Yellow mosaic disease (YMD) caused by mungbean yellow mosaic virus (MYMV) is one of the most destructive biotic production constraints in mungbean. Development and introduction of resistant cultivars are considered as the most economical and eco-friendly option to manage YMD, for which availability of stable sources of resistance is a pre-requisite. A set of 14 mungbean genotypes including a susceptible check were evaluated for responses to YMD under natural infection across three seasons and under challenged inoculation in glasshouse for one season. None of the genotypes were immune to YMD and produced different degrees of response to MYMV in terms of yellow mosaic symptoms (YMS). Based on the delayed appearance of initial YMS, and lower estimates of per cent disease index and area under disease progressive curve (AUDPC) in response to natural infection and challenged inoculation, five genotypes namely AVMU 1698, AVMU 1699, AVMU 16100, AVMU 16101 and KPS 2 were identified as resistant to YMD. Failure of detection of MYMV through polymerase chain reaction (PCR) using MYMV coat protein gene-specific primer and successful detection of the same through rolling circle amplification-PCR suggested latent infection of MYMV in resistant genotypes. The resistance response of the five genotypes could be attributed to enhanced activities of enzymes such as peroxidase, polyphenol oxidase and phenylalanine ammonia lyase and increased concentration of total phenols. These results are discussed in relation to strategies to breed mungbean for resistance to YMD.

Given the increasing importance of data quality for the ex situ conservation and utilization of plant genetic resources (PGR), an indicator was created that quantifies the level of completeness of passport data. This passport data completeness index (PDCI) uses the presence or absence of data points in the documentation of a genebank accession, taking into account the presence or value of other data points. For example, a wild accession should have a well-defined collection site but no variety name. Any type of accession, wild, landrace, breeding material or modern variety, can attain a maximal score of ten for this index. The applicability of this index was tested on the complete contents of EURISCO, the European catalogue of ex situ maintained PGR containing over one million records. Analysis of the PDCI of the material in EURISCO provided valuable insight in the data quality of European collections. The PDCI can be used to identify datasets that might need additional attention and improvement or datasets that need more careful interpretation than others.

Climate change forecasts point to increased frequency of droughts which may affect plant growth. For protein crops such as lentil, genetic improvement of both water use and drought tolerance is necessary. Wild lentil species are known to have evolved in drought prone areas and can be introgressed into cultivated lentil, making them candidates for the evaluation of high transpiration efficiency (TE) and drought tolerance. We assessed TE, water use and drought tolerance at the plant level for five wild lentil species and in cultivated lentil. Under fully watered and moderate drought conditions, wild lentil genotypes consumed significantly less water to fix similar or more dry matter compared with their cultivated counterparts. Under severe drought conditions, the wild lentil genotype L. ervoides IG 72815 had significantly higher TE compared with L. culinaris Eston. Lens ervoides L-01-827A, had significantly higher yield compared with all other species in the presence or absence of drought and showed significantly higher (α = 5%) TE under moderate drought. Drought susceptibility index was identified as a tool to identify drought-tolerant lentil genotypes grown under severe drought. The numerous small seeds of wild lentil made it difficult to estimate drought indices that are weight based and require formulae that incorporate seed numbers.

Comprehensive screening of rice (Oryza sativa L. subsp. japonica Kato) germplasm resources with different nitrogen (N) efficiency levels is effective for improving N use efficiency (NUE) while reducing pollution and providing high quality, yield, and efficiency agriculture. We investigated 14 indices of 38 varieties under three N application levels to assess differences among genotypes. Rice varieties were classified for screening and identifying N efficient. Descriptive statistical analysis results indicated significant differences in relative yield, and also in NUE indices (agronomic utilization rate and partial productivity of N fertilizer). The genotype main effects and genotype–environment interaction effects (GGE) biplot analysis was used to evaluate suitable varieties, compare the stable and high yield capabilities of different varieties, find the ideal variety, and describe the correlation, discrimination and representativeness of the indices under different N application levels. Descriptive statistical, discrimitiveness and representativeness and factor analysis were used to select indices, in which the panicle number per plant and soil and plant analyzer development (SPAD) value were the key indices for evaluation and identification. Heatmap and hierarchical cluster analysis based on the average value of evaluation indices, and scatter plot based on the comprehensive value of N efficiency (P) according to formula showed that all varieties could be divided into five types under different N treatments. Our findings work toward developing N efficient rice varieties to improve NUE, reduce N fertilizer application and thus N waste, consequently mitigating the effects of rice production on the environment to ensure food security and sustainable agricultural development.

Miscanthus is a promising bioenergy crop due to its high productivity and broad environmental adaptability to tropical and temperate climates. As important Miscanthus species such as M. sinensis and M. sacchariflorus are native to East Asia, implying more diverse Miscanthus genetic resources in this region, in this study, we collected about 300 Miscanthus accessions from East Asia, mainly in Korea. From the whole collections, 66 Miscanthus accessions representing geographical location and latitude were selected and tested through a 3-year field trial to investigate genetic diversity in their agronomic traits. Five agronomic traits associated with biomass production were assessed to investigate the relationships of agronomic traits with biomass yield and latitudes of locations where Miscanthus accessions were collected. Plant height, stem diameter, stem dry weight and heading date exhibited a significantly positive correlation with biomass yield with r= 0.465, 0.780, 0.817 and 0.450, respectively. Stem diameter (r= − 0.495), stem dry weight (r= − 0.393), heading date (r= − 0.914) and estimated yield (r= − 0.425) exhibited a significantly negative correlation with latitudes of the collection sites. The results of the study revealed the existence of considerable genetic diversity in agronomic traits in the Miscanthus accessions collected. The presence of a significant relationship between latitudes and agronomic traits suggests that accessions collected from different geographical latitudes will provide more genetically diverse materials for breeding. Therefore, the results of the present study can provide useful information and materials for Miscanthus breeding programmes.

Low temperature is a major constraint for crop productivity. To cope with this challenge, plants have developed several mechanisms to adapt to low temperature. Developing breeding strategies to enhance cold stress tolerance in crops requires an understanding of the mechanisms by which plants perceive and transmit cold stress-related signals to their cellular machinery, thereby activating adaptive responses. Only one quantitative trait locus for tolerance to low-temperature germination, qLTG3-1, has been narrowed down to the gene level in rice. A 71 bp indel that can be used to distinguish between tolerant and susceptible parents has been identified. We tested the 71 bp indel on 65 diverse rice genotypes including those adapted to colder climates of North and Northeastern India to find evidence of the tolerant allele (insertion) and to see whether it is associated with low-temperature germinability in these genotypes. Our results show that 48% of the rice genotypes tested carried the tolerant allele. The insertion was found to be significantly associated with cold tolerance during germination. Moreover, several landraces/improved varieties known for their superior performance in other abiotic stress conditions such as drought and high salinity conditions, and which were previously never exposed to low temperature, carry the beneficial allele for qLTG3-1, suggesting an additional role of this allele in adverse climatic conditions. This study enhances current understanding of the distribution of the tolerant allele qLTG3-1 in rice germplasm, which could help in the identification of suitable donors for potential marker-assisted breeding programmes.

Momordica charantia L. (Cucurbitaceae) is a commonly cultivated functional food plant. In the present study, karyological variation among 34 accessions of M. charantia originating from the Indian subcontinent (Bangladesh, India and Pakistan) and Thailand was evaluated. Ploidy levels ranging from diploid (2n= 22) to hexaploid (2n= 66) were observed. Hexaploidy in M. charantia is reported herein for the first time. Chromosome length ranged from 0.8 to 2.9 μm. The hexaploid accessions had submetacentric and subtelocentric chromosomes. All accessions harboured median and submedian chromosomes. Only one hexaploid accession (TOT1140) had chromosomes with subterminal centromeres. There was considerable variation in chromosome length and chromosome arm ratio.

Seeds of 15 diverse rice accessions, representing aus, indica, temperate japonica and tropical japonica subpopulations, were produced under temperate climate conditions in Korea and used for vitamin E analysis and seed storage experiments at 45°C and 10.9% seed moisture content. High γ-tocotrienol was significantly positively correlated with seed longevity. In addition, a high β-tocopherol proportion relative to δ-tocopherol was significantly negatively correlated with seed longevity. Using high-density single-nucleotide polymorphism marker data, DNA haplotype analysis showed clear allelic variations in the region of two S-adenosylmethionine synthetase genes: LOC_Os04g42095 and LOC_Os11g15410, which regulate the conversion of δ-tocopherol into β-tocopherol. Four indica accessions with rare and subpopulation-specific alleles showed a 2.3-fold lower β-/δ-tocopherol ratio compared with accessions from other subpopulations.

Advances in genomics have provided technologies for high throughput analysis of plant genomes with potential for use in gene discovery in germplasm collections. The establishment of DNA banks facilitates this screening by making DNA from large numbers of plant accessions widely available. DNA banks require the development of appropriate policies for access and benefit sharing. Tools for automating sample and data handling are essential. Standard molecular methods for fingerprinting DNA accessions for international comparisons need to be determined. New screening technologies are required to take advantage of the emerging availability of large DNA collections. The Australian Plant DNA Bank aims to collect DNA from all Australian plant species and to sample the diversity within each species. DNA from all individuals of the species is being stored for rare species. Domesticated or economically important species from all countries are also being collected and stored. International networking of DNA banks will be a key step in linking genomics tools to global plant diversity.

The genetic relationships among 13 melon inodorus populations that were collected in southern Italy were assessed using 100 inter-simple-sequence repeat (ISSR) primers and 15 morphological traits. The dihaploid line Nad-1 and the cultivar Charentais-T, both of which belong to the botanical variety cantalupensis, were used as reference accessions in the molecular analysis. A total of 358 polymorphic bands were obtained from 39 of the 100 ISSR primers used, and 15 phenotypic traits were scored and used for genetic-similarity calculations and cluster analysis. The resulting dendrograms based on the ISSR and phenotypic data allowed almost all of the melon genotypes to be distinguished on the basis of the skin colour of the fruits. Mantel's test revealed a good correlation between the morphological and molecular data in their ability to detect genetic relationships among melon ecotypes (r = 0.50, P = 0.99). The data obtained confirm the effectiveness of this approach, and open new perspectives to reveal possible molecular associations with the phenotypic traits analysed.

Successful development of new sorghum cultivars and hybrids to ensure sustainable production depends largely on the availability of genetic resources with desirable traits such as pest resistance. Our recent research has focused on improvement of crop protection against greenbugs using the worldwide germplasm collection and genomics-based approaches. First, we conducted the systematic evaluation of a worldwide germplasm collection in order to identify new sources of greenbug resistance. Twenty-one resistant lines were identified, which offered new sources of resistance to sorghum breeding. Molecular markers used to assess the genetic diversity among those resistant lines suggested relatively diverse resistant sources in the sorghum germplasm collection. More recently, a mapping project was executed to associate the resistance genes with sorghum chromosomes. The mapping data indicated one major and a minor quantitative trait loci reside on chromosome 9 and are responsible for resistance to greenbug. In addition, cDNA microarrays were used to monitor greenbug-induced gene expression in sorghum plants. This study has developed a transcriptional profile for sorghum in response to greenbug attack, which provides us with useful molecular information for discovery of greenbug resistance genes and a better understanding of the genetic mechanisms controlling host defences in sorghum.

Mango (Mangifera indica L.) is an important fruit crop with a long cultivation history in Myanmar. This study evaluated the genetic variation within two economically important traditional varieties, ‘Yin Kwe’ and ‘Sein Ta Lone’, and the relationship between genetic variation and propagation practices. Genetic variation was estimated by genotyping 94 individuals with 12 single sequence repeat markers. ‘Yin Kwe’ (n = 53) showed higher levels of observed heterozygosity (Ho = 0.59) and average genetic distance among individuals (Da = 0.29) than did ‘Sein Ta Lone’ (n = 41; Ho = 0.45; Da = 0.09). The differences between the two varieties at the DNA level were significant (Fst = 0.44). The broader genetic background in ‘Yin Kwe’ compared with ‘Sein Ta Lone’ was also demonstrated by neighbour-joining and principal coordinates analyses. Differences in variety uses and propagation practices were determined by interviewing local specialists in Lower Myanmar (southern Myanmar). ‘Yin Kwe’ was often used as a rootstock for ‘Sein Ta Lone’. Clonal propagation by grafting was observed frequently for ‘Sein Ta Lone’ but never for ‘Yin Kwe’. The differences in genetic variation between these two varieties might have been caused by the propagation practices for each variety, which result from their respective uses.

Germplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop's improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype × environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.

Sugarbeet cultivars are almost exclusively hybrids, which are produced using the sole source of cytoplasmic male sterility (CMS), the so-called Owen CMS. Several alternative sources of CMS have been described. One of these, I-12CMS(3), was derived from wild beets collected in Pakistan, and another CMS source, GCMS, has a cytoplasmic origin in wild sea beets from France. During the past decade, male sterility-associated mitochondrial genes have been identified in these three CMS systems. Moreover, the recent development of a variety of DNA markers has permitted the genetic mapping of nuclear restorer-of-fertility genes for both Owen and GCMS. This review focuses on the mechanism of CMS in beets.

Ilex paraguariensis, commonly known as yerba mate, is a tree species native to South America. Its commercial value is due to the manufacturing of teas, with potential also in the pharmacological and cosmetic industries. Vegetative propagation of yerba mate is considered an innovation to the traditional production systems based on sexual propagation. The present study aimed to evaluate the rhizogenic potential and chemical attributes of mini-cuttings from 15 yerba mate genotypes, as well as to verify the correlation between phytochemical and rooting-related variables. Mini-cuttings were collected from a pre-existing mini-clonal hedge and the experimental design was completely randomized, with 15 treatments (genotypes), four replications and 10 mini-cuttings per plot. After 120 days, mini-cuttings were assessed regarding rooting, mortality, callogenesis and leaf retention percentages, percentage of mini-cuttings with both calluses and roots, number of roots and average root length. At the time of collection, subsamples from each plot were used for phytochemical analyses including total phenolic compounds, protein, caffeine and theobromine contents and antioxidant activity. Rooting percentages ranged from 5 to 72.5%, with significant variation among genotypes. Adventitious rooting and phytochemical profile of yerba mate mini-cuttings are genotype-dependent. Leaf retention is a relevant factor in the rooting of yerba mate mini-cuttings and the levels of total phenolic compounds, antioxidants and theobromine present in mini-cuttings are negatively correlated components to Ilex paraguariensis adventitious rooting.

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.

Cocoa butterfat and cocoa powder are key economic products from the seeds of the cacao tree (Theobroma cacao L.). In this study, 323 accessions (comprised mainly of Upper Amazon Forasteros and Refractarios) from the International Cocoa Genebank, Trinidad were characterized for one biochemical and five morphological seed-derived traits. The data were analysed using non-parametric statistics including correlation analysis to identify promising parental candidates for future cacao breeding programmes. The Upper Amazon Forastero group had the greatest proportion of accessions with high butterfat content in cotyledons, whereas Refractario and Trinitario groups tended to contain more accessions with high butterfat content per fruit. The correlation of butterfat content of cotyledons with the dry mass of cotyledons was inconsistent in significance and direction. However, consistent significant positive correlations between butterfat content per fruit, cotyledon size and dry mass of cotyledons were found. The results suggested that butterfat content is a likely trait for independent selection but that selection for increased cotyledon size could lead to the selection of genotypes for high butterfat yield. Several promising accessions exhibited favourable levels of multiple traits and MATINA 1/7, CRU 51, AM 2/91 [POU], CRU 133, EET 58 [ECU] and POUND 18/A [POU] could be recommended as good choices for parental stock in breeding programmes for improving cacao butterfat content.

Woad (Isatis tinctoria L.) was the most important source of natural blue indigo, a pigment used mainly for dyestuff until the beginning of the 20th century, when the increased use of synthetic dyes by the industry lead to a decrease in the interest of natural dyes and to the abandonment of dye crops. The aim of this study was to characterize, according to morphological and agronomical traits, 11 woad accessions from different countries and to quantify the indigo precursor content by high-performance liquid chromatograph-diode array detection (HPLC-DAD). Qualitative traits revealed a low variability and a great variation was observed in quantitative traits. Principal component analysis (PCA) diagrams divided the accessions into four groups, primarily according to their geographic origin. The first three components of the PCA accounted for 76.8% of the total variation. Reciprocal interactions between indigo precursors and fresh leaf weight were compared through genetic diversity, with significant differences in isatan B (0.5–5.1 g/kg), indoxyl (0.3–2.0 g/kg) and residual indigo (0.3–0.5 g/kg). This information, together with genetic data, can be used to assist local farmers to re-introduce Isatis species in the European agricultural system, not only indicating the higher indigo yielding genotypes, but also the most suitable harvest time.

Error-prone repair of radiation-induced DNA double-strand breaks (DSBs) results in DNA mutation that is essential for mutation breeding. Non-homologous end joining might be the principal DSB repair mechanism in eukaryotes, which is mediated and activated by Ku protein, a heterodimer of 70 and 80 kDa subunits. In this study, on the basis of complementary DNA (cDNA), the genomic sequences of TaKu70 and TaKu80 genes in all the three genomes of wheat were characterized. Only single-nucleotide substitutions and no insertions or deletions were detected in the exons of TaKu70 and TaKu80 genes. The size of the introns exhibited a slight variation between the sequences. Yeast two-hybrid analysis demonstrated that TaKu70 and TaKu80 formed a heterodimer, and electrophoretic mobility shift assays revealed that this heterodimer bound to double-stranded DNA, but not to single-stranded DNA. The quantitative polymerase chain reaction analysis revealed that the expression of TaKu70 and TaKu80 genes was up-regulated under γ-ray irradiation in a dose-dependent manner in the seedlings of wheat. These results suggest that TaKu70 and TaKu80 form a functional heterodimer and are associated with the repair of the induced DSBs in wheat.

Germination tests are performed on a routine basis to determine the viability of genebank accessions. The results determine which accessions have to be rejuvenated. The reliability of the germination test results used by the Centre for Genetic Resources, the Netherlands was determined by the retesting of 641 random samples anonymously, in the same year and by the same testing agency as the original tests. Results showed alarmingly low reliabilities, with error levels much higher than expected based on sampling effects. The result of a germination test of a random sample with a germination of 80% was shown to have a 95% confidence interval from 63 to 97%. The errors differed strongly over crops and testing years, and were larger for crop wild relatives than for crop species.