The re-sequencing of the genomes of wild crop relatives is a rapid method to determine the likely utility of the germplasm in crop improvement. The conservation of genetic resources both in situ and ex situ can be guided by information on the novelty of specific populations at the whole-genome and specific allele levels. The analysis of Australian wild relatives of rice, coffee, Macadamia and Eucalypts is being used to support crop improvement and enhance food and energy security. Rice populations that are novel sources of diversity in the A genome of rice have been characterized at the whole-genome level. This has demonstrated the novelty of these species and will support taxonomic revisions of the Oryza species. Variation in the genomes of plants from diverse environments defines strategies that might be employed to develop climate-resilient crop varieties. Eucalypt sequencing aims to support the selection of species and genotypes for use as new energy crops.

India is the second most populous nation in the world after China, and its plant genetic resources are an important basis for crop improvement to meet human population needs. An important legume in the diet of the Indian population is common bean (Phaseolus vulgaris L.). Common beans are one of the many important legumes grown in India, but unlike others, its centre of origin is not in Asia but in the Americas. The objective of this study was to evaluate two collections of Indian common beans: one for an internationally available collection of Food and Agriculture Organization (FAO)-protected accessions and one from the north-western Himalayan region. In total, 149 Indian landraces were evaluated with a total of 24 microsatellites across the two collections, and these represented all common bean-growing states of India. A population structure analysis was used to find groups in each collection, and this was compared across the collections. The genetic analysis of the two sets of Indian accessions with neighbour-joining trees and principal component analysis categorized the landraces into Andean and Mesoamerican gene pool groups. The Andean genotypes dominated the north-western Himalayan collection while the FAO-protected accessions were predominantly Mesoamerican. The Indian subcontinent can be considered as a region of high bean diversity; however, very little introgression was observed between the gene pools in both the germplasm sets. Gene pool identity was further substantiated by the comparison of seed traits, particularly seed size. The role of the landraces in plant breeding programmes is discussed.

Information on genetic diversity and genetic relationships among taxa of Brassica rapa (n = 10, AA genome) is currently limited. Grown for oil, vegetable and fodder use in Europe and Asia, previous studies have indicated western and eastern groups corresponding to independent centres of origin. This study evaluated patterns and levels of genetic diversity in 93 accessions [includes 25 Agriculture and Agri-Food Canada (AAFC) breeding lines (BL)] of B. rapa based on 307 amplified fragment length polymorphisms (AFLP), testing subspecific separateness and the affiliation of four previously unassigned AA genome species (B. perviridis, B. purpuraria, B. ruvo and B. septiceps). AFLP data revealed three main clusters (I, II, III) corresponding to European (I), Indian (III), and a mixed Asian/European/Indian (II) purported origins of the taxa, with several subclusters observed in I and II. Mean AFLP polymorphism levels for Asian, European, Indian and AAFC-BL accessions were 79, 74, 66 and 62%, respectively. Few of the subspecies formed unique clusters and some, particularly subspecies chinensis and pekinensis, were assigned to several clusters. AFLP-based genetic distance information can be used by breeders to select diverse genotypes for cultivar development and fingerprinting of genotypes/cultivars. For example, a single AFLP primer pair was sufficient to uniquely identify all breeding lines in the AAFC B. rapa breeding programme.

The purpose of this study is to identify key home garden species in order to address basic research questions aimed at understanding farmers' home gardens management practices. The study was conducted in two contrasting Hill and Tarai sites in Nepal with households (HHs) ranging from 355 to 634. Unlike larger production systems, home gardens harbour many species in small areas often with a few crop varieties and species that are not well represented in larger fields. Given the number of species and their small population sizes, species and genetic diversity are best studied by identifying representative key species characterizing the complex productive niches within farms. Although species diversity within community is large (172–342), 24 key species were identified for the study. There is no fixed size of a home garden. The log of home garden size and species richness was positively correlated (r = 0.42, P < 0.001). Species richness was significantly higher in vegetable followed by fodder, fruits and spices. This paper also explores the diversity in home gardens to identify the composition and characteristics of the key species and how they are managed, used and conserved. Most of the farmers save the seeds of these home garden species for their own use, but many also exchange and buy and sell seed in local weekly market. Farmers' practices for selecting seed vary according to the reproductive biology of the key home garden species. Home gardens provide the HH with fresh and diverse supply of nutritious food, which improves their self-sufficiency, while conserving diversity on-farm. Despite this, they are neglected in research and development by policy makers and researchers.

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

A world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

Eruca vesicaria subsp. sativa (syn. E. sativa) is a cruciferous vegetable and oilseed crop that is high in erucic acid. It occurs throughout the Mediterranean region and western Asia, and has been naturalized elsewhere as a crop/weed escape. It is closely related to subsp. vesicaria and subsp. pinnatifida, which are endemic to Spain and north-western Africa, respectively. This study evaluated patterns and levels of diversity in the three subspecies based on 234 amplified fragment length polymorphisms (AFLP), and evaluated agronomic and seed quality data in a field trial in western Canada. AFLP data revealed three main clusters: ‘Sativa’ (33 accessions of subsp. sativa), ‘Vesicaria’ (nine accessions of subsp. vesicaria) and a ‘Pinnatifida’ cluster (one accession of subsp. pinnatifida and three Moroccan accessions of subsp. sativa). The Sativa cluster separated into Mediterranean and Asian groups, likely reflecting differences in origin (wild versus cultivated) or primary usage, vegetable versus seed oil. The origin of the introduced Mexican population was confirmed as subsp. sativa. The highest levels of diversity were found in the Sativa cluster (88% AFLP polymorphisms) and the least in the Vesicaria (56%) and Pinnatifida (39%) clusters. Extensive variation was observed among the 159 subsp. sativa accessions evaluated in the field trial, and overall findings indicated a favourable agronomic potential.

Regional distributions of crop diversity are important to take into account for the spatial design of in situ, farmer-participatory interventions in crop genetic management. Regional seed flows are an important factor in shaping geographical distributions of crop diversity. This study contributes to the insight in these seed flows, focusing on maize (Zea mays L.) in Chimaltenango, an area in the western highlands of Guatemala. A social survey of 257 households on different aspects of seed management produced information on cultivar naming, seed sources, reasons and causes of the discontinuation of seed lots, and important explanatory variables associated with different seed sources. A small portion of the reported seed lots originated from regional seed sources. The main motivation of regional seed exchange and the discontinuation of seed lots was to achieve change in plant characteristics of the crop, especially to obtain lower plants and shorter growing cycles. It is argued that farmer selection fails to achieve such change, and in fact leads to an equilibrium with high plants and long growing cycles. Seed exchange functions as an escape to this trend. Other factors of influence on seed exchange are altitude and ethnicity. The study also highlights the issue of geographical directionality in seed exchange patterns.

Mungbean seeds, despite being protected inside the pod, are susceptible to pre-harvest sprouting (PHS) following rainfall due to lack of fresh seed dormancy (FSD), which deteriorates the quality of the seed/grain produced. Therefore, development of mungbean cultivars with short (10–15 days) period of FSD has become important to curtail losses incurred by PHS. In this study, we investigated variations in PHS, fresh seed germination (FSG) and activity of α-amylase enzyme in diverse mungbean genotypes. There was a wide variation in PHS tolerance and FSG among 163 genotypes examined and 14 genotypes were found to be tolerant (<20%) to PHS. Seed germination in a pod, a measure used to evaluate PHS, varied from 7.14% in germplasm accession Chamu 4 to 82.52% in cultivated variety IPM 2–3. There was a marked increase in α-amylase activity in genotypes showing high FSG and PHS, especially at 48 and 72 h after germination as compared with PHS tolerant genotypes. Therefore, α-amylase can be used as an effective biochemical marker to evaluate a large number of mungbean genotypes for FSD and PHS. Also, the variation in seed germinability as found in this study could be further used for mungbean improvement programme.

Onobrychis viciifolia (sainfoin) is a forage legume crop with many positive agronomic, environmental, nutritional and nutraceutical attributes. Farmers also benefit from its drought tolerance in areas of low rainfall and light free draining soil, mainly due to its deep taproot. It is resistant to most common pest and diseases and is a valuable resource for pollinators, specifically cultivated for honey production in some regions. It has many benefits for animals, being highly palatable and without danger of bloat, which can be life-threatening to livestock. Its decline in Northern Europe started during the Green Revolution and was impacted by changes towards more intensive farming. Unlike other forage legume crops such as red clover and lucerne, sainfoin does not respond well to inputs and is difficult to establish and maintain. Sainfoin could be classified as an ‘orphan crop’ with very little genetic improvement or agronomic studies in the past 60 years. In the past 5–10 years, however, there has been a resurgence in interest and this has given rise to a number of studies and initiation of systematic improvement of the crop, which is indispensable to its reintroduction into the farmed environment. Interest has been driven in part by considerable evidence to suggest that condensed tannins present in the legume foliage, together with other polyphenol compounds, have positive effects on animal nutrition together with anthelmintic properties. These compounds are also thought to play a role in environmental benefits. There remain many challenges to address in order to optimize the potential for cultivation of sainfoin and its use as a beneficial forage crop. This review makes particular reference to a recently completed project; ‘Legume Plus’, funded by the European Union and embracing a multi-disciplinary approach to both understand and improve the crop for farmers. The present review covers results from both this project and other studies during the past 5 years, also drawing on historic studies of etymology, taxonomy, genetics, agronomy and botany, aiming to be a useful resource for research and for practical plant breeders and agronomists.

Thirty-one accessions of Citrullus spp. belonging to Citrullus lanatus var. lanatus, C. lanatus var. citroides and Citrullus colocynthis were subjected to phylogenetic analysis using combined datasets of amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs). Tree topologies inferred by neighbour-joining analysis have resolved the phylogenic relationships among the species with special reference to established taxonomic classification. In this study, we have clearly resolved species boundaries of various taxa of citroides, lanatus and colocynthis into three well-supported clusters. Clustering pattern of principal component analysis with the shared polymorphisms using the subsets of data between any two taxon combinations helped to elucidate the introgression and interrelationships among the species. We report two major groups of C. lanatus taxa, one of which has undergone wide introgressions with the taxa of C. lanatus var. citroides and C. colocynthis. In this paper, we identified 583 AFLP bands that are polymorphic within the var. lanatus of C. lanatus, which is the largest set ever reported. The species-specific diagnostic SSRs and polymorphic AFLPs that are informative within and between the taxa reported in this paper would be immensely useful for future studies of these economically important genera.

Helianthus annuus and H. petiolaris (Asteraceae) are wild sunflowers native to North America but have become naturalized in central Argentina covering an area of about 5 million hectares. Wild H. annuus has been recognized as invader species in several countries, but no research has been done to study the ecological determinants of their distribution. In a survey covering seven provinces between 31°58′–38°S and 60°33′–69°W, we described the ecology of the main wild populations. Wild Helianthus populations were located in three of the 18 ecological regions of Argentina, on five Mollisol and seven Entisol soil groups. The associated plant communities were comprised 60 species belonging to 16 families, all being frequent components of the native flora. Disease symptoms were seldom observed in wild populations, with Alternariahelianthi being the most commonly observed pathogen. Population size varied from less than 100 to more than 100,000 plants, covering from 100 to more than 60,000 m2 with densities most frequently up to 3 plants/m2, but reaching 80 plants/m2 at certain sites. Intermediate plant phenotypes between wild species and cultivated sunflower were found in one-third of the populations providing evidence of intense gene flow. Hybrid swarms were found at three localities with population sizes between 100 and 10,000 individuals.

Castor (Ricinus communis L.) is an important non-edible oilseed crop that can potentially be used as feedstock for biodiesel production. There are 1033 accessions in the United States Department of Agriculture (USDA) castor germplasm collection. The range of oil content in these accessions has never been surveyed. For exploiting castor as a feedstock for biodiesel production, the entire USDA castor collection was procured from the National Plant Germplasm System (Germplasm Resources Information Network) and the oil content was measured with nuclear magnetic resonance. The variation of oil content among all castor accessions ranged from 37.2 to 60.6% with an average of 48.2%. One hundred seed weights were determined and seed-coat colour was also recorded from each accession. One hundred seed weight ranged from 10.1 to 73.3 g with an average of 28.3 g. There was a significant correlation between seed weight and oil content but the correlation value was low (r = 0.1572, P < 0.0001). Fifty accessions with a wide range of oil content were selected to be field grown for further evaluation. The results obtained from this survey will be useful for castor breeders seeking germplasm accessions with high oil content in the collection.

Snow mould caused by Microdochium nivale (Fr.) Samuels & Hallett is the most widespread seedling disease in winter cereals. Due to the complexity of the resistance mechanisms, a poorly understood genetic background and strong interaction with winter weather conditions, it is difficult to assess the resistance of triticale cultivars via conventional inoculation methods. Genetic resistance is the most economical and environmental friendly way to control M. nivale infection; therefore, the objective of this study was to detect the quantitative trait loci (QTLs) associated with resistance components of winter triticale in a mapping population derived from a cross of the ‘Modus’ (partly resistant) and ‘SaKa 3006’ (sensitive) varieties. High-resolution mapping was conducted by using 1518 molecular markers (diversity arrays technology, simple sequence repeat and amplified fragment length polymorphism). Partial resistance components assessed in this study, i.e. candidate QTLs, were detected on chromosomes 1B, 2A, 3A, 3B, 5A, 5B, 6A, 6B and 7B, whereas QTLs describing overall seedling vitality in non-infected control plants were located on chromosomes 1B, 2B, 3A, 5A, 7B and 7R.

The Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

The present study is the first to compare the trait-level differentiation (Qst) and the molecular-level differentiation (Fst) between Malus× domestica and Malus sieversii. A set of 115 accessions representing M.× domestica (99) and M. sieversii (16) were genotyped using the International RosBREED SNP Consortium apple 8K SNP array and phenotyped for eight fruit quality traits in a clonally replicated experiment. A set of 3521 single nucleotide polymorphisms (SNPs) with an average call rate of 98% was retained following SNP data quality filters. About 86% of the total SNPs were polymorphic in M. sieversii, while all but three SNPs were polymorphic in M. × domestica. The patterns of linkage disequilibrium were different, especially at the longer distances, between the two species. No differentiation (Fst= 0) was observed for nearly 23% of the SNPs, but about 20% of the SNPs exhibited a high genetic differentiation (Fst≥ 0.15). A highly significant (P< 0.001) genome-level Fst= 0.12 was observed between M. × domestica and M. sieversii. The average estimated Qst value was 0.20 (range 0.08–0.40), and for three of the eight studied traits (crispness, flavour intensity and fruit weight), Qst value was more than twice the estimated genome-level Fst value. A higher Qst value than Fst value for four of the eight fruit quality traits indicated differential (or directional) selection for these traits in M. × domestica. The average posterior probability of assignment of M. × domestica accessions to the M. sieversii gene pool was 11%, supporting the hypothesis of M. sieversii being one of the progenitors of the domesticated apple.

Wild and managed bees are needed to move sunflower (Helianthus annuus L.) pollen, both to create hybrid seed and to encourage high, consistent yields when those hybrids are subsequently grown. Among floral traits that influence bee preference, floret size may be critical, as the depth of the corolla affects the accessibility of nectar. Sampling and observation of inbred maintainer (HA) lines were used to assess variation in floret size, and to measure any effects of floret size on pollinator visitation. Among 100 inbreds sampled, there was significant variation among the lines, with floret lengths of 6.8–9.9 mm. Floret length, measured before anthesis, was closely related to corolla depth during anthesis and was consistent between 2 years (environments). Pollinator observations on 30 inbred lines showed floret size explained a majority (52%) of the variation in wild bee preference, with a reduction in floret length of 2 mm more than doubling pollinator activity. Though honey bee, Apis mellifera L., colonies were located ≈ 60 m from the plots, near-zero honey bee activity in the sunflowers precluded an assessment of how strongly this managed pollinator is affected by floret length. Production of inbreds and hybrids with smaller florets could enhance sunflower pollination, but genetic markers for floret size are needed to facilitate selection, and an understanding of potential trade-offs also is required. Information on variation and heritability of other traits, such as pollen and nectar rewards, could help explain residual variation in wild bee visitation to sunflowers.

Triticum boeoticum is a valuable gene source for tolerance to drought stress. In order to study the effect of drought stress on this plant, and to understand its adaptive mechanisms at the molecular level, 10 accessions of T. boeoticum were evaluated under non- and drought stress conditions. Evaluation of 31 different phenological, morpho-physiological and root-related traits showed that there were significant differences between accessions. Using the bi-plot resulting from the PCA, the studied traits and accessions were separated in different groups. The most tolerant (B5) and susceptible (B6) accessions to drought stress were identified, so these accessions were used for assessment of changes in the TaNAC2 and TaNAC69-1 transcription factors (TFs) expression. The results showed that in the most tolerant and susceptible accessions, TaNAC2 and TaNAC69-1 expression levels increased between non-stress and stress conditions significantly, but the increased level of these two genes expression in the most tolerant accession was much higher than the most susceptible accession. According to the obtained results, T. boeoticum can be a suitable and promising gene source for improving modern wheat. In addition, the results of TFs expression could improve our understanding about the complex mechanisms associated with drought tolerance in wheat, especially wild wheat.

Soft wheat (Triticum aestivum L.) improvement could be enhanced by the identification of germplasm with superior end-use quality traits. Due to the geographic and historical separation of eastern and western US soft wheat germplasm ‘pools’, genetic differences in end-use quality may exist among cultivars arising from these two pools. To identify such differences, 30 US soft wheat cultivars were evaluated in ‘head-to-head’ trials over 3 years in Washington state. Cultivars were classified as: eastern soft red winter (SRW), eastern soft white winter (ESWW), western soft white (WSWW) and western Club. These four soft wheat cultivar classifications clearly differed systematically for some of the quality traits examined. The Club wheat cultivar group had the highest flour yield and flour ash. The Club group also had the lowest mixograph dough water absorption. Milling score (which incorporates break flour yield) was highest for Club and ESWW. Eastern soft red and white wheat cultivar groups had lower flour ash and alkaline water retention capacity (AWRC) compared to the western Club and soft white wheats; ESWW had the lowest AWRC of any classification. Cookie diameter was greatest for the ESWW group, followed by the SRW and Club groups (which were not significantly different), and then by the WSWW group. Individual cultivars with exceptional quality traits were also identified. These results indicate that the four US soft wheat germplasm pools differ, and they may be valuable genetic resources for ‘inter-pool’ wheat improvement.

Grapevine cultivar identification is based mainly on two complementary methodologies: microsatellite (simple sequence repeat (SSR)) DNA analysis and traditional ampelography. Here, we report a direct multiplex PCR approach that allows the simultaneous amplification of 11 SSR loci from crude samples, i.e. bypassing DNA extraction, by using an engineered DNA polymerase improved to tolerate plant PCR inhibitors. Many different plant tissues were successfully amplified: leaf, root, wood, berry flesh and skin, stalk and must, from wine and table grape varieties, and rootstocks. The direct multiplex PCR that we propose is quicker and cheaper than the methodologies used until now, and provides accurate results. Thus, SSR DNA analysis becomes economically more accessible to a larger number of potential users in addition to research institutes.