An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Obesity, overweight and central obesity and sedentary behaviour coexist with undernutrition, and have become a public health problem in all the five cities of India. The prevalence of obesity and sedentary behaviour was significantly greater in Trivandrum, Calcutta and Bombay compared to Moradabad and Nagpur. Sedentary behaviour was significantly associated with obesity compared to non-obese subjects in both sexes, which may be due to greater economic development in metro cities.

BackgroundDrought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance research work. Screening for drought tolerance stress under hydroponic conditions at seedling stage with air exposure is an efficient technique to select genotypes with contrasting traits. Transcriptome analysis provides valuable resources, especially for lentil, as here the information on complete genome sequence is not available. Hence, the present studies were carried out.ResultsThis study was undertaken to understand the biochemical mechanisms and transcriptome changes involved in imparting adaptation to drought stress at seedling stage in drought-tolerant (PDL-2) and drought-sensitive (JL-3) cultivars. Among different physiological and biochemical parameters, a significant increase was recorded in proline, glycine betaine contents and activities of SOD, APX and GPX in PDL-2 compared to JL-3while chlorophyll, RWC and catalase activity decreased significantly in JL-3. Transcriptome changes between the PDL-2 and JL-3 under drought stress were evaluated using Illumina HiSeq 2500 platform. Total number of bases ranged from 5.1 to 6.7 Gb. Sequence analysis of control and drought treated cDNA libraries of PDL-2 and JL-3 produced 74032, 75500, 78328 and 81523 contigs, respectively with respective N50 value of 2011, 2008, 2000 and 1991. Differential gene expression of drought treated genotypes along with their controls revealed a total of 11,435 upregulated and 6,934 downregulated transcripts. For functional classification of DEGs, KEGG pathway annotation analysis extracted a total of 413 GO annotation terms where 176 were within molecular process, 128 in cellular and 109 in biological process groups.ConclusionThe transcriptional profiles provide a foundation for deciphering the underlying mechanism for drought tolerance in lentil. Transcriptional regulation, signal transduction and secondary metabolism in two genotypes revealed significant differences at seedling stage under severe drought. Our finding suggests role of candidate genes for improving drought tolerance in lentil.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3596-7) contains supplementary material, which is available to authorized users.

One hundred and sixty two genotypes of different Lens species were screened for salinity tolerance in hydroponics at 40, 80 and 120 mM sodium chloride (NaCl) for 30 d. The germination, seedling growth, biomass accumulation, seedling survivability, salinity scores, root and shoot anatomy, sodium ion (Na+), chloride ion (Cl-) and potassium ion (K+) concentrations, proline and antioxidant activities were measured to evaluate the performance of all the genotypes. The results were compared in respect of physiological (Na+, K+ and Cl-) and seed yield components obtained from field trials for salinity stress conducted during two years. Expression of salt tolerance in hydroponics was found to be reliable indicator for similarity in salt tolerance between genotypes and was evident in saline soil based comparisons. Impressive genotypic variation for salinity tolerance was observed among the genotypes screened under hydroponic and saline field conditions. Plant concentrations of Na+ and Cl- at 120 mM NaCl were found significantly correlated with germination, root and shoot length, fresh and dry weight of roots and shoots, seedling survivability, salinity scores and K+ under controlled conditions and ranked the genotypes along with their seed yield in the field. Root and shoot anatomy of tolerant line (PDL-1) and wild accession (ILWL-137) showed restricted uptake of Na+ and Cl- due to thick layer of their epidermis and endodermis as compared to sensitive cultigen (L-4076). All the genotypes were scanned using SSR markers for genetic diversity, which generated high polymorphism. On the basis of cluster analysis and population structure the contrasting genotypes were grouped into different classes. These markers may further be tested to explore their potential in marker-assisted selection.

Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource (http://webtom.cabgrid.res.in/pmdtdb/) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.

Aluminium (Al) stress was imposed on 285 lentil genotypes at seedling stage under hydroponics to study its effects on morpho-physiological traits where resistant cultigens and wilds showed minimum reduction in root and shoot length and maximum root re-growth (RRG) after staining. Molecular assortment based on 46 simple sequence repeat (SSR) markers clustered the genotypes into 11 groups, where wilds were separated from the cultigens. Genetic diversity and polymorphism information content (PIC) varied between 0.148–0.775 and 0.140–0.739, respectively. Breeding lines which were found to be most resistant (L-7903, L-4602); sensitive cultivars (BM-4, L-4147) and wilds ILWL-185 (resistant), ILWL-436 (sensitive) were grouped into different clusters. These genotypes were also separated on the basis of population structure and Jaccard’s similarity index and analysed to study Al resistance mechanism through determination of different attributes like localization of Al and callose, lipid peroxidation, secretion of organic acids and production of antioxidant enzymes. In contrast to sensitive genotypes, in resistant ones most of the Al was localized in the epidermal cells, where its movement to apoplastic region was restricted due to release of citrate and malate. Under acidic field conditions, resistant genotypes produced maximum seed yield/plant as compared to sensitive genotypes at two different locations i.e. Imphal, Manipur, India and Basar, Arunanchal Pradesh, India during 2012–13, 2013–14 and 2014–15. These findings suggest that Al stress adaptation in lentil is through exclusion mechanism and hybridization between the contrasting genotypes from distinct clusters can help in development of resistant varieties.

Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

Heat stress is one of the most severe abiotic stresses affecting yield of agricultural crops. Its effects can be minimized through development of heat‐tolerant genotypes. In this study, the populations were developed through crossing heat‐stress‐sensitive (‘JL‐3’ and E‐153) and tolerant (PDL‐1 and PDL‐2) lentil (Lens culinaris Medik.) genotypes for studying the genetics and molecular mapping of heat tolerance. The parents, F1, F2, F3, and backcross populations were exposed to heat stress at seedling (35/33°C) and reproductive (35/20°C) stages under hydroponic assay. The F1s were found tolerant, indicating dominance of heat tolerance based on seedling survival and pod set per plant. The segregation ratios obtained for heat tolerance in the F2, F3, and backcross populations were 3:1, 1:2:1, and 1:1 based on seedling survival and pod set per plant. This suggested the presence of a single dominant gene for seedling survival and pod set related to heat tolerance in PDL‐1 and PDL‐2. This matched with one major quantitative trait locus (QTL) in each trait (i.e., seedling survival and pod set per plant). Out of 495 simple sequence repeat markers used in this study, 13 distinguished the parental lines. However, tolerant and sensitive bulks could be distinguished by seven markers, which were used for genotyping the F2 mapping population. The QTL analysis using data for genotyping and phenotyping identified two major QTLs, qHt_ss and qHt_ps, with 12.1 and 9.23% phenotypic variance explained for seedling survival and pod set, respectively. These QTLs would provide further opportunities to dissect candidate genes and development of molecular markers for improving lentil cultivars with heat tolerance.