Sesame (Sesamum indicum L.) is one of the world's oldest oil crops and has been cultivated in Asia from ancient times. India has a rich diversity of this crop and a landrace collection is maintained at the National Genebank at the National Bureau of Plant Genetic Resources (NBPGR). The breeding potential of this germplasm has been hardly exploited to date. The major hindrance for the utilization of these resources is the transfer of diversity into a form that can be easily used by breeders and farmers. As part of a core collection strategy, a selection was made of 24 of the most diverse and unadapted parental lines, including one accession of the wild species S. mulayanum, and these were intercrossed in various combinations to maximize genetic diversity and to develop locally adapted pools of genetic resources. A weak and decentralized selection regime was maintained at four selected target sites on the progeny of 103 crosses. The range of variation in the selected F4 progenies was assessed, and promising types with desired plant characteristics and high seed yield were selected. Realized genetic gains, especially for yield-related traits, were also assessed. Only a limited fraction of the existing diversity held in the genebank was used in the present study and there is much more diversity available for large-scale genetic enhancement of sesame in the future.

Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.

Amphidiploids serve as a bridge for transferring genes from wild species into wheat. In this study, five amphidiploids with AABBUU and AABBNN genomes were produced by spontaneous chromosome doubling of unreduced triploid F1 gametes from crosses between diploid Aegilops (A. umbellulata accessions CIae 29 and PI 226500, and A. uniaristata accession PI 554419) and tetraploid Triticum turgidum (ssp. durum cultivar Langdon and ssp. dicoccum accessions PI 94 668 and PI 349045) species. The composition of high-molecular-weight glutenin subunits (HMW-GS) in these amphidiploids and in their parental A. umbellulata and A. uniaristata species was analysed. As expected, the amphidiploids from T. turgidum ssp. dicoccum accession PI 944668 or PI 349045 and A. umbellulata accession CIae 29 or PI 226500 and A. uniaristata accession PI 554419 showed the same HMW-GS patterns as those of their Aegilops parents, because HMW-GS genes were all silenced in the T. turgidum ssp. dicoccum parents. The amphidiploids from CIae 29 and Langdon inherited all of the HMW-GS genes from their parents except for the Uy type. Using 10 and 15% sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) and 10% urea/SDS–PAGE, 11 Ux and ten Uy types in 16 combinations were observed in 48 A. umbellulata accessions, and two Nx and two Ny types in two combinations were detected in six A. uniaristata accessions. These novel HMW-GS variants may provide new genetic resources for improving the quality of wheat.

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.

False brome grass, Brachypodium distachyon (L.) Beauv, has been proposedas a new model species to bridge rice and temperate cereal crops for genomics research.However, much basic information for this species is still lacking. In this study, sixdiploid B. distachyon(2n = 2x = 10)accessions (Bd1-1, Bd2-3, Bd3-1, Bd18-1, Bd21 and BD29) were evaluated for their responseto infestation by two cereal aphid pests of common wheat (Triticumaestivum L.): the greenbug, Schizaphis graminum Rondani, and theRussian wheat aphid (RWA), Diuraphis noxia Mordvilko. Through databasemining of B. distachyon expressed sequence tag (EST) and genomic DNAsequences, 160 EST- and 21 genomic microsatellite markers were developed and used toevaluate genetic diversity among the B. distachyon accessions. All sixaccessions were resistant to RWA biotype RWA1 but showed distinct responses to feeding bygreenbug biotypes C and E, as well as RWA2 RWAs. Although microsatellite-based geneticdiversity among different accessions was generally low, Bd1-1 and BD29 were the mostdiverged from the other four lines. The genetic divergence was correlated withgeographical distances between the Brachypodium accessions. Comparison ofsimple sequence repeat polymorphisms in three inbred lines (Bd2-3, Bd3-1 and Bd18-1) withtheir respective original parental lines revealed no effect of inbreeding on geneticdiversity. Phylogenetic analysis suggested that Aegilops tauschii (Coss.)Schmal., the D genome donor of common wheat, was closer to B. distachyonthan to rice. The greenbug - B. distachyon system seemsto be a model of choice for plant–aphid interaction studies in the grassgenome.

trans-Resveratrol (trans-3,4′,5-trihydroxystilbene), a polyphenolic compound uniquely identified in plants, is believed to greatly contribute to human health. Peanut (Arachis hypogaea L.) seeds of 20 germplasm accessions were harvested from the same field and used for resveratrol analysis by high-performance liquid chromatography. trans-Resveratrol content in air-dried peanut seeds was on average about 0.5 μg/g and a statistically significant variation (from 0.125 to 1.626 μg/g, at least a ten-fold difference) was detected among the accessions analysed. The average weight for 100 seeds was 52.84 g. A statistically significant variation in seed weight (from 22.30 to 87.94 g, at least a four-fold difference) was observed. There was no significant correlation between trans-resveratrol content and seed weight. The information about the levels of trans-resveratrol in peanut seeds will be useful for peanut cultivar development and peanut product processing. Breeders could use germplasm accessions containing a high amount of resveratrol to develop new nutritionally improved peanut cultivars and food processors could use these new cultivars to manufacture high resveratrol peanut products.

This study is the first assessment of the entire soybean [Glycine max (L.) Merr] collection of the United State Department of Agriculture National Plant Germplasm System (USDA) reporting quantitative and population genomic parameters. It also provides a new insight into soybean germplasm structure. Germplasm studies enable plant breeders to incorporate novel genetic resources into breeding pipelines to improve valuable agronomic traits. We conducted comprehensive analyses on the 19,652 soybean accessions in the USDA-ARS germplasm collection, genotyped with the SoySNP50 K iSelect BeadChip SNP array, to elucidate the quantitative properties of existing subpopulations inferred through hierarchical clustering performed with Ward's D agglomeration method and Nei's standard genetic distance. We found the effective population size to be approximately 106 individuals based on the linkage disequilibrium of unlinked loci. The cladogram indicated the existence of eight major clusters. Each cluster displays particular properties with regard to major quantitative traits. Among those, cluster 3 represents the tropical and semi-tropical genetic material, cluster 5 displays large seeds and may represent food-grade germplasm, and cluster 7 represents the undomesticated material in the germplasm collection. The average FST among clusters was 0.22 and a total of 914 SNPs were exclusive to specific clusters. Our classification and characterization of the germplasm collection into major clusters provides valuable information about the genetic resources available to soybean breeders and researchers.

Drought stress restricts the production of agricultural crops through morphological, physiological and biochemical changes in plants. This study explored the genetic control of physiological traits related to drought in coriander. In a diallel analysis, all six parents, their 15 F1 hybrids and 15 F2 populations were subjected to different irrigation regimes including well-watered, mild and severe water deficit stress. Drought stress decreased the relative chlorophyll content (RCC), the relative water content (RWC), chlorophyll a (Chla), chlorophyll b (Chlb), total chlorophyll (TChl) content, carotenoids (Car) and essential oil yield (EOY) in F1 and F2 generations. General combining ability (GCA) and specific combining ability effects were highly significant for all traits in F1 and F2 generations. Additive gene action was predominant for Chla, Chlb, TChl and Car under well-watered condition while non-additive gene effects were more important under mild and severe water deficit stresses in F1 and F2 generations for the above traits. Additive gene effects were more important for RCC, RWC and electrolyte leakage (EL) traits in both F1 and F2 generations under mild and severe water deficit stresses. In conclusion, the high narrow-sense heritability and significant genetic correlations between EOY and RCC, RWC and EL suggest that these traits can be used as surrogates to identify superior genotypes for arid and semi-arid regions. Also, the parental lines, P4 and P6 had the best GCA for RCC, RWC, Chla, Chlb, TChl, Car, essential oil content and EOY.

We analysed the natural variation of drought response in 11 Tunisian populations of Medicago truncatula sampled from environments that varied in soil composition, salinity and water availability. Plants were cultivated in a greenhouse under well-irrigated and water-deficit treatments (50% of field capacity), and a number of traits associated with drought response were measured. Variance analysis indicated that the variation of phenotypic traits was explained by the effects of population, line, treatment, and population × treatment and line × treatment interactions, with treatment being the one with the greatest effect. A large degree of phenotypic variation for most traits in the two water treatments was found within populations. Most of the measured characters showed higher broad-sense heritabilities (H2) in well-irrigated treatment than in water-deficit treatment. Furthermore, the largest population differentiation (QST) for most of the measured traits was observed under drought stress. Most of the correlations between measured traits under both treatments were positive. Four groups of lines differing in drought tolerance were identified, with 45 susceptible, 14 moderately susceptible, 31 tolerant and 23 most tolerant lines. The tolerant group experienced lowest reductions in the length of plagiotropic axes, length of stems, number of internodes and number of leaves. The large phenotypic variation of M. truncatula in response to drought stress can be used to identify genes and alleles important for the complex trait of drought tolerance.

Population structure and linkage disequilibrium (LD) were investigated in a set of 395 bread wheat landraces including 154 spring, 193 winter, two facultative wheat and 46 unknown growth type collected from different geographical regions of Iran. A total of 53 microsatellite markers distributed in three genomes of wheat were assayed for polymorphism. The 312 polymorphic alleles were served to estimate population structure and analyse the genome-wide LD. The number of alleles ranged from 2 to 18 with an average of 5.89 alleles/locus. Mean of polymorphic information content was 0.6 with a range of 0.15–0.86 and gene diversity varied from 0.16 to 0.88 with an average of 0.64. The population of landraces was highly structured and based on distance-and model-based cluster analyses the 395 landraces were assigned into eight subpopulations: SG1–SG8. Population structure estimates based on simple sequence repeat (SSR) marker data were quantified in a Q matrix and used in calculation of LD between pair of markers. A low overall LD level found in 12–13% (166) of the SSR marker pairs showed significant pairwise LD in r2 ≥ 0.01 and P ≤ 0.001 and six pair showed r2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

In order to utilize germplasm resources more efficiently for peanut (Arachis hypogaea L.) genetic improvement, a core collection of 576 accessions and a primary mini core collection of 298 accessions were developed previously from a collection of 6839 cultivated peanut lines stored at the Oil Crops Research Institute of Chinese Academy of Agricultural Sciences at Wuhan. For an efficient evaluation and characterization of the most useful agronomic and disease-resistant traits, an even smaller collection of peanut accessions that represent a spectrum of phenotypes could be more desirable. For this reason, a mini-mini core collection with 99 accessions from the core accessions was developed based on the analysis of 21 morphological traits. It was demonstrated that there were no significant differences between the core and mini-mini core collections in 20 out of the 21 morphological traits studied. Further, the mini-mini core collection captured the ranges of all of the 21 traits displayed in the core collection. The newly developed mini-mini core collection was assessed for resistance to bacterial wilt disease caused by Ralstonia solanacearum. Two accessions showing a high level of resistance to bacterial wilt were identified, demonstrating the usefulness of the mini-mini core collection. The mini-mini-core collection provides a more efficient means of germplasm evaluation and will be resequenced as part of the International Peanut Genome Consortium sequencing project at the UC-Davis Genome Center.

Dwarfing genes play an important role in improving yield and adaptability of wheat cultivars in most production environments. Understanding the allelic distribution at dwarfing loci is very important for any wheat-breeding programmes. In this study, we reported the allelic constitution at microsatellite locus Xgwm261 and the two major height-reducing genes Rht-B1 and Rht-D1 among a set of 56 bread wheat cultivars and nine landraces, based on diagnostic polymerase chain reaction assays. With respect to Rht-B1, 37% of the accessions carried the dwarfing allele Rht-B1b, while at Rht-D1, only one accession carried the dwarfing allele Rht-D1b. The allelic state at Rht8 was assayed indirectly by genotyping for the linked microsatellite locus Xgwm261. About 26% of the accessions carried the 192 bp allele (linked with Rht8 gene in some cases), whereas 35 and 12% genotypes carried 165 and 174 bp allele at the microsatellite locus Xgwm261. Cultivars released from 1980 onwards increasingly carried either Rht-B1b or Rht8. This information should allow for a more rational use of this collection for the purpose of wheat improvement in Turkey.

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.

DNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

Selecting desired agronomic traits may lead to a loss of genetic diversity in crop species. A molecular investigation was conducted to determine how well a set of olive (Olea europaea L.) accessions sampled in Moroccan traditional orchards represented the entire Moroccan olive diversity range. We therefore collected, in traditional agroecosystems from northern and central Morocco, a total of 88 olive trees chosen for their agronomic traits based on local farmers' knowledge. Using 12 SSR loci, 45 trees (51.1%) had a genotype identical to the ‘Picholine Marocaine’ variety, while the remaining samples were classified into 27 different SSR profiles. Two categories of genotypes were identified: (i) genotypes closely related to the ‘Picholine Marocaine’ variety and probably resulting from intensive vegetative propagation from a limited number of clones, and (ii) genotypes displaying a high number of dissimilar alleles which may have originated from selected spontaneous seedlings. A significant difference in allelic richness was revealed between the 28 on-farm selected genotypes and the overall olive diversity, represented by 57 local genotypes, indicating that the on-farm selected trees represented a subsample of Moroccan genetic diversity. This could be explained by the prevalence of ‘Picholine Marocaine’ in traditional orchards, while some original genotypes with favourable agronomic traits resulting from local farmers' selection were also identified. Applying an ethnobotany approach combined with criteria to fulfil farmers' household needs could be particularly relevant and better explain the obtained results.

Plant genetic resources are raw materials and their use in breeding is one of the most sustainable ways to conserve biodiversity. The ICRISAT has over 120,000 accessions of its five mandate crops and six small millets. The management and utilization of such large diversity are greatest challenges to germplasm curators and crop breeders. New sources of variations have been discovered using core and minicore collections developed at the ICRISAT. About 1.4 million seed samples have been distributed; some accessions with specific attributes have been requested more frequently. The advances in genomics have led researchers to dissect population structure and diversity and mine allelic variations associated with agronomically beneficial traits. Genome-wide association mapping in sorghum has revealed significant marker–trait associations for many agronomically beneficial traits. Wild relatives harbour genes for resistance to diseases and insect pests. Resistance to pod borer in chickpea and pigeonpea and resistance to rust and late leaf spot in groundnut have been successfully introgressed into a cultivated genetic background. Synthetics in groundnut are available to broaden the cultigen's gene pool. ICRISAT has notified the release of 266 varieties/cultivars, germplasm, and elite genetic stocks with unique traits, with some having a significant impact on breeding programs. Seventy-five germplasm lines have been directly released for cultivation in 39 countries.

Chickpea (Cicer arietinum L.) is an important grain legume nutritionally balanced for human consumption. The physical properties of chickpea seeds are important for processing and storage as well as for assessing seed quality and the hydration properties related to cooking quality. The chickpea mini core collection (211 accessions) and four control cultivars were evaluated for seed morphological (seed colour, shape, dots on seed coat and surface texture); physical (seed moisture content, 100-seed weight, seed coat content, length, width, thickness, geometric mean diameter (GMD), surface area, sphericity, shape aspect, volume, bulk density, true density and porosity); and hydration traits (hydration capacity, hydration index, swelling capacity and swelling index). Highly significant differences were observed for all the seed traits in the mini core collection. Correlation coefficients indicated that accessions with high or more seed weight, GMD, sphericity, seed shape aspect, swelling capacity and swelling index would be useful for utilization in research. The results of this study have refined the seed traits of chickpea and resulted in identifying several desirable accessions in the mini core. Some of these accessions were previously identified as promising sources for important agronomic and nutritional traits and for resistance to biotic and abiotic stresses and will be useful sources to develop high-yielding cultivars with desirable seed physical and hydration quality.

In a germplasm bank collection the conservation and characterization of genetic resources is a prerequisite in order to use the material in breeding projects aiming the creation of new cultivars. In the present study, 54 Prunus salicina domestica and Prunus domestica genotypes (including seven Greek cultivars), maintained in the ex situ National Genebank Collection of Greece, were classified using microsatellite (simple sequence repeat, SSR) markers on high resolution melting (HRM) analysis. The SSR primer pairs were chosen from the published literature as originally designed on Prunus species. This combined approach was used to genotype all plum accessions of the collection highlighting the benefits of either method (HRM and SSRs) for cultivar identification. Dendrograms for P. domestica and P. salicina and a combined one with all the genotypes assayed were produced. A total of 15 from the 19 P. domestica accessions analysed, including all the Greek accessions but ‘Avgati Skopelou’, were grouped into the same clade in the combined dendrogram, whereas the remaining four were dispersed into the P. salinica clades. Bayesian structure analysis confirmed that ‘Avgati Skopelou’ differs from the rest of the Greek plum cultivars since it was not grouped into the same cluster. The combination of HRM and SSRs, provided a considerably faster, cost-effective, closed-tube microsatellite genotyping method for molecular characterization of plum cultivars.

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.

Characterization of high-molecular-weight (HMW) glutenins is an important criterion for identifying genotypes with good bread-making quality. In synthetic hexaploids (SHs), the D-genome encodes several allelic variants of HMW glutenins that require proper identification prior to their utilization for bread wheat (BW) improvement. In this study, SHs with promising agronomic features were characterized for HMW glutenin composition. Seven different allelic variants were observed at the Glu-Dt1 locus, three of which (1Dx1.5+1Dy10, 1Dx1.5+1Dy12.2 and 1Dx2.1+1Dy10) have not been previously reported in existing BW germplasm. The results also showed a variety of D-genome-encoded subunits along with superior glutenin alleles in the B-genome (1Bx7+1By8, 1Bx6+1By8 and 1Bx13+1By16). About 63% of these SHs encoded favourable allelic variants of HMW glutenins, which make them a good choice for improvement in wheat bread making. Glu-Dt1 encoded favourable allelic variants (1Dx5+1Dy10 and 1Dx1.5+1Dy10) that are frequently observed in SHs can be easily incorporated into BW through recombination breeding.