A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.

BackgroundSalinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes.ResultsOur analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5’UTRs (21.1%), introns (14.3%) and 3’UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species.ConclusionWe have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1476-1) contains supplementary material, which is available to authorized users.

Thirty-three soybean [Glycine max (L.) Merill] genotypes, comprising 14 black-seeded and 19 yellow-seeded ones, were selected on the basis of their reported storability for the biochemical phenotyping to establish the role of lipid peroxidation and antioxidant enzymes in seed longevity. The present study revealed clear genotypic variability with respect to storability among different soybean genotypes. Good-storer genotypes with lower electrolyte leakage were characterized by smaller seed size with black testa color. The level of volatile aldehydes released and lipoxygenase II enzyme activity were higher in the yellow-seeded genotypes than in the black-seeded genotypes, though it increased in all during ageing. A sharp increase in the release of volatile aldehydes and lipoxygenase II activity, concomitant with the reduction in germination under uncontrolled laboratory conditions of storage indicated the role of lipid peroxidation in seed longevity behavior (r = -0.6638** and r = -0.7639**, respectively). No significant difference was noted in the mean hydroperoxide lyase activity of black and yellow-seeded genotypes. However, maintenance of high hydroperoxide lyase activity during storage resulted in higher release of volatile aldehydes and poor storability of seeds. Significantly higher antioxidant enzyme activity was recorded in the black-seeded genotypes than in the yellow-seeded ones, though there was a reduction in hydroperoxide lyase activity during storage in all the genotypes. The viability of black-seeded genotypes after storage for 1 year was better than the yellow-seeded genotypes.

Blumeria graminis (DC). E.U. Speer f.sp. tritici Em. Marchal (Syn. Erysiphe graminis DC f.sp. tritici, Em. Marchal), a causal organism of powdery mildew (PM), is one of the important diseases of wheat worldwide. A comprehensive evaluation of wheat germplasm accessions (19,460) conserved in the National Genebank of ICAR–National Bureau of Plant Genetic Resources was conducted to identify sources of resistance to PM. Accessions belonging to the three wheat species—bread wheat (Triticum aestivum L. subsp. aestivum) (15,944), durum wheat (T. durum Desf.) (3,359), and emmer wheat (T. dicoccum Schrank ex Schübl.) (157)—were screened at Wellington, a hotspot location for PM, for two consecutive seasons. Screening results indicated that 7271 (45%) from bread wheat, 756 (22%) from durum wheat, and 22 (14%) from emmer were resistant. Out of 8094 PM‐resistant accessions, 60% were indigenous, while majority of the 40% exotic were from CIMMYT. Focused identification of germplasm strategy (FIGS), which identifies a set of similar plant genotypes with a greater possibility of containing specific target traits, was used to form a subset of 52 accessions (from 19,460) that have the potential to contain new PM resistance genes. Resistant accessions identified in the study have enriched the existing gene pool for PM resistance in wheat and will serve as a potential source for resistance in future.

The entire collection of cultivated barley germplasm accessions conserved in the Indian National Genebank (INGB) was characterized for nine qualitative and 8 quantitative traits to assess the nature and magnitude of prevailing genetic variability and to develop a core set. A wide range of variability was observed for days to spike emergence (51–139 days), days to physiological maturity (100–152 days), plant height (45.96–171.32 cm), spike length (3.44–13.73 cm), grain number/spike (10.48–82.35), and 100-grain weight (1.20–6.86 g). Initially, seven independent core sets were derived using 3 core construction tools– MSTRAT, PowerCore, and Core Hunter 3 by employing the maximization method, heuristic sampling, and optimisation of average genetic distances, respectively. The core set-3 generated by Core Hunter 3 by simultaneous optimisation of diversity and representativeness, captured maximum genetic diversity of the whole collection as evident from the desirable genetic distance, variance difference percentage (VD; 87.5%), coincidence rate of range (CR; 94.27%) and variable rate of coefficient of variance (VR; 113.8%), which were more than threshold value of VD (80%), CR (80%), and VR (100%) required for good core collection. The coefficient of variation and Shannon–Weaver diversity indices were increased in the core set as compared with the whole collection. The low value of Kullback-Leibler distance (0.024–0.071) for all traits and quantile-quantile plots revealed a negligible difference between trait distribution patterns among the core set and entire assembly. Correlogram revealed that trait associations and their magnitude were conserved for most of the traits after sampling of the core set. The extraction of the INGB barley core set and identification of promising accessions for agronomically important traits in different genetic backgrounds will pave the way for expedited access to genetically diverse and agronomically important germplasm for barley breeding.

Plant genetic resources, the source of genetic diversity provides a broad genetic foundation for plant breeding and genetic research, however, large germplasm resources are difficult to preserve, evaluate and use. Construction of core and mini core collections is an efficient method for managing genetic resources and undertaking intensive surveys of natural variation, including the phenotyping of complex traits and genotyping of DNA polymorphisms allowing more efficient utilization of genetic resources. A mega characterization and evaluation programme of the entire cultivated gene pool of wheat conserved in the National Genebank, India was undertaken. Wheat accessions with limited seed quantity, were multiplied in the off-season nursery at IARI Regional Station, Wellington during rainy season 2011 and the entire set of 22,469 wheat accessions were characterized and evaluated at CCS HAU, Hisar, Haryana during winter season 2011-12 for 34 characters including 22 highly heritable qualitative, and 12 quantitative parameters. The core sets were developed using PowerCore Software with stepwise approach and grouping method and validated using Shannon-Diversity Index and summary statistics. Based on Shannon-Diversity index, PowerCore with stepwise approach was found better than PowerCore with grouping. The core set included 2,208 accessions comprising 1,770 T. aestivum, 386 T. durum, and 52 T. dicoccum accessions as a representative of the total diversity recorded in the wheat germplasm. The core set developed will be further validated at different agro-climatic conditions and will be utilized for development of mini core set to enhance the utilization by wheat researchers and development of climate resilient improved varieties.

The use of untapped plant genetic resources of wheat (Triticum spp.) can enhance its productivity. In the present study, we characterized 22,416 accessions of three different species of wheat conserved in the Indian National Genebank using 23 qualitative and 12 quantitative traits to develop a core set. These accessions were highly diverse on the basis of range, coefficient of variation, and Shannon–Weaver diversity index. Initial grouping was done on the bases of species and origin, and thereafter, agromorphological data were used to develop core sets for each species group using the heuristic approach with PowerCore. Finally, a composite core set was constituted comprising 2,226 accessions, which included 1,779 accessions of bread wheat (T. aestivum L.), 394 of durum wheat [T. turgidum L. subsp. durum (Desf.) van Slageren], and 53 of emmer wheat [T. dicoccon Schrank; syn. T. turgidum L. subsp. dicoccon (Schrank) Thell]. The core set was validated under field conditions. Also, the coincidence rate of range (CR) (bread wheat, 85.78%; durum wheat, 87.52%; and emmer wheat, 95.34%) and variable rate of the coefficient of variation (VR) (bread wheat, 174.9%; durum wheat, 136.5%; and emmer wheat, 105.81%) were more than the threshold values of 80 and 100%, respectively. The phenotypic correlations among different traits attributable to coadapted gene complexes and total variation shown by principal components in the entire set were also mostly preserved in the core set. The composite wheat core and the trait‐specific germplasm sets identified would serve as valuable resources for global wheat improvement programs.

Leaf rust ( Puccinia triticina Eriks.) is a fungal disease of wheat ( Triticum spp.), which causes considerable yield loss. Adult plant resistance (APR) is one of the most sustainable approaches to control leaf rust. In this study, field-testing was carried out across ten different locations, followed by molecular screening, to detect the presence of APR genes, Lr34 +, Lr46 +, Lr67 + and Lr68 in Indian wheat germplasm. In field screening, 190 wheat accessions were selected from 6,319 accessions based on leaf tip necrosis (LTN), disease severity and the average coefficient of infection. Molecular screening revealed that 73% of the accessions possessed known APR genes either as single or as a combination of two or three genes. The occurrence of increased LTN intensity, decreased leaf rust severity and greater expression of APR genes were more in relatively cooler locations. In 52 lines, although the presence of the APR genes was not detected, it still displayed high levels of resistance. Furthermore, 49 accessions possessing either two or three APR genes were evaluated for stability across locations for grain yield. It emerged that eight accessions had wider adaptability. Resistance based on APR genes, in the background of high yielding cultivars, is expected to provide a high level of race non-specific resistance, which is durable.