59%). The Shannon weaver diversity index and principal component analysis revealed the maximum diversity captured in the core from the base collection. This re-defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in yam improvement programs.

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

We report on identification of core collection from 192 accessions collected from 12 Indian states and five other countries based on 109 polymorphic amplified fragment length polymorphism (AFLP) markers. Pairwise Jaccard's similarity coefficient for accessions varied from 0.25 to 1 with a maximum genetic distance of 0.75 obtained between accessions Jc428 (from Mexico) and J204 (from Madurai, Tamil Nadu). Both UPGMA (Unweighted Pair Group Method of Arithmetic Averages) clustering and principal coordinate analyses showed similar grouping of accessions in three major clusters in which Mexican accessions clustered separately from Indian, Chinese and African accessions. Results obtained from analysis of molecular variance indicated that 59% of the genetic variation was distributed among the populations, while 41% of variation was within the populations. A total of 16 (8.3% of the entire collection) core accessions were identified, which contained the entire allelic diversity of 192 accessions with respect to the sampled AFLP loci. The core accessions would be highly useful for future genetic improvement of Jatropha. To the best of our knowledge, this is the first report on identification of core accessions in Jatropha.

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size.

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

Ziziphus mauritiana Lam. is an important fruit crop of the Thar Desert of India. About 330 accessions and cultivars collected from various parts of India are currently being maintained at a farm in the Central Institute for Arid Horticulture. Utilization of such a large collection of germplasm for breeding and crop improvement is difficult. Therefore, in the present study, using a heuristic approach based on phenotypic characters, we identified 52 accessions that represented a core collection, with a coverage of 100% and a coincidence rate of 98.1%. No significant difference was observed with respect to either the Shannon–Weaver or the Nei diversity index for qualitative traits, mean values and ranges for quantitative traits or clustering patterns between the core and whole collections. The core collection represents the entire range of diversity with minimum redundancy and should be useful for the conservation and utilization of Z. mauritiana germplasm.

Three hundred and seventeen grape accessions from the National Active Grape Germplasm Site in India were analysed with 25 microsatellite markers. A total of 411 alleles were detected, of which 42% were rare alleles. Unique alleles for 56 genotypes were also identified. The analysis of microsatellite data identified 63 duplicate accessions and only 254 accessions were unique genotypes. Several cases of misnomers, synonymy and homonymy were identified. Parental genotype for a few clonal selections was ascertained. Population structure analysis grouped 254 unique genotypes into four major clusters. The analysis also revealed the presence of admixtures with only 79% of pure ancestry. A core collection comprising 80 genotypes was identified, which represented all the alleles and genetic diversity. A user-friendly and interactive computer application software was developed for storage and the retrieval of molecular data. A molecular database for the 254 genotypes was created. This analysis will help in the rationalization and better management of germplasm. Information on genetic diversity and population structure will form the basis for varietal improvement programmes.

The narrow genetic base of existing commercial oil palm cultivars has prompted oil palm breeders to give increased importance to augmenting these genetic resources because the sustainable development of the crop depends largely on the availability of genetic diversity and its use. Therefore, the purpose of this study was to conduct a molecular characterization of an ex situ collection of oil palm Elaeis guineensis Jacq. populations from the Republic of Cameroon using microsatellite molecular markers. Overall, 31 simple sequence repeats were polymorphic, with a total of 223 alleles, 78.4% of which were found at low frequency. The total genetic diversity was relatively high (HT= 0.673). The genetic differentiation between geographical regions was low (GST= 0.023, P= 0.001), and between families it was high (GST= 0.166, P= 0.001), showing greater variation between families than among geographical regions. The molecular data indicate that genetic diversity among the genotypes evaluated is mainly distributed within regions, suggesting that there is no isolation by geographical distance and that all the sampled individuals form a single diverse population. Therefore, it was concluded that a relatively low number of accessions (120 in the analysed case) that includes at least one representative of each family would allow us to efficiently collect almost the entire genetic diversity of Cameroon within the collection studied. This will allow for the efficient use of genetic resources and a reduction in morpho-agronomic characterization costs.

Flavour is one of the most highly demanded consumer traits of tomato at present; poor flavour is one of the most commonly heard complaints associated with modern varieties of tomato. In order to combine flavour with other desirable fruit traits in improved cultivars, it is important to determine how much variability exists in the crucial compounds that contribute most to flavour. The objective of the present study was to determine the variability of flavour-contributing components including total soluble solids (TSS) and total titratable acids (TTA) among other subjective traits related to flavour in a core collection of tomato accessions. The core collection was comprised of 173 tomato accessions with a wide genetic background from the United States Department of Agriculture (USDA), Agricultural Research Services (ARS) Plant Genetic Resources Unit repository. The TTA varied from 0.20 to 0.64%, whereas the TSS ranged from 3.4 to 9.0%, indicating the availability of broad variation for these traits. Rinon (PI 118783), Turrialba, Purple Calabash and LA2102 were among the high TTA (>0.45%) containing accessions, whereas those with high TSS (>7.0%) were AVRDC#6, Sponzillo and LA2102. A positive correlation of overall flavour with TTA (r= 0.33; P< 0.05) and TSS (r= 0.37; P< 0.05) indicated that these two components play an important role in determining the overall flavour in tomato. Subjectively measured other traits including fruity odour and fruity flavour had positive correlations with overall flavour. Overall flavour is discussed in the context of other traits including fruit firmness. Information obtained from this study may be useful for tomato breeders aiming to improve tomato flavour.

Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of diverse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular diversity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4–35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic diversity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was >0.50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most diverse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of diverse parents for breeding cultivars and the development of mapping populations.

International Institute of Tropical Agriculture maintains 2544 cassava accessions (Manihot esculenta Crantz) from 28 countries in its field bank. Being vegetatively propagated, this poses challenges in maintenance in terms of cost as well as in labour requirements. A core collection representing the range of phenotypic diversity present in the entire collection would enhance the conservation aspects and increase the potential for its exploitation in crop improvement programmes. The present study aimed to establish a core collection using 40 agro-morphological traits evaluated at two locations using a different number of accessions in each location. To meet the challenges generated by the types of variables and include maximum diversity in the core collection, a sequential strategy based on five major concepts was used: hierarchical multiple factor analysis allowing the mixture of variables of different kinds; three-way analysis that included the effect of genotype × environment interaction in the clustering process; linear discriminant function to assign all those individuals who were included in one location but not in the other to the groups that were generated from the common number of accessions evaluated in both locations; and D-allocation method to select samples from each cluster. The representativeness of the core subset to the entire collection was further estimated by comparing means and variances, range, and distances between accessions. The established cassava core collection consisted of 428 accessions that conserved 15% higher phenotypic diversity with no redundancies. The phenotypic diversity represented in this core collection will be a guide to users of cassava germplasm in their crop improvement programmes.

The purpose of the study was to support the selection process of the most valuable currant and gooseberry accessions cultivated in Northern Europe, in order to establish a decentralized core collection and, following the selection, to ensure sufficient genetic diversity in the selected collection. Molecular analyses of the material from nine project partners were run at seven different laboratories. The results were first analysed for each partner separately, and then combined to ensure sufficient genetic diversity in the 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 Peru, 17 from Ecuador, 14 from Mexico and four from other countries).

The tribe Fabeae (formerly Vicieae) contains some of humanity's most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

A total of 1968 accessions of cultivated eggplants, belonging to Solanum melongena and Solanum aethiopicum and procured from the IVC/JAAS (Nanjing) and IVC/ZAAS (Hangzhou), China, were examined for 23 morphological traits, such as characteristics of plant, stems, leaves, flowers, fruits and original geographic information. A comprehensive numerical classification methodology, including two types of genetic distance, viz. Mahalanobis (Ma) distance and Euclidean (Eu) distance; four clustering methods, viz. unweighted pair group average (UPGA), Ward's (W), complete linkage (CL) and single linkage (SL) methods; three sampling strategies, viz. random (R), preferred (P) and deviation (D); and four sampling sizes (10, 15, 20 and 30% of initial collection), was used to divide all accessions into main groups and subgroups for the establishment of candidate collections. The evaluation of these candidate collections showed that a combination of Eu distance, UPGA clustering method, and R or P sampling strategy with sampling size at 15–20% was suitable for establishing the core collection, providing an adequate and representative genetic diversity of the initial collection of the cultivated eggplants.