Annual wild soybean characterized with more number of branches and pods may contain favourable exotic genes/alleles for improving the yield potential of cultivated soybeans. To evaluate the wild alleles/segments, the chromosome segment substitution line population SojaCSSLP3 comprising 158 lines with N24852 (wild) as the donor and NN1138-2 (cultivated) as the recurrent parent was tested under three environments. The phenotypic data along with 198 simple sequence repeat markers were analysed for qualitative trait loci (QTL)/segments associated with the number of branches on the main stem (BN) and number of pods per plant (PN) using the inclusive composite interval mapping procedure (RSTEP-LRT-ADD model) of ICIM version 3.0. The analysis was carried out for individual environments due to a significant G × E interaction. A total of eight QTL/segments associated with BN and eight QTL/segments associated with PN were detected under the three environments, with all the wild segments having positive effects. Among these, two QTL/segments for each of the two traits could be detected under two or three environments and three QTL/segments could be detected for both traits. Four QTL/segments associated with BN and one QTL/segment associated with PN were identified only in SojaCSSLP3, not reported for cultivated crosses in the literature. The detected wild segments may provide materials for further characterization, cloning and pyramiding of the alleles conferring the two traits.

Millefolii herba is one of the oldest and most important drugs in Lithuania, used both in folk and official medicine. The raw material is usually gathered from spontaneous populations. It would be reasonable to develop methods to identify the populations which produce high plant biomass and accumulate high levels of proazulenes. The quantitative variation of proazulenes and their relationships with phytosociological dependence and morphological characters of Achillea millefolium from wild populations has been examined. The vegetation records were made at 140 growing sites of A. millefolium. The species was found in 29 types of community representing different growing habitats. The resources of milfoils prevailed in dry grasslands of Arrhenatheretalia communities and ruderal habitats of Dauco-Meliliotion. The data on productivity and morphological characters were subjected to multivariate statistical analysis. A hierarchical cluster analysis indicated that higher productivity of A. millefolium populations was associated with their dependence on ruderal and segetal communities. The testing of A. millefolium plants revealed high variation for proazulenes in different communities. The proazulene-containing plants have been identified in 38% of all analysed cases. In the highest segetal and wasteland communities of Agropyretalia repentis, Sisybietalia, Digitario-Setarion, Aperion spicae-venti, Senecion fluviatilis only proazulene-free plants were found. Results of the ANOVA showed the proazulene-containing and proazulene-free plants significantly differed (P<0.05) for width of leaves and number of nodes. The presence of nodes in high number and narrow leaves in high proazulene-containing plants distinctly marked them from the proazulene-free plants. The study raised the possibility that selection based on the two morphological marker traits (node number and leaf width) and proazulene distribution in the populations would be effective for rapid identification of highly productive population(s) of pharmaceutical importance.

To date, very limited molecular knowledge and molecular tools are available on grass pea (Lathyrus sativus L.). Herein, we present a genetic diversity analysis of 20 grass pea accessions collected from various regions of Ethiopia by means of seven newly developed Lathyrus expressed sequence tag-derived simple sequence repeat (EST-SSR) markers and four cross-transferable EST-SSRs derived from Medicago truncatula L. Forty-five alleles were detected among all the analyzed accessions. The number of alleles/locus ranged from two to seven with an average of four alleles/locus. The observed heterozygosity (Ho) ranged from 0.320 to 0.504, while the expected heterozygosity (He) ranged from 0.354 to 0.470. FST values estimated by analysis of molecular variance were 0.01, 0.15 and 0.84 for among regions, among accessions and within accessions, respectively, indicating that most of the variation (84%) resides within accession. The model-based cluster analysis grouped the accessions into three clusters grouping accessions, irrespective of their collection regions.

Rice is a salt-sensitive species with enormous genetic variation for salt tolerance hidden in its germplasm pool. The EcoTILLING technique allows us to assign haplotypes, thus reducing the number of accessions to be sequenced, becoming a cost-effective, time-saving and high-throughput method, ideal to be used in laboratories with limited financial resources. Aiming to find alleles associated with salinity tolerance, we are currently using the EcoTILLING technique to detect single nucleotide polymorphisms (SNPs) and small indels across 375 germplasm accessions representing the diversity available in domesticated rice. We are targeting several genes known to be involved in salt stress signal transduction (OsCPK17) or tolerance mechanisms (SalT). So far, we found a total of 15 and 23 representative SNPs or indels in OsCPK17 and SalT, respectively. These natural allelic variants are mostly located in 3′-untranslated region, thus opening a new path for studying their potential contribution to the regulation of gene expression and possible role in salt tolerance.

Fonio (Digitaria exilis (Kippist) Stapf) and Bambara groundnut (Vigna subterranea (L.) Verdc.) are native crops grown at a small scale in Mali that have potential to support agricultural productivity under climate change. A community biodiversity management approach was explored in this study as a means to reinforce the cultivation of these crops by increasing farmers' access to intraspecific diversity and developing capacities of community institutions for their management. The research involved six communities in Ségou and Sikasso regions. Multiple varieties of fonio (10–12) and Bambara groundnut (8–12) were established in diversity fields in each site over 2 years where farmers engaged in experiential learning over the crop cycle. Significant adoption of fonio and Bambara groundnut was detected in several study sites. The precise drivers of adoption cannot be definitively determined but likely include increased seed access and awareness gained through the diversity field fora, seed fairs and community seed banks. No significant yield advantage was detected for any of the varieties in the diversity fields, which showed variable performance by site and year. The number of varieties registered and managed by community seed banks in each site increased from 1–5 varieties of each crop to 11–12 varieties following the interventions. The number of Bambara groundnut varieties cultivated in farmers' fields also increased, while there was evidence of a slight decline in fonio diversity in some communities. The results of this study can inform efforts to strengthen seed systems and cultivation of neglected and underutilized species in Africa.

The dwarfing wheat (Triticum aestivum L.) breeding has promoted a dramatic increase in yields. Since the utilized dwarfing genes in wheat are very limited, identification of novel dwarfing genes is necessary for improving the genetic diversity of wheat. In this study, more than 300 dwarfing wheat lines from induced mutation were screened by kompetitive allele-specific PCR and gibberellin (GA) treatment. The 17.49% of Rht-D1b and 1.37% of Rht-B1b dwarfing mutants were identified in this mutant group. Additionally, Rht-D1b mutants showed more effective in reduction of plant height and higher 1000-grain weight comparing with that of Rht-B1b mutants. By combing with comparison of yield components and expression profile of GA biosynthetic genes with wild-type, the GA-responsive mutant dm15 without directly involvement in GA metabolism, significantly increased 1000-grain weight but no change of other yield components in two locations of field experiments. Meanwhile, another elite mutant dm11 with change of GA biosynthetic genes expression was also identified. These mutants will be promising candidates for dwarfing wheat breeding.

Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

Here we review the potential of ILB 938 (IG 12132 – doi: 10.18730/60FD2), a unique faba bean accession originating from the Andean region of Colombia and Ecuador, maintained at ICARDA – International Center for Agricultural Research in the Dry Areas, with resistance to multiple biotic and abiotic stresses and carrying some useful morphological markers. It has been used as a donor of leaf-related drought adaptation traits and chocolate spot (Botrytis fabae) resistance genes in faba bean breeding programmes worldwide. From generated populations of recombinant inbred lines, quantitative traits loci associated with these useful traits have been mapped. Other markers, such as a lack of stipule-spot pigmentation and clinging pod wall, show the presence of unusual changes in biochemical pathways that may have economic value in the future.

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.

To reduce the level of redundancy in a collection of cultivated lettuce, data from 160 amplified fragment length polymorphism (AFLP) fragments and 10 polymorphic microsatellites were used in combination with passport data and morphological data, the latter obtained from an experimental field trial performed for verification purposes. Based on the observed distribution of the number of marker differences between and within accessions, a minimum of three AFLP differences and two microsatellite differences were regarded as levels warranting distinction between accessions in the redundancy analysis. The strategy followed in the redundancy analysis was mainly based on the confirmation of duplication by each of two independently generated data sources. The molecular data were used for the validation as well as the identification of potential duplicates, revealing a total number of 198 redundancies, corresponding to 12.9% of the total collection. Trueness to type, number of characterization and evaluation data, and collection management considerations, such as available seed quantities and germination percentages, were used as primary, secondary and tertiary criteria to decide which accession from duplication groups to maintain in the collection. Removal of accessions showed negligible effects on total collection diversity, as quantified for AFLPs and microsatellites, characterization and evaluation traits and resistance profiles against downy mildew pathotypes, indicating that the applied strategy was effective.

The sequence-specific amplified polymorphism (S-SAP) method was used to genotype 198 Nordic bread wheat landraces and cultivars from the 19th to the 21st centuries. It was shown that the Sukkula-9900-LARD retrotransposon primer was highly suitable for resolving closely related wheat materials. Cluster analysis was generally consistent with pedigree information and revealed a clear separation for growth habit but not for countries. A principal coordinates analysis (PCoA) showed a separation into different time periods (before 1910, 1910–1969 and 1970–2003). These results are consistent with the breeding history and pedigree information, indicating that little hybridization has occurred between winter and spring wheat, in contrast to frequent exchange of germplasm between the Nordic countries. Estimates of gene diversity, the PCoA results, and changes in band frequencies across time indicate that plant breeding has led to substantial genetic shifts in Nordic wheat. Diversity was reduced through selections from landraces during the early 20th century, followed by a period of relatively lower genetic diversity, and a subsequent increase and net gains in diversity from the late 1960s onwards through the use of exotic germplasm. Thus, an anticipated loss of overall genetic diversity was found to be negligible, although allele losses have occurred at specific loci.

In recent years, there has been an increased interest in Europe and in the USA in grafting watermelon onto bottle gourd, Lagenaria siceraria (Mol.) Standl. In this study, genetic diversity and relationships were examined [using 236 sequence-related amplified polymorphism markers] among 56 United States plant introductions (PIs) of L. siceraria and PIs of important cucurbit crops [including Cucurbita maxima Duchesne (winter squash), Cucurbita pepo L. (squash and pumpkin), Citrullus spp. (watermelon), Cucumis melo L. (melon) and Cucumis sativus L. (cucumber)]. The analysis showed that L. siceraria is distinct and has similar genetic distances to the cucurbit species examined herein. The L. siceraria PIs were assembled into two major clusters. One cluster includes groups of PIs collected mostly in South Asia (India) and a few PIs collected in the Mediterranean region and in Northeast Africa. The second cluster includes groups of PIs collected mainly in Southern Africa and in North, Central and South America, and PIs collected in China, Indonesia and Cyprus. All L. siceraria PIs in this study were susceptible to the southern root-knot nematode (RKN) [Meloidogyne incognita (Kofoid and White) Sandground]. However, several PIs, among them a group of closely related PIs collected in Mexico and Florida, were less infected with southern RKNs. All L. siceraria PIs were infested with whiteflies [Bemisia tabaci (Gennadius)], while several PIs were less infested than others and need further evaluation and selection for developing breeding lines that may be less appealing to this pest. Most of the PIs that showed resistance to zucchini yellow mosaic virus and tolerance to powdery mildew were collected in India and belong to the same phylogenetic groups (PGs). Experiments with L. siceraria PIs representing different PGs showed similar grafting compatibility with watermelon. Findings from this study should be useful for the development of superior L. siceraria rootstock lines with enhanced resistance to diseases and insect pests of cucurbit crops.

Molecular investigations of qualitative and quantitative changes in the genetic diversity of cultivated crops are useful for plant breeding and the management of crop genetic resources. A genotyping study, based on 28 genomic (g-SSR) and 13 expressed sequence tag-derived (e-SSR) microsatellite markers uniformly distributed across the barley genome, was conducted on samples of cultivated barley (Hordeum vulgare L.) collected at intervals of 40–50 years in three comparable geographical regions in Austria, Albania and India. The analysis indicated an absence of any significant differences either in the total number of alleles per locus or in g-SSR and e-SSR polymorphic information content (PIC) values from the Indian and Austrian materials. However, a slight reduction in genetic diversity was noted among the materials collected in Albania. The trend in numbers of collection mission-specific SSR alleles suggests significant allele flow over the time interval sampled. The g-SSRs yielded a higher mean number of alleles per locus and a superior PIC than the e-SSR markers. We conclude that a qualitative, rather than a quantitative shift in diversity has taken place over time, and that g-SSR markers detect more diversity than do e-SSR markers.

A coiled coil-nucleotide binding site-leucine-rich repeat gene RB/Rpi-blb1 isolated from Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans and is currently employed in potato breeding for durable late blight (LB) resistance. RB homologues were reported in several Solanum species; some of them retained defence function. Here, we report additional evidence on RB-like sequences in 21 Solanum species of the section Petota. The panel of Solanum species was screened with three RB-related PCR markers. RB-like sequences were found in every tested Solanum accession, suggesting universal distribution of RB structural homologues among Solanum genomes, while locus-specific RB-629 was found only in 15 species. Phylogenetic analysis of RB-629 sequences suggested a highly conservative pattern of polymorphisms that was neither species- nor series-specific. Apparently, duplication and evolution of RB-like loci preceded Solanum speciation. Marker presence and particular haplotypes were not immediately associated with high LB resistance.

Development of core collection representing the diversity in the entire germplasm creates a better access and enhanced utilization of the main collection thus allowing rapid evaluation in crop improvement programs. Core collections are dynamic in nature and needs revisiting when additional germplasm and information becomes available. In the current study, an attempt was made to re-define the previously developed yam (Dioscorea spp) core collection using 56 morphological traits. Information on additional acquired germplasm and presence of duplicates or mislabelled accessions in the entire collection was also used. The re-defined core collection consisted of 843 accessions and represented about 20% of the entire collection. It included six Dioscorea species, of which accessions of Dioscorea rotundata are in the majority (73.54%) followed by Dioscorea alata (21.35%), Dioscorea bulbifera (1.66%), Dioscorea cayenensis (1.42%), Dioscorea dumetorum (1.42%) and Dioscorea esculenta (0.59%). The Shannon weaver diversity index and principal component analysis revealed the maximum diversity captured in the core from the base collection. This re-defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in yam improvement programs.

Legume flavonoids have received considerable attention due to their beneficial effects on human health. Flavonoid content in the seeds of 36 germplasm accessions of guar [Cyamopsis tetragonoloba (L.) Taub.] was quantified by high-performance liquid chromatography (HPLC). On a per 100 g basis, the seed contained, on average, 1.114 mg (0–2.355) daidzein, 0.700 mg (0–1.685) genistein, 0.553 mg (0–1.250) quercetin and 14.460 mg (10.70–19.82) kaempferol. A significant positive correlation was observed between the content of daidzein and genistein; however, significant negative correlations existed between the content of kaempferol and daidzein and of kaempferol and genistein. Compared to soybean seeds, guar seeds contained very low amounts of daidzein and genistein, but a high amount of kaempferol. The information about the levels of flavonoids in guar seeds will be useful to breeding programmes for improving guar seed quality. Furthermore, the high kaempferol content of guar seeds may expand its nutraceutical and pharmaceutical utilization.

Periwinkle [Catharanthus roseus (L) G. Don] has become one of the very extensively investigated medicinal plants after the discovery of two powerful anti-cancer alkaloids, vinblastine and vincristine, in its leaves more than 50 years ago. These alkaloidal drugs are still in clinical use. Also, periwinkle is still the only source of these alkaloids and their precursors, catharanthine and vindoline. Low concentrations of these alkaloids in the plant and, therefore, high costs of their extraction have led to tremendous efforts towards understanding their biosynthesis and exploration of alternate ways of their production such as, chemical synthesis, cell, tissue and hairy root cultures, and metabolic engineering of heterologous organisms. Literature on this plant is quite voluminous, with an average of about 80 publications per year during last three decades (1985–2015). Nearly 60% of these publications are on physiology, biochemistry, cell and tissue culture, phytochemistry, metabolic and genetic engineering aspects. In spite of these efforts, an economically viable alternative to field-grown periwinkle plants as a source of these alkaloids has not yet been found. Biosynthesis of C. roseus alkaloids is a complex process involving many genes, enzymes, regulators, inter- and intra-cellular transporters, cell types, organelles and tissues and its current understanding is still considered to be incomplete to produce C. roseus alkaloids through metabolic engineering/synthetic biology. Till such time, breeding periwinkle varieties with higher concentrations of anti-cancer alkaloids for cultivation can be an alternate approach to meet the demand for these alkaloids and reduce their costs. While literature on cell and tissue culture, phytochemistry, metabolic and genetic engineering aspects of periwinkle has been reviewed periodically, crop production and plant breeding aspects have received little attention. In this paper, an attempt has been made to bring together published information on genetics and breeding of periwinkle as a medicinal plant. Some probable constraints which may have hindered taking up periwinkle breeding are identified. Initially, quite a few attempts have been made at genetic improvement of periwinkle through induced polyploidy, and subsequently through induced mutagenesis. Mutations, both natural and induced, provide a valuable resource for use in breeding and in functional and reverse genomics research. It is only during last 6–7 years, genetic diversity has been assessed using molecular markers and very recently molecular markers have been identified for marker-assisted selection for alkaloid yield.

Mineral concentration levels in cultivated vegetables have received very little concern in the context of biodiversity despite the fact that most vegetables have a rich micronutrient composition. Swiss chard is an important salad crop which is high yielding and rich in minerals, vitamins and phenolic compounds. It is also extremely easy to grow. However, there is a lack of information on the genetic variability of mineral concentration of Swiss chard. Mineral composition diversity of 54 genetically diverse Swiss chard accessions, representative of all Turkish Swiss chard genetic resources, was investigated using multivariate analysis. These traits are useful in evaluating germplasm diversity in the nutritional concentration context and for use in further breeding programmes which will focus on improving mineral concentrations in Swiss chard cultivars. The results displayed significant differences among accessions and remarkably high nutrient contents. The data gathered were analyzed using principal components (PCs) and cluster analysis and revealed five major groupings. The data also observed 74.39% of total variation. The first three PCs accounted for 49.86% of the total variation in the population. Present values provided great variability among accessions and the results demonstrate that it is possible to identify genetic differentiation among Swiss chard accession for some nutritional elements. The genetic resources that exist indicate that potentially important accessions could be used as a gene source due to their high levels of K, Ca, Cu and Zn in breeding programmes.