The study of unknown and therefore unexploited genetic material from landraces and wild relatives could be essential to help modern plant breeders to respond to ongoing requirements and new challenges in food production. The present study evaluates the most relevant physicochemical values and nutrient contents of a genetically unique array of traditional melon varieties, cultivated in Spain at least since the 19th century, and compares them with modern melon hybrids available on the market. This research is complemented with an assessment of variety, environment and repetition effects on each trait to determine their stability. Spanish melon landraces displayed extraordinary diversity with respect to juiciness (70.59–95.97 g/100 g water fresh weight), firmness (20.75–149.89 N), soluble solids content (9.57–16.53 °Brix), pH (5.04–6.38), total sugars (360.21–877.36 mg/g dry weight), carotenoids (0.01–2.05 μg/g fresh weight) and ascorbic acid values (7.55–44.33 mg/100 g fresh weight). A subset of these landraces, belonging to Piel de Sapo and Rochet market classes, revealed remarkably superior values of ascorbic acid in comparison with all commercial varieties, doubling ascorbic acid values with respect to their corresponding market class. Furthermore, most of these landraces exhibited high acidity and accumulated high levels of sugars, fulfilling those sensory and physicochemical characteristics that researchers and breeders have spent many years seeking. The possibilities of these landraces to be used in improvement projects are innumerable; they should be surely taken into account in the near future.

Annual wild soybean characterized by low 100-seed weight (100SW), high protein content (PRC) and low oil content (OIC) may have favourable exotic genes/alleles for broadening the genetic base of the cultivated soybean. To evaluate the wild alleles/segments, a chromosome segment substitution line population comprising 151 lines with N24852 (wild) as the donor and NN1138-2 (cultivated) as the recurrent parent was analysed using single-marker analysis, interval mapping, inclusive composite interval mapping and mixed linear composite interval mapping. On 14 segments of ten chromosomes, 17 quantitative trait loci (QTL) were identified, with two segments each containing two QTL for 100SW and OIC and one segment containing two QTL for PRC and OIC, respectively. All the seven wild alleles/segments for 100SW were associated with negative effects and three were associated with positive effects, but one was associated with a negative effect for PRC, and five were associated with negative effects, but one was associated with a positive effect for OIC. Except Satt216 and Sat_224 for 100SW, the identified QTL/segments have been reported from cultivated soybean mapping populations. The detected wild segments may provide materials for further characterization, cloning and pyramiding of the alleles conferring the seed-quality traits.

Cultivated soybeans [Glycinemax (L.) Merr.] have various flower colours such as dark purple, purple, light purple, pink, magenta, near white and white. About one-third of the soybean accessions in the United States Department of Agriculture – Germplasm Resource Information Network (USDA-GRIN) Soybean Germplasm Collections have white flowers and are the second dominant accessions after the purple-flowered accessions. Earlier studies have shown that the w1 recessive allele of the W1 gene encoding flavonoid 3′,5′-hydroxylase produces white flowers. In the present study, we aimed to understand why the white-flowered accessions have become abundant among the cultivated soybeans and what their genetic and regional origin is. For this purpose, 99 landraces with white flowers and 39 landraces with purple flowers from eight Asian countries and Russia were analysed with regard to the nucleotide sequences of the W1 locus. We not only found that the w1 alleles of the 99 white-flowered landraces were identical to those of the white-flowered Williams 82, but also found that these w1 alleles displayed no polymorphism at all. By carrying out a phylogenetic analysis, we were able to identify a group with W1 alleles from which the w1 allele might have diverged.

Soybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Seed composition, including the protein, lipid and sucrose contents of 334 accessions of wild soybean (Glycine soja) collected in Japan, was evaluated using near-infrared reflectance spectroscopy (NIRS) technology. The distribution of protein, lipid and sucrose contents and correlations among these three classes of seed components were determined. Protein, lipid and sucrose levels ranged in accessions from 48.6 to 57.0, 9.0 to 14.3 and 1.24 to 3.53%, respectively. Average levels of protein, lipid and sucrose in the accessions were 54, 11 and 2.5%, respectively. High negative correlations were observed between the protein and lipid contents, and the protein and sucrose contents. Mean levels of the three constituents were compared among collection sites classified by climatic conditions. The total protein content of accessions from regions with a high annual mean temperature was high. The protein content of accessions from the II-1 region was higher than those from the III-3 region, and the sucrose content from the II-1 region was lower than those from regions III-2 and IV-3. The lipid content of plants from the II-1 region was lower than those from other regions, and the accessions in region II had a higher protein content and lower sucrose and lipid contents than the other regions. These results provide diverse and wide-ranged protein, lipid and sucrose contents information of Japanese wild soybean resources according to climatic region; thus, providing a foundation for the future development and selection of new soybean varieties with desired traits in global environmental changes.

Research on resistance to black pod caused by Phytophthora megakarya has been carried out in Cameroon for 40 years. It has yielded a significant database which is currently being exploited for the modelling of disease resistance levels of the major clones selected as candidate parents for the creation of new resistant and consequently more productive cocoa varieties. These outputs are expected to meet the increasing need of producers for improved planting material to extend cultivation into emerging cocoa-growing areas or to renew old cocoa production basins. These outputs have been made possible through an international collaborative effort and, more recently, within the scope of regional or international initiatives sponsored by CFC/ICCO/IPGRI and by CAOBISCO. New selection approaches and methodologies, such as rapid field assessment and early screening tests, have been promoted, along with the use of molecular tools for genome mapping and disease resistance quantitative trait locus (QTL) identification. Promising material has been introduced, evaluated in the laboratory and on-farm, and compared to the local cocoa germplasm. The basic knowledge developed from this local database has enabled the definition of an empirical disease resistance sorting and subsequently a prediction of the yield gains expected from the use of different cocoa clones and possible combinations (progenies) available on-station and in farmers' stands in different agro-ecological growing conditions; or which have to be created following strategies in the new breeding programme.

Genebanks are important suppliers of genetic resources to the genomics research community, and access to the resulting information will allow traditional genebank users to better select genetic material for their breeding and scientific programmes. We discuss herein a possible solution to interconnect these data automatically based on semantic web technology.

Tomato is a pivotal vegetable crop worldwide concerning human nutrition, economy and in service to biotechnology. Tomato leaf curl virus (ToLCV) is a begomovirus transmitted through the whitefly (Bemisia tabaci) and is responsible for severe losses in tomato production. In this context, the current investigation was carried out to determine heterotic combiners with high yield, resistance to ToLCV and mode of gene action for economically important traits. For this, 11 prescreened inbred lines were crossed in a half diallel fashion to generate 55 F1 hybrids. The 55 crosses with 11 parents and commercial checks were evaluated for different horticultural traits and resistance to ToLCV. The molecular validation with SCAR markers TG0302 and SCAR1 confirmed the presence of ToLCV-resistant genes in parents and their crosses. The hybrid IIHR-2902 × IIHR-2852 showed the presence of both Ty-2 and Ty-3 alleles in the homozygous state. The estimation of σSCA2 and σGCA2 was significant. It also indicated that the genetic control of target traits was under additive and non-additive gene effects. The values of σA/D2 along with σGCA2/σSCA2 found to be less than unity indicates the preponderance of non-additive gene action in the expression of the studied traits except for percent disease incidence. The parental line IIHR-2919 was the best combiner for fruit and yield traits. The cross combinations IIHR-2913 × IIHR-2898 exhibited significantly higher economic heterosis for yield along with the presence of Ty-2 and Ty-3 genes. The study paves the way for breeding high yielding and ToLCV-resistant hybrids in tomato.

Niger harbours a wealth of diversity of Africa's rice (Oryza glaberrima) and its related wild species. We therefore engaged in a collecting mission of rice species across growing regions and agrosystems in Niger. A total of 270 rice accessions were assembled, including 177 Asian rice (O. sativa) cultivars, 67 African rice landraces (O.glaberrima), 25 O. barthii and one O.longistaminata. We found most accessions (80.7%) along the Niger River and its tributary the Dallol Maouri. Many of the accessions, except those belonging to the wild O. barthii initially found around the Lake Chad region, were also collected along the Niger River. Drought, insects, birds, rice yellow mottle virus and bacterial blight were noted as major constraints on rice production. Accession naming by farmers was consistent within regions but seldom across regions. Based on the recorded agro-morphological traits, the germplasm was classified into three clusters: (1) O. longistaminata with floating African landraces and late-maturing floating Asian rice; (2) lowland O.barthii and African landraces; (3) a mixture of irrigated Asian rice with lowland accessions of both cultivated species. The phenotypic variability of the germplasm collection, as measured by the Shannon–Weaver diversity index, was relatively high (H′ = 0.69), with accessions in the irrigated agrosystem being less diverse than those in the traditional agrosystems. There was no significant difference in the magnitude of diversity between the main eco-geographical zones and between the clusters. However, some traits contributing the most to this diversity were different. This study suggested a substantial germplasm exchange between regions in Niger.

Spelt (Triticum spelta L.) is hulled wheat which was widely cultivated in Spain until the first half of the 20th century and is still cultivated in Asturias (northern Spain). Much of the variability of this species has been preserved, but little evaluation has been carried out. We describe the characterization of some of these spelt lines for several quantitative traits, including plant height and awnedness.

Acetohydroxyacid synthase (AHAS) inhibiting herbicides have played a significant role in effective weed control in the cultivation of sunflower since their discovery. The development of sunflower lines and hybrids resistant to these herbicides made their post-emergence application possible. In this study, wild Helianthus species were screened phenotypically for imidazolinone (IMI) and sulfonylurea (SU) resistance by herbicide spray and for allelic variations at Ahasl1 (Ahas1 large subunit) locus using simple sequence repeat and single nucleotide polymorphism markers. Helianthus praecox accession 1823 plants showed promising resistance to three classes of SU-based herbicides and Helianthus nuttallii accession NUT05 plants remained green for a longer time after imazethapyr spray. A total of 50 accessions belonging to 21 wild Helianthus species of different ploidy levels were analysed for allelic variation along with some parents of commercial sunflower hybrids. None of the wild species showed the resistant allele (Ahasl1-1) similar to SCG101 (IMI-resistant line), although it is present in some of the parental lines of hybrids. However, the parental lines having Ahasl1-1-type allele failed to survive the field dose of imazethapyr spray. Inter-species and inter-accessional allelic variation could be observed among the species. PRA1823 and NUT05 showed repeat length variations at Ahasl1 locus. Sequencing of full length Ahasl1 gene from both these accessions did not reveal any resistance mutations in the protein sequences. The molecular basis of the phenotypes identified in this study could be explored further and utilized in breeding programmes for imparting herbicide resistance in cultivated hybrids across sunflower growing regions of the world.

In this study, 15 morphological traits and 16 microsatellite markers were used to assess the morphological variability and structure of 68 (33 local and 35 foreign) almond accessions (Prunus dulcis (Mill.) D.A. Webb). Extensive phenotypic diversity was found among the accessions, and results indicated a high variation in leaf and fruit traits. Varieties were separated into two distinct groups with a similarity coefficient of 0.761. Morphological traits were categorized by principal component analysis into five components, which explained 86.5% of the total variation. Nut and kernel traits were dominant in the two first components, accounting for 49.4% of the variation. By contrast, leaf traits accounted for 18.4% of the variation in the third component. The results of molecular analysis (Bayesian clustering approach) did not correspond to morphological groupings, and the second approach was more discriminate. The combination of both approaches revealed the richness among the collected plant materials, which will be useful in breeding programmes of this species.

Cultivated pigeonpea has a narrow genetic base. Wild relatives play an important role in the efforts to broaden its genetic base. In this report, we present a successful wide-cross between the cultivated pigeonpea and Cajanus lanceolatus, a wild relative from the secondary gene pool, native to Australia, with desirable traits such as frost and drought resistance. A range of F1 progeny were obtained and the resultant F1 hybrid plants set mature pods and seeds. The hybrids had intermediate morphology, sharing the traits of both the parents. All the F1 hybrids flowered profusely. Some of the hybrids were completely male sterile and some were partially fertile with pollen fertility ranging from 35 to 50 %. Meiotic analysis of the fertile F1 hybrids revealed a high degree of meiotic chromosome pairing between the two parental genomes. Meiotic analysis of the sterile F1 hybrids revealed that the breakdown of microsporogenesis occurred at the post-meiotic stage after the formation of tetrads. Fertile plants formed regular bivalents with normal disjunction, except for occasional asynchrony at meiotic II division.

Amylose-free (waxy) maize has been a vegetable (cooked ears) and staple food in Southeast Asia for centuries, resulting in hundreds of landraces (LRs) across the region. The recessive waxy allele induces soft grains with preferred cooking and flavour properties. We hypothesized that eating preferences resulted in the additional selection for different starch properties, reflected in altered starch granule morphology or amylopectin structure. A total of 41 LRs were available as starting material that had been used by different ethnic groups in Vietnam and Thailand. Unluckily, some LR were not pure waxy, but we successfully regained the original pure waxy status for most. Twenty LR were chosen for analysis of starch traits according to their purity. Four different waxy mutations were identified, including two unknown alleles. This is a strong proof for parallel independent selection of waxy maize in the region. Starch granule morphology and size were similar among all LRs. Gelatinization properties differed only between waxy and wild-type LR, and all waxy LR were comparable to a commercial waxy hybrid. The fine structure of waxy amylopectin had fewer short chains compared with that in wild-type. So far, the differences observed in starch properties are likely associated exclusively with the waxy trait. Despite the strong selection for amylose-free starch, there was no evidence for additional region wide selection for other special starch properties in our collection. In conclusion, all analyses did not encourage further targeted research on allelic variation of other starch metabolism genes for future use in the food and feed industry.

The genebank at ICRISAT, India that serves as a world repository for sorghum germplasm conserves 39,234 accessions from 93 countries, including 6249 from seven South Asian countries: Afghanistan (6), Bangladesh (9), India (6101), the Maldives (10), Nepal (8), Pakistan (90) and Sri Lanka (25). A total of 5340 georeferenced accessions were used to identify gaps, and 5322 accessions that were characterized at ICRISAT were used to assess the diversity in the collection. Accessions of basic races varied widely than those of intermediate races for flowering in the postrainy season, plant height in both rainy and postrainy seasons, panicle exsertion, panicle length and width, seed size and 100 seed weight. Landraces from India were late flowering, tall and produced stout panicles and larger seeds. Landraces from Pakistan flowered early in both seasons and produced stout panicles and those from Sri Lanka were late flowering and tall in both seasons, produced more basal tillers and stout panicles. A total of 110 districts in 20 provinces of India, 13 districts in three provinces of Pakistan, three districts in Bangladesh and five districts in four provinces of Sri Lanka were identified as geographical gaps. Sorghum bicolor subsp. verticilliflorum, S. halepense and S. propinquum were identified as taxonomic gaps in the collection. Therefore, it is suggested to explore the districts identified as gaps to enrich the variability in the world collection of sorghum at ICRISAT.

Low-temperature stress is an important factor affecting the growth and development of rice in temperate and high-elevation areas. In this study, 220 germplasm lines were used for screening of tolerant genotypes, validation of molecular markers and identification of robust markers for seedling-stage chilling stress tolerance to be used in marker-assisted breeding (MAS) programme. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling stages of the germplasm lines. The genotypes were classified into six classes: those having susceptible genotypes were classified into moderately and highly susceptible types, while tolerant types into moderately tolerant, tolerant, highly tolerant and very highly tolerant classes. Genotypes namely Langma, Umleng-1 and Geetanjali showed survival up to 25 d, which were better than the positive check Kalinga-III surviving up to 20 d under chilling stress. Ten simple sequence repeat (SSR) markers were tested for differentiation of genotypes. Individual use of SSR markers like RM284, RM286, RM85, RM341 and RM5746 can be applied in MAS breeding including combination use of non-pair markers like RM284, RM239 and RM85, which was even better than the combined use of RM284 and RM85. However, combined use of all ten markers can most effectively be employed for cold tolerance through MAS breeding.

Purple- and red-fleshed potato cultivars constitute a great source of phenolic compounds, which may promote human health. Since the characterization of potato germplasm is a key step during the breeding process, the classification of high anthocyanin-producing tetraploid genotypes may facilitate the incorporation of phenolic-related traits in a potato breeding programme. A set of 18 high anthocyanin-producing underutilized tetraploid cultivars, which have been previously classified in terms of phytochemical content, have been characterized by both microsatellite markers (simple sequence repeat, SSR) and morphological descriptors. A wide genetic variability was found using 11 highly discriminatory SSR markers. The collection also displayed a large amount of variation for most morphological traits. The neighbour-joining trees defined by SSR markers and morphological descriptors revealed genetic and phenotypic relatedness of the potato genotypes. Despite the complexity of tetrasomic inheritance, high anthocyanin-producing tetraploid cultivars should be considered for potato breeding since they are adapted to long-day conditions and do not present undesirable characteristics that are found in native accessions or landraces.

Cereal crops are one of the most widely consumed and most valuable crops for humankind. The species have been domesticated for over 10,000 years and as such have lost much of the genetic diversity that is present within their wild relatives. Future breeding efforts will require the use of genetic diversity from crop wild relatives (CWRs) to help improve our cereal crops. This study aims to identify an in situ conservation network within the Mediterranean Basin and west Asia for the four cereal crops, barley (Hordeum L.), oat (Avena L.), rye (Secale L.) and wheat (Aegilops L., Amblyopyrum L., Triticum L.). This region is a centre of diversity for these taxa and an area of potentially high genetic diversity, which if left unprotected will not be available for plant breeders to utilize in the future. Presence point data for a total of 90 taxa were collected from GBIF and resulted in 76,343 individual presence points across the 44 countries in the study region. Geographic Information System (GIS) software was used to identify potential in situ reserve networks per crop genepool and for all crops combined. Results indicate a network of 10 locations across the region which would protect over 80% of the taxa. The number one priority reserve is found within the Fertile Crescent region on the border of Israel, Syria and Jordan. This proposed reserve location contains 93 currently protected areas (i.e. National Parks) and as such, it may only be necessary to alter management plans to effectively protect CWR populations. For taxa not found within protected areas ex situ conservation may be more appropriate and should be implemented as a backup to the in situ reserve network.

The red algal genus Porphyra is sister to the genus Pyropia, the single most valuable marine crop in the Orient. We developed microsatellite loci for the red alga Porphyra umbilicalis, a widespread species in the Northern Atlantic. Enriched DNA libraries were constructed and 68 loci were screened for amplification and polymorphism. Seven polymorphic microsatellite markers were isolated using 44 individuals collected from four natural populations. The number of alleles per locus ranged from two to 12. Null alleles were detected in three loci. Among the markers reported, we tested also cross-amplification with two other Porphyra spp. These polymorphic microsatellite markers should be useful for investigating population genetic structure of P. umbilicalis in the North East Atlantic.

Rhubarb includes approximately 60 species in the genus Rheum. It has been utilized for thousands of years for medicinal purposes, but only recently identified for its culinary use. In the mid 1700s, edible petioles were discovered on seedlings from rhubarb species. Hundreds of cultivars have since been identified for a wide range of uses from tarts to wine. Unfortunately, propagation by seed and irregular naming has resulted in a plethora of similarly named cultivars and multitude of phenotypes. Fifteen morphological characters were evaluated to differentiate rhubarb cultivars in the USDA, ARS Rheum collection in Palmer, Alaska. Two years of morphological data, focusing on horticultural characteristics indicated variation between the years. To improve cultivar resolution, the results suggest using 1 year's data instead of combining data from different years. The mean °Brix observed was 3.8, with a range from 2.2 to 6.1. Flesh colour and basal skin colour were poorly correlated (R2 = 0.462); overall skin colour was more red at the base than in the middle of the petiole. Rhubarb character categories, in particular petiole number and petiole base thickness, need to be modified to better anticipate the range of expected values, and thereby contribute improved reproducibility and reliability to separate cultivars based on morphological characters.