Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

New races of Phytophthora infestans rapidly defeat potato late blight (LB) resistance based on Solanum demissum germplasm, and breeders search for new sources of durable LB resistance. We developed and verified six sequence characterized amplified region markers recognizing the race-specific genes R1 and R3 of S. demissum and the broad-spectrum resistance gene RB of S. bulbocastanum and the germplasms of these species and used them to screen 209 accessions of 21 wild Solanum species. In addition to S. demissum, homologues of R1 and R3 were found in several species of series Demissa,Longipedicellata and diploid Tuberosa; R3 homologues were also detected in S. bulbocastanum,S. cardiophyllum and S. ehrenbergii. The RB homologues were found in a wider range of Solanum species. The markers of R1 and R3 genes reliably discerned between germplasms of S. tuberosum ssp. tuberosum and wild sources of LB resistance. Following introgression, the species-specific markers of demissum and bulbocastanum germplasm were rapidly lost, whereas the markers of R1 and R3 genes lasted through several meiotic generations and were maintained at high frequencies in modern potato cultivars. The presence of these markers in demissoid potato cultivars was significantly associated with LB resistance, presuming that both genes contribute to overall defence response.

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

Medicinal plants are the vital source of numerous structurally diverse pharmacologically active metabolites collectively called as secondary metabolites finding extensive applications in traditional systems of medicine and in pharmaceutical industries. Several distinctive and complex pathways operate in an interactive manner via metabolic networks that are responsible for the accumulation of such highly specialized metabolites. Secondary metabolites are believed to play a wide spectrum of physiological and functional roles in plants, many of which being investigated and supported by the experimental studies. Biosynthetic pathway related studies on various aspects in these medicinal plants have been found very tedious owing to several issues in plants such as considerably lower metabolite concentrations in native tissues, existence at different locations, and highly complex multi-step pathways, etc. Pathway elucidation and gene/enzyme discovery for studying metabolic pathway evolution and subsequent engineering could be better achieved by mining various pathway databases and reconstruction of metabolic networks available at different omics databases. Though medicinal plants have a limited range of genomic sequences available, however recently, next generation sequencing is being widely used to generate a comprehensive transcriptomic resource for these plants. It is anticipated that databases and resources generated from these studies are likely to play a key role towards the study and exploitation of metabolites from medicinal plants in near future. In this review, we have discussed next generation sequencing approaches, which were used for the generation of transcriptomic resources for several medicinally important plants. The relevance of transcriptomic approaches in curation of the pathways linked with the synthesis of major secondary metabolites along with their precursors of pharmaceutical importance in medicinal plants is also comprehensively analysed.

The evolutionary diversity of wild potato species makes them excellent materials for improving the narrow genetic basis of the cultivated potato Solanum tuberosum. Understanding their genetic diversity is important not only to choose the best parents for breeding, but also to design proper crossing schemes and selection strategies. The objectives of this study were to determine the resistance response to Ralstonia solanacearum, Potato virus Y and low temperatures of 21 clones of 12 potato species, and to determine their genetic diversity through simple sequence repeat (SSR) markers. Sources of resistance have been found for all the investigated traits, with high resistance variability not only between but also within species. Combined resistances were also identified, with positive implications for efficient breeding. SSR analysis allowed the detection of 12 loci and 46 alleles across all genotypes, with an average value of 3.8 alleles per locus. Both unique and rare alleles useful for marker-assisted selection were found. SSR-based cluster analysis revealed that resistant genotypes were distributed among all clusters, suggesting that genetically different resistant genotypes were identified. The information obtained in this study is discussed from a breeding perspective.

Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic relationships among members of the Saccharum species. A panel of 31 SRAP primer combinations were used to score 30 genotypes of Saccharum officinarum, Saccharum spontaneum, Saccharum robustum, Saccharum sinense, Saccharum barberi and sugarcane hybrids, with Miscanthus and Erianthus included as outgroups. The amplifications produced 1364 DNA fragments for an average of 44 per primer combination, with 83% (1135) being polymorphic and 8.7% (119) being species specific. Based on the Dice index, all 30 genotypes were differentiated from each other with genetic similarity (GS) estimates ranging from 0.60 to 0.96 (mean = 0.79). Both the dendrogram [obtained by the unweighted pairgroup method with arithmetic mean or (UPGMA)] and the non-metric multidimensional scaling method grouped the genotypes according to their phylogenetic relationships. Erianthus and Miscanthus were separated as two outgroups (at GS levels of 0.56 and 0.72, respectively) into two major clusters: cluster I separated the S. robustum, S. sinense, S. barberi and hybrids as different subgroups with each one including some S. officinarum clones, while cluster II included the S. spontaneum clones, exclusively. A S. officinarum–S. spontaneum sequence comparison of some of the monomorphic and polymorphic bands revealed 65–90% homology with rice, corn or sugarcane sequences deposited in databases. The high discriminatory power coupled with the possibility that most of the amplicons may be amplifying gene-rich regions of the genome makes SRAP a potentially robust tool for genetic mapping aimed at marker-assisted introgression in sugarcane.

With the numbers of new varieties of potato obtaining Plant Breeders' Rights increasing yearly, the reliable maintenance of large culture collections is becoming more problematic. Additionally, the differentiation of cultivars based on morphological characteristics is a highly skilled and time-consuming task and for these reasons a rapid and robust method for variety differentiation has become highly desirable. By screening a number of microsatellite (simple sequence repeat, SSR) markers we have developed a set of six that can be used to differentiate over 400 cultivars, including those on the UK National List, but excluding somaclonal variants (e.g. Red King Edward and King Edward). The whole process from tuber to accurate identification can be carried out in a single day.

This study evaluates the agronomic and morphological traits, chemical composition and traits related to consumer perception of local tomato landraces mostly collected in the suburban area of Madrid. Results showed remarkable variability at all the studied levels in this small area – intra- and inter-accession variability, and in morphological, agronomical and quality traits – and was often dependent on the environmental conditions where the crop was grown. However, few morphotypes could be defined. Some morphological traits of the studied samples seemed to be associated. For instance, ribbed fruits ripened with green shoulder and dark flesh accumulated more soluble solids. Consumer appreciation and fruit morphology, i.e. traits related to fruit size and shape, seemed to be the main determinants of tomato-type definition, although nutrient content also played an important role. Consumers positively received heirloom tomatoes, especially when they were cultivated in the open-field near their area of selection where they express their full potential in the nutrient synthesis and sensory properties. Although total soluble solids content seems to be the main trait related to appreciation, some morphological traits could be determinant in consumers’ choice. Furthermore, some consumers were more interested in different tomato typologies and nutritional characters like acidity.

We report the morphological typing of 13,337 accessions of bread wheat. The individual characters assessed were: awnedness, awn colour, glume colour, presence/absence of glume hairs, spike type, spike density, spike branching, grain colour, stem type (hollow/solid) and presence/absence of ligules. We have associated these morphological data with accession provenance, to analyse global patterns of the traits. Whereas some of the traits (awnedness, awn colour, glume colour, presence/absence of hairs on glumes, stem type) are concentrated in distinct geographical regions, others (spike type, spike density, grain colour, presence/absence of ligules) appear to be randomly distributed. Spike branching was not observed. Possible reasons for the geographical distributions of the characters, in the light of their inheritance, are discussed.

A set of 68 simple sequence repeat (SSR) markers were selected from existing databases (including Medicago, soybean, cowpea and peanut) for the purpose of exploiting the transferability of SSRs across species and/or genera within the legume family. Primers were tested for cross-species and cross-genus fragment amplification with an array of 24 different legume accessions. Nearly one-third (30.78%) of the SSR primers screened generated reproducible and cross-genus amplicons. One hundred and seventeen cross-species polymorphic amplicons were identified and could be used as DNA markers. These polymorphic markers are now being used for characterization and evaluation of our collected and donated legume germ- plasm. The transferability of SSRs, mis-/multiple-primings, homologous/heterologous amplifications, single/multiple-amplicons and application of these amplicons as DNA markers are discussed. The transfer of SSR markers across species or across genera can be a very efficient approach for DNA marker development, especially for minor crops.

Transformations that farmers bring to their traditional farming systems and their impacts on the conservation and evolution of maize varieties over a 12-year period are investigated using a longitudinal analysis. Despite the increased introduction and supply of improved maize variety seeds in the Yucatan Peninsula, Mexico, over the last 12 years farmers continue to maintain a substantial amount of traditional maize variety diversity. Even with the increased availability of hybrid seeds, farmers in the community of Yaxcaba on average plant more than three quarters of their milpa fields to traditional maize varieties, with the latter one fourth predominately planted to a locally improved variety Nal Xoy, a farm cross of a traditional variety and an improved variety. We observed a significant reduction in yellow – x-Nuuk nal, a long-cycle traditional landrace, paralleled by an increase in short- and intermediate-cycle locally adapted improved maize varieties. We found great differences in the distribution of maize varieties by soil type, with modern varieties being targeted for the rarer, deeper and fine-grained soils, while traditional varieties predominate on the more prevalent stony and thin soils. Our results provide a picture in which most traditional maize varieties in Yaxcaba continue to be maintained by farmers, coexisting with locally adapted improved varieties on the same landscape, and allowing the continued evolution of maize populations.

The worldwide spread of barley cultivation required adaptation to agricultural environments far distant from those found in its centre of domestication. An important component of this adaptation is the timing of flowering, achieved predominantly in response to day length and temperature. Here, we use a collection of cultivars, landraces and wild barley accessions to investigate the origins and distribution of allelic diversity at four major flowering time loci, mutations at which have been under selection during the spread of barley cultivation into Europe. Our findings suggest that while mutant alleles at the PPD-H1 and PPD-H2 photoperiod loci occurred pre-domestication, the mutant vernalization non-responsive alleles utilized in landraces and cultivars at the VRN-H1 and VRN-H2 loci occurred post-domestication. The transition from wild to cultivated barley is associated with a doubling in the number of observed multi-locus flowering-time haplotypes, suggesting that the resulting phenotypic variation has aided adaptation to cultivation in the diverse ecogeographic locations encountered. Despite the importance of early-flowering alleles during the domestication of barley in Europe, we show that novel VRN alleles associated with early flowering in wild barley have been lost in domesticates, highlighting the potential of wild germplasm as a source of novel allelic variation for agronomic traits.

Aegilops species provide an invaluable source of genes for the improvement of cultivated wheats. This paper illustrates how the existing geo-referenced passport data associated with Aegilops species can be used to identify gaps in current conservation and also to develop a more systematic conservation strategy for the genus. Taxonomic, ecological, geographic and conservation information for the 22 Aegilops species were collated from ICARDA, EURISCO, GRIN and SINGER datasets, synthesized and analysed. The combined database contained 9866 unique geo-referenced observations collected between 1932 and 2004. Patterns of specific distribution based on the germplasm accession data and the predicted distribution using climatic models were compared in conservation gap analysis using GIS tools. The ex situ conservation status of each taxon was assessed and used to provide a priority ranking. Future ex situ collection is recommended in Cyprus, Egypt, Greece, Iran, Israel, Libya, Spain, Syria, Tajikistan, Tunisia, Turkey, Turkmenistan and Uzbekistan. The species identified with the highest ex situ conservation priority are as follows: Aegilops bicornis, Aegilops comosa, Aegilops juvenalis, Aegilops kotschyi, Aegilops peregrina, Aegilops sharonensis, Aegilops speltoides, Aegilops uniaristata and Aegilops vavilovii. Patterns of species richness based on the germplasm accession passport data are presented and five complementary regions of Aegilops diversity were identified in west Syria and north Lebanon, central Israel, north-west Turkey, Turkmenistan and south France. Within these areas, 16 IUCN-recognized protected areas are found and these are identified as potential sites to establish genetic reserves. However, the premier Aegilops hotspots on the Syrian/Lebanese border are not coincident with any existing internationally recognized protected areas, and here there is a need to establish a novel protected area.

Fifty morphological characteristics, fruit production over 3 years (from 1999 to 2002) and the amplified fragment length polymorphism (AFLP) technique were used to analyse a set of 48 guava (Psidium guajava L.) accessions cultivated in Mexico, in order to characterize their genetic relationships. Germplasm was collected from the Calvillo-Cañones region and planted in Huanusco, Mexico. The study included two P. cattleianum (Sabine) and two P. friedrichsthalianum (Berg-Niedenzu) accessions from Costa Rica as outgroups. Principal component analysis (PCA) explained less than 30% of total variation and 14 characteristics from trees (1), leaves (2) and fruits (11) were the most informative. PCA analysis separated the germplasm into three major groups of accessions based on fruit size and weight, stem diameter and leaf size. Significant differences in fruit yield were detected among accessions and years, where P. guajava produced 36 kg/year/tree of fresh fruit while P. cattleianum and P. friedrichsthalianum showed fruit yield lower than 7 kg/year/tree. The fruit yield broad sense heritability was 0.25. The AFLP analysis produced two clusters of Psidium accessions, the first included P. cattleianum and P. friedrichsthalianum, and the second P. guajava accessions. This is the first report about the use of AFLP marker methodology for the genetic characterization of Mexican native guava germplasm and the results based on phenotypic and productive characteristics suggest that germplasm was selected from open pollinated trees.

Having knowledge on genetic similarity and DNA profile of potato genotypes facilitates a breeder's decision for parent selection and provides accurate variety identification. Fingerprinting and identification of genetic similarity among 151 potato genotypes were achieved using an inter-primer-binding sites (iPBS) retrotransposon marker system. Our study is the first application of iPBS markers for fingerprinting and distinguishing large numbers of Solanum tuberosum genotypes. Initially, 16 potato genotypes were screened using 45 iPBS retrotransposon markers to identify polymorphisms. Seventeen of these primers were selected for fingerprinting the whole set of accessions due to strong, reproducible and polymorphic bands. The 17 iPBS primers produced 290 scorable bands of which 224 were polymorphic. The number of bands per primer ranged from 10 to 26 with an average of 17.1. The number of polymorphic bands per primer was between 6 and 21. The polymorphism percentage per primer ranged from 46.2 to 100.0% with an average of 77.2% per primer. The mean polymorphism information content (PIC) values of iPBS primers varied from 0.12 to 0.31 per primer. Genetic similarity based on Jaccard's coefficient of potato genotypes ranged from 0.61 to 0.93 with an average of 0.73. The data produced herein may be used for selection of appropriate parents and variety description in the future. The findings of the present study suggest that iPBS retrotransposons are powerful and easy DNA markers for fingerprinting the large samples of potato germplasm.

Artichoke, Cynara cardunculus var. scolymus is a diploid outcrossing species, originated in the Mediterranean basin, which has been much appreciated both for its tasty heads and pharmaceutical properties since ancient times. The species includes two more botanical varieties: C. cardunculus var. altilis, the cultivated leafy cardoon and C. cardunculus var. sylvestris, the presumed wild progenitor of artichoke, which are completely interfertile with the cultivated globe artichoke and all together they form the primary gene pool of artichoke. The secondary gene pool includes at least seven wild Cynara species. A high level of morphological variation, essentially in head shape and size, is observed in artichoke varieties. Amplified fragment length polymorphism (AFLP) markers were used in order to assess genetic variation and relationships among artichoke varieties and between these and some of their wild relatives. A selected group of wild and cultivated artichoke accessions belonging to different clusters detected on a morphological basis and from various geographical origins was chosen for the analysis. Twenty-four primer combinations were initially tested to evaluate their ability to detect polymorphism between samples. Nine primer combinations were chosen for further analysis on 39 cultivated artichokes, two wild progenitors, one cultivated cardoon, one sample of C. cornigera, one of C. humilis and two samples of C. syriaca. A high level of polymorphism was observed for AFLP markers. The polymorphic bands obtained were scored and used to assess genetic similarity among wild and cultivated accessions and finally to construct a UPGMA dendrogram and principal co-ordinate (PCO) analysis based on Jaccard's similarity index. The artichoke wild progenitor was quite distantly related to the cultigen and occupied a separate branch in the dendrogram. However, wild C. cardunculus was more similar to the artichoke than were the other wild species, corroborating the idea that it is the wild progenitor of cultivated artichokes. Within the cultivated artichoke, the dendrogram derived from AFLP analysis produced branches which roughly corresponded to the groups obtained on the basis of morphological and physiological characteristics. The groups were homogeneous enough, except for the ‘Romaneschi’ types, which proved to be quite genetically variable, and did not cluster in a single branch. This is interpreted on the grounds of the possible selection pathway of this more modern morpho-group.

To date, there are only a few sequenced-tagged site (STS) markers associated with genes controlling fruit quality in watermelon. A normalized cDNA library for watermelon fruit (Citrullus lanatus var. lanatus) was constructed. Sequence analysis of the cDNA clones resulted in the development of 4700 non-redundant ESTs (EST unigenes) expressed in watermelon fruit (http://www.ncbi.nlm.nih.gov, http://www.icugi.org). One hundred of these EST unigenes [including 40 EST unigenes that contain simple sequence repeat (SSR) motives (EST-SSRs) and 60 customary EST unigenes (not containing SSR motives)] were used for designing primer pairs for PCR experiments. The EST primer pairs were tested in PCR experiments with genomic DNA of 25 watermelon heirloom cultivars and 13 United States Plant Introductions (US PIs) of Citrullus sp., including four C. lanatus var. lanatus, five C. lanatus var. citroides PIs and four Citrullus colocynthis PIs. The 40 EST-SSR and 60 EST primer pairs produced 108 and 142 EST-PCR markers, respectively, among the Citrullus PIs and watermelon cultivars. A large number of the EST-PCR markers were polymorphic between the Citrullus PIs and the watermelon cultivars, but significantly less polymorphic among the cultivars. Of the 108 EST-PCR markers associated with EST-SSRs, 103 exist in the Citrullus PIs and 64 in the cultivars. Of these 64 markers, 45 (70.3%) were polymorphic among the cultivars. Of the 142 EST-PCR markers associated with customary ESTs, 134 exist in the Citrullus PIs and 108 in the cultivars. Of these 108 markers, 86 (79.6%) were polymorphic among cultivars. The results in this study indicate that polymorphism exists in coding regions of genes expressed in fruits of watermelon cultivars. In total, 131 polymorphic EST-PCR markers (45 associated with EST-SSRs and 86 associated with customary ESTs) related to watermelon fruit genes were generated using the above data. These markers should be useful for DNA fingerprinting of cultivars and breeding lines, for assessing genetic relationships and for genetic mapping of watermelon.

Crop biofortification is increasingly being recognized as a cost-effective and sustainable approach to address the widespread micronutrient malnutrition arising from Fe and Zn deficiencies. Pearl millet as a cereal crop species has higher Fe density than all other major cereals. Earlier studies in pearl millet have shown that breeding lines, hybrid parents, improved populations and composites having high Fe and Zn densities were often based largely or entirely on iniadi pearl millet germplasm. In an attempt to identify additional sources of high Fe density in this group of germplasm, 297 accessions were screened using Perl's Prussian Blue staining, of which 191 accessions (118 from Togo, 62 from Ghana and 11 from Burkina Faso) were re-evaluated during the 2010 rainy and 2012 summer seasons using the inductively coupled plasma atomic emission spectroscopy method. On the basis of the mean performance over the two seasons (environments), large variability was observed for both Fe (51–121 mg/kg) and Zn (46–87 mg/kg) densities. There was a highly significant and positive correlation between the two micronutrients (r= 0.77, P< 0.01). Of these re-evaluated accessions, 49% had higher Fe density than the high-Fe control commercial cultivar ICTP 8203 (81 mg/kg), and most of these accessions also had Zn density ≥ 61 mg/kg (59 mg/kg for ICTP 8203). A total of 27 accessions (20 from Togo and seven from Ghana) having a Fe density of 95–121 mg/kg (1 standard error of difference above that for ICTP 8203) and a Zn density of 59–87 mg/kg were selected as a valuable germplasm resource for genetic improvement of these two micronutrients in pearl millet.

Guava (Psidium guajava) and araçá (Psidium spp.) plants are important for the Brazilian economy, as their fruit is both accepted by the consumers, and makes a beneficial contribution to the human diet thanks to their content in vitamin C, carotenoids and phenolic compounds. Here, we report the content in the fruit of free ascorbic acid, lycopene, β-carotene, flavonoids and phenolic compounds, and the total antioxidant activity present in a collection of guava and araçá accessions curated at the Embrapa Semiarido germplasm bank. Guava fruits with a red-coloured pulp flesh contained a significant amount of carotenoids, especially lycopene, and a high concentration of phenolic compounds. These compounds were largely responsible for the antioxidant activity of the araçá accessions. Among the guava accessions, phenolic compounds were also responsible for the antioxidant activity. High levels of free ascorbic acid were present in most accessions. In both guava and araçá, there is substantial potential to develop cultivars with a good level of consumer acceptability.

Although the concept of ‘sustainable development’ has been hailed for its reconciliatory poten- tial, it has failed in practice to resolve enduring conflicts. Exploring the evolution of the concept—from its 19th-century antecedents through Brundtland to contemporary ‘Panglossian’ interpretations—the paper argues that difficulties of implementation are not transient but have deep roots. No conception of sustainable development can be adopted without making fundamental ethical and political choices, but the debate about such choices is nevertheless of great importance. It is argued that we should abandon our search for a singular, consensual definition of sustainability, but try as best we can to make progress in the absence of consensus.