The genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

With regard to the survey data of Korean researchers using genetic resources from three genebanks administered by the Korea Research Institute of Bioscience and Biotechnology, we conducted conjoint and cluster analyses to estimate the relative importance of genetic resource (microbial, plant and animal) attributes among the researchers. Our results indicate that Korean researchers view price (cost of acquiring an accession), high new functionality (functional properties of germplasms for specific applications and uses) and completely uncovered genomic information (about mutation, genetic transformation, genomic function and pathways) as far more important in decision-making about R&D use of microbial, plant and animal genetic resources, respectively, than other attributes. Furthermore, this study shows that researchers conducting R&D in the microbial and plant genetic resource sectors especially prefer resources from specific domestic environments and Korean indigenous species, respectively. The study also sheds light on different patterns of researcher segments in terms of utilities of attributes and subgroups of researchers who have common needs in the three genetic resource sectors. We proposed some policy and strategic implications based on the results of this study.

Safflower is a multi-purpose oilseed crop, primarily known for good quality oil containing highest polyunsaturated fatty acid content (>80%) among edible oils. In this study, a core subset of 148 safflower accessions representing 15 countries, predominantly of Indian origin, was evaluated for agronomic traits and characterized for genetic diversity, population structure and linkage disequilibrium (LD) using 44 simple sequence repeat (SSR) loci across 11 linkage groups to enable its utilization in breeding and genetic mapping purposes. The collection had substantial variation for seed yield-related traits. SSR allelic variation was low as indicated by average number of alleles (3.6) per locus, gene diversity (0.314) and polymorphism information content (0.284). Cluster analysis (neighbour-joining tree) revealed five major genotypic groups with very low bootstrap support. STRUCTURE analysis showed recognizable population structure; based on membership coefficients ( ≥ 0.75), 52% accessions were classified into four populations (K= 4) and the remaining 48% accessions into admixture group. High Fst values (0.30–0.48) suggested that the populations were substantially differentiated. Analysis of molecular variance results showed that maximum of genetic variation (85%) was explained between individuals within the population suggesting that the population structure was only weak. About 1.9% of SSR locus pairs were in LD, which appeared to be low. High phenotypic variation, mild population structure and low level of LD among unlinked loci suggested that the core subset can be explored for association mapping of seed yield components in safflower.

Ex situ seed banks provide an effective conservation and utilization system for crops and their wild relatives. Efforts are made to reduce genetic drift in conservation, where regeneration is a critical step. In the present study, we examined eight wild populations of red clover (Trifolium pratense L.) according to 13 morphological and phenological traits. Samples of original collected seed were grown and compared with plants from first and second ex situ generation, with commercial cultivars and landraces being included for purposes of comparison. Variance analysis and Tukey multiple comparisons of means showed that the commercial cultivars and landraces were clearly distinct from the wild populations and were excluded from the further analysis. Despite the fact that the wild accessions were collected from a geographically delimited region in Norway, they exhibited significant differences in several of the measured traits. The main phenotypic patterns remain after ex situ regenerations. However, the mean values for four of the examined traits (across accessions) did change significantly from one generation to the next. Two of the eight accessions had significantly changed from one generation to the next, a tendency was observed across all the studied traits. The results were discussed in terms of regeneration circumstances. Observed changes appeared to be directional, going from populations with predominantly wild morphological types towards plants more closely resembling the commercial cultivars. Such a directional change implies that selection or gene flow has been acting on the accessions during regeneration, rather than random changes owing to genetic drift.

Safflower is a traditional oilseed crop in the world. Its seed oil is a healthy edible oil containing high amount of unsaturated fatty acids. Genetically diverse exotic cultivars are valuable germplasm for introducing new diversity in safflower improvement programmes. In this study, we characterized safflower cultivars of India (30) and Mexico (23) comprising varieties, hybrids and advanced lines developed over 50 years for genetic distinctiveness using 38 simple sequence repeat (SSR) loci. Genetic diversity estimates across cultivar groups (total, India and Mexico) were as follows: mean number of alleles (3.2, 3.1, 2.6), expected heterozygosity (0.42, 0.37, 0.37) and polymorphism information content (0.36, 0.33, 0.32) respectively, which suggested narrow SSR allelic diversity within and between cultivar groups. However, distance-based cluster analysis (neighbour-joining tree) and model-based STRUCTURE analysis revealed that safflower cultivars of India and Mexico, with the exception of a few, form two genetically distinct groups. High level of genetic variation explained between the populations (40%) and Fst estimate (0.4) suggested that the cultivar groups were highly differentiated with limited gene flow supporting a strong genetic structuring. High oil (~38%) and high oleic (73–79%) contents of a subset of Mexican safflower varieties and advanced lines were confirmed in field trials in India. These exotic sources from Mexico are valuable for safflower breeding programmes in India to develop new cultivars with high oil yielding potential and high oleic acid content, which is the current market demand.

Andean arracacha (Arracacia xanthorrhiza Bancr.) is a valuable but poorly known vegetatively reproduced root crop whose origin is still unresolved. Wild tuberous forms are present in the presumed areas of domestication and have a perennial or monocarpic life history. To elucidate the origin of the cultivated form, we surveyed a molecular analysis with amplified fragment length polymorphisms (AFLPs) in a representative sample of this crop and its wild relatives from Ecuador and Peru, the presumed areas of domestication. Wild species with tuberous and non-tuberous roots were included, as well as the perennial and monocarpic forms of the presumed wild ancestor. While the two wild varieties of A. xanthorrhiza were closest to the cultivars, they were distinguished by AFLPs. Unexpectedly, two clearly distinct groups were formed among the cultivars, one of which was significantly closer to the monocarpic wild form. However, the chloroplast DNA survey revealed greater similarity between all of the cultivars and the wild perennial A. xanthorrhiza. These results combined with the morphological and life history features, confirms the hypothesis that arracacha domestication started from the wild perennial form. We suggest this scenario of domestication followed by an unsuspected introgression in the cultivation, resulting in two cryptic genetic groups, well distinguished at the molecular level. This is an important revelation with implications in genetic resource conservation and breeding standpoints in this promissory crop.

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

Knowledge of pollen movement and frequency of interspecific hybridization in fragmented populations of rare species is a prerequisite for the implementation of conservation measures. In a large-scale study area (14,000 hectares) we analysed 297 Malus sylvestris trees with nine nuclear microsatellite markers. After open pollination of 564 offspring from 51 mother trees located in seven harvesting sites were investigated and genetic paternity analysis was performed. The paternal parent was identified for 213 offspring and the pollen dispersal distances between mother and pollen source were calculated. A large proportion of detected pollination events (42.4%) were observed within a radius of 50 m of the mother tree. The comparison of different tree densities indicated that with decreasing density the pollen dispersal distances increase. We observed pollination over long distances with a maximum of 10.7 km which is probably one of the reasons for a low spatial genetic structure within the M. sylvestris population and a stable genetic diversity in the offspring. Incorporating microsatellite data of 21 apple cultivars, a hybridization frequency of nearly 8% was determined. With decreasing tree density the number of hybridization events increased. Based on the results of our study an enhancement of the density of existing M. sylvestris populations is recommend to reduce the likelihood of hybridization. The production of young plants originated from seeds collected after open pollination is not advisable. Instead of that the seedlings for further reintroduction measures should be produced by controlled crossings in seed orchards to ensure ‘true type’ M. sylvestris individuals.

Drought remains the most important factor that affects rice productivity, especially in rainfed areas, worldwide. Upland rice is one of the crop choices of farmers in the rainfed environment. Although upland rice varieties require less water than lowland rice varieties, yields often remain limited by drought, particularly in the period of early growth. The aims of this study were to identify the traits related to early drought tolerance in upland rice varieties, and to identify the potential sources of germplasm for early drought tolerance. A total of sixty upland rice varieties were planted in a factorial experiment with a randomized complete block design with 3 replications in the rainy seasons of 2011 and 2012, under greenhouse conditions. Based on the drought tolerance index (DTI), the test germplasm sources were classified into three groups: (i) susceptible; (ii) moderately tolerant; (iii) tolerant to drought stress. Grain yield (GY) showed significant negative correlations with the leaf rolling score (r= − 0.623, P< 0.01), the leaf death score (LDS) (r= − 0.673, P< 0.01) and the recovery score (r= − 0.746, P< 0.01), while leaf dry matter (r= 0.698, P< 0.01) and leaf water potential (r= 0.618, P< 0.01) had significant positive correlations with GY. These findings indicate the suitability of the DTI as the selection criteria for early drought tolerance in a breeding programme. In addition, the upland rice germplasm accessions KKU-ULR011, KKU-ULR012, KKU-ULR125, KKU-ULR199 and KKU-ULR292 were identified as having high levels of stability for drought tolerance in both the 2011 and 2012 experiments, suggesting their potential for further use for rice variety improvement for drought tolerance.

Brassica species have an economic and medicinal importance. Estimation of the amount and distribution of genetic diversity within Brassica species is essential for establishing efficient management, conservation and breeding practices. This review discusses the taxonomy, gene pool, and Brassica-derived phytochemicals and their nutraceutical importance. It also surveys the recently advanced studies of the genetic diversity and phylogenetic studies of Brassica species at the level of morphological, cytological, biochemical and molecular markers that have proven to be useful for evaluating the genetic variation, taxonomic relationships and species identity, and could be useful for improving Brassica crops through future promising breeding programmes.

Seedling emergence is the preliminary factor defining wheat adaptability and stability under salt stress. This study was led to assess the salinity tolerance amongst 226 synthetic hexaploid wheats (SHWs) evaluated against two check cultivars, the tolerant ‘S-24’ and the susceptible ‘PBW-343’ at three sodium chloride treatments (0, 100 and 200 mM). Highly significant and positive correlation was observed between germination % and germination index (r = 0.85), and between seedling height and weight (r = 0.85). All four traits across three treatments were transformed into the salt tolerance trait index and salt tolerance index (STI). STI had significant positive correlation with all four parameters indicating reliability of this index for ranking the tolerance levels. STI-based 20 best performing genotypes were known as being promising candidates for wheat breeding. Local tolerant check was amongst the top three tolerant accessions. Two SHWs, AUS30288 {Croc_1/Aegilops squarrosa (466)} and AUS34444 {Ceta/Ae. squarrosa (872)} outperformed S-24 with STI of 61.8 and 55.7, respectively. SHW with same durum parents were included in tolerant and susceptible categories indicating that tolerance is contributed by the Ae. squarrosa syn. tauschii parent of SHWs. In conclusion, this baseline study revealed that continuous variation in the seedling emergence traits under salt stress is a conduit towards implementing genome-wide association studies. Likewise, new diversity has implications in development of salt tolerance germplasm after genetic dissection permitting unique Ae. squarrosa accessional diversity validation to target SHW donors for breeding.

Yams (Dioscorea spp.) are one of the main root and tuber crops in the world, especially within the species complex Dioscorea cayenensis/D. rotundata. Few studies have been conducted in Brazil with these species, including genetic diversity. The objective of this study was to characterize the genetic diversity of local varieties of D. cayenensis and D. rotundata using morphological and molecular markers, and provide information on the management and use of the crop by family farmers from different regions in Brazil. Thus, yam tubers were sampled from several municipalities in the South, Southeast and Northeast regions. Eighteen morphological traits and ten microsatellite loci were used to analyse 47 yam accessions (23 D. cayenensis and 24 D. rotundata). Species identification was carried out after field morphological evaluation. Spatial genetic analysis indicated significant structure among the local varieties, mostly between regions and species. Both cluster and Bayesian analyses showed a separation of the accessions into two distinct groups: group I with accessions originated from the Southeast region and group II with accessions originated from the Northeast region, while accessions from the South region were intermediate or included in either group. The results showed a separation between D. cayenensis and D. rotundata accessions in Brazil, and that D. cayenensis occurs predominantly in the Southeast region, while D. rotundata occurs in the Northeast region. Further studies with larger sampling would be welcome in order to confirm these findings. Also, this study highlights the importance of family farmers in the genetic diversity conservation of these species in Brazil.

Molecular variability of vanilla (Vanilla planifolia) and three wild species was assessed to explore the possible sources of variation that can be used for crop improvement. A total of 154 ISSR loci were analysed by the UPGMA, assignment tests of individuals (STRUCTURE) and indices of genetic diversity. The assignment tests were done at two levels: first considering the four species and then only the accessions of V. planifolia. The molecular analysis indicated 99.3% polymorphism among all species and 70.45% within V. planifolia. The UPGMA showed the separation of these four species into three groups and grouped V. planifolia accessions into three subgroups. The more genetically differentiated accessions were of the Rayada morphotype and a wild accession was from Oaxaca, followed by a wild accession from Quintana Roo; all the commercial accessions of V. planifolia (Mansa morphotype) were grouped together. The STRUCTURE analysis differentiated between V. planifolia and the three wild species, and among the accessions of the Mansa and Rayada morphotypes and the wild accessions. The STRUCTURE analysis also indicated the presence of mixed individuals. These results are of great importance since the accessions of V. planifolia that are genetically more differentiated are the most threatened due to the scarcity of these individuals, the destruction of habitat and replacement by the commercial morphotype. These individuals should be salvaged and used to expand the genetic background of vanilla.

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

About 40% of the global arable land is acidic, and in India, majority of these acidic soils are in the north-eastern region. Soil acidity leads to high phosphorus (P) fixation that causes P deficiency; therefore, there is a need to characterize the identified potential donors for acidic soils for P-deficiency tolerance. We evaluated rice genotypes for nucleotide variation in two loci reported for low P tolerance, namely PSTOL1 and PupK20-2. Sequence comparison for PSTOL1 revealed two distinct haplotypes. Genotypes with higher P uptake such as LR 19 and LR 23 had the desired Kasalath-type haplotype, whereas those with lower P uptake such as UR 29 and LR 39 showed a mixed haplotype. A total of four novel nucleotide variations were observed in 3′-UTR (untranslated region). Sequencing of PupK20-2 revealed a total of 28 SNPs and one insertion–deletion, of which 24 SNPs were novel. The discovery of novel SNPs across both PSTOL1 and PupK20-2 suggests the existence of novel haplotypes in genotypes adapted to acidic soil conditions. We reported for the first time the characterization of the donors being used in breeding programmes for acidic soils at the molecular level. The implications in breeding programmes are discussed.

Identification and characterization of the farmers’ named crop varieties cultivated around the world is a major issue for conservation and sustainable use of plant genetic resources. Intraspecific diversity is strongly determined by farmers’ socio-cultural environment, but this has little been documented. In this paper, we tested, on a contact zone among three ethnolinguistic groups located on the Mount Kenya region, whether farmers’ socio-cultural differences have an impact on the morphological characteristics of the farmers’ named sorghum varieties. Eighteen qualitative morphological traits of the panicles were measured. We first compared the morphological diversity of the named varieties among ethnolinguistic groups using multivariate analysis of homogeneity of groups’ dispersion and tested their differentiation using permutational multivariate analysis of variance. Discriminant analysis of principal components was then used to categorize the morphological diversity without a priori, and this classification was compared with farmers’ local taxonomy (vernacular names) in the three ethnolinguistic groups. Our results show that some morphotypes are peculiar to some ethnolinguistic groups and that a morphotype can bear different variety names while the same variety name can be used to identify different morphotypes. Morphological differentiation that was explained by ethnolinguistic groups was higher for local landraces than for improved varieties. Our findings imply that socio-cultural diversity of farmers and the criteria they use to identify and maintain landraces need to be considered in studying and sampling crop diversity for in situ as well as for ex situ conservation.

A total of 27 accessions from ten Vicia species were investigated for flavonoid contents, total polyphenol contents, and DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS [2,2′-azinobis(3-ethylbenzothiazoline 6-sulfonic acid)] free radical-scavenging activities. The results revealed that NAC17 (V. monantha) and NAC14 (V. hyrcanica) had the highest total flavonoid content (1.42 ± 0.09 mg/g) and total polyphenol content [124.2 ± 0.5 μg/gallic acid equivalents (GAE) mg], respectively. Among four flavonoids, naringenin was detected at high concentrations in Vicia species. The DPPH and ABTS assays showed values in the range of 57.2 (IC50) (NAC13, V. faba) to 6530.0 (IC50) (NAC24, V. sativa subsp. nigra) and 19.1 μg/Trolox mg (NAC7, V. cracca) to 253.4 μg/Trolox mg (NAC13, V. faba), respectively. Among ten Vicia species, V. monantha and V. hyrcanica had the highest flavonoid content (1.31 ± 0.09 mg/g) and total polyphenol content (116.5 ± 2.0 μg/GAE mg), respectively. The highest antioxidant activity was detected in V. faba. These results will expand the flavonoid database and provide valuable information on Vicia species for the development of functional foods or feed-additive resources.

A study was carried out between 2008 and 2011 to investigate the potential risks of gene flow and its consequences in the crop–wild–weed S. bicolor complex in Ethiopia to aid efforts to conserve genetic diversity. Morphological measurements and genomic DNA samples were taken in situ from 30 wild and eight cultivated populations representing a total of 760 samples from five regions. Genetic diversity, gene flow, population structure and outcrossing rates of wild populations were computed using phenotypic measurements and/or polymorphic simple sequence repeat (SSR) markers. Moreover, morphological analyses of fitness of crop–wild hybrids were studied. High diversity was observed among the wild/weedy sorghum populations for phenotypic traits and SSRs. SSR diversity was high in both wild and cultivated populations, but the magnitude was greater in the former. Gene flow between the wild and the cultivated sorghum was observed to be higher than that within either pool. Wild sorghums exhibited variation in the multilocus outcrossing rate (range = 0.31–0.65) and fitness was not compromised in most wild × crop hybrids. The study indicated that crop-to-wild gene flow is possible in Ethiopia. Thus, genes from transgenic sorghum are expected to enter into the wild and non-transgenic cultivated populations and may spread and persist, if transgenic sorghum is deployed in Ethiopia and in other countries of Africa, which may pose risk of introduction of unwanted effects, which in turn may lead to loss of genetic diversity.

Knowledge on genetic diversity is necessary to determine the relationships among the genotypes, which allow the selection of individual accessions for crop breeding programmes. The present study aimed at assessing the extent and pattern of genetic diversity within a set of 251 sorghum genotypes using SSR markers. A total of 393 alleles were detected from the 251 genotypes, with the number of alleles ranging from 2 (Xcup11) to 24 (Sb5-206) and an average of 10.07 alleles per primer pair. Pairwise Wright's FST statistic and Nei's genetic distance estimates revealed that the race and geographical origin were responsible for the pattern of diversity and structure in the genetic materials. In addition, the analysis also revealed high genetic differentiation between the rainy and post-rainy sorghum groups. Narrow diversity was observed among the different working groups in the rainy (restorers and varieties) and post-rainy (varieties and advanced breeding lines) sorghum groups. Neighbour-joining and STRUCTURE analysis also classified 44 elite lines broadly into two distinct groups (rainy and post-rainy). However, limited diversity within the rainy and post-rainy sorghum groups warranted an urgent need for the utilization of diverse germplasm accessions for broadening the genetic base of the Indian breeding programme. The diverse germplasm accessions identified from the mini-core accessions for utilization in breeding programmes are discussed.

Ultra-dry storage, storing orthodox seeds at ambient temperatures with moisture contents below 5%, can maintain seed viability for long periods with low input. Optimum moisture contents for ultra-dry storage exist and vary substantially among different seed lots due to their differences in desiccation tolerance, which is associated with the accumulation of protective compounds. To study the relationship between moisture contents of ultra-dry stored species, seed composition and the free-radical scavenging activity (FRSA). Eleven seed lots of maize, wheat, pepper, peanut, Chinese cabbage, and cucumber were chosen and multiple stepwise regression analysis was applied. In general, analysis of the seed lots revealed that optimum moisture contents for highest seed viability are below equilibrium moisture at 13% relative humidity and 20°C. Nevertheless, seed composition differed significantly among species. Lipids, flavonoids and the FRSA were significantly negatively correlated with the optimum moisture content of ultra-dry stored whole seeds and accounted for 97.7% of the total variation in the optimum moisture content. Lipids had the highest effect (90.0%) on the optimum moisture content of ultra-dry storage, which is consistent with the previous results. The FRSA and flavonoids accounted for 4.8 and 2.9% of total variation of optimum moisture content of ultra-dry stored whole seeds, respectively. The FRSA and flavonoids were also significantly negatively correlated with the optimum moisture content for non-lipid fraction of ultra-dry stored seeds, and accounted for 74.1 and 15.3% of the total variation in the optimum moisture content, respectively.