Mutagenesis is a powerful tool used for studying gene function as well as for crop improvement. It is regaining popularity because of the development of effective and cost efficient methods for high-throughput mutation detection. Selection for semi-dwarf phenotype during green revolution has reduced genetic diversity including that for agronomically desirable traits. Most of the available mutant populations in wheat (Triticum aestivum L.) were developed in post-green revolution cultivars. Besides the identification and isolation of agronomically important alleles in the mutant population of pre-green revolution cultivar, this population can be a vital resource for expanding the genetic diversity for wheat breeding. Here we report an Ethylmethane Sulfonate (EMS) generated mutant population consisting of 4,180 unique mutant plants in a pre-green revolution spring wheat cultivar ‘Indian’. Released in early 1900s, ‘Indian’ is devoid of any known height-reducing mutations. Unique mutations were captured by proceeding with single M2 seed from each of the 4,180 M1 plants. Mutants for various phenotypic traits were identified by detailed phenotyping for altered morphological and agronomic traits on M2 plants in the greenhouse and M3 plants in the field. Of the 86 identified mutants, 75 (87%) were phenotypically stable at the M4 generation. Among the observed phenotypes, variation in plant height was the most frequent followed by the leaf morphology. Several mutant phenotypes including looped peduncle, crooked plant morphology, ‘gritty’ coleoptiles, looped lower internodes, and burnt leaf tips are not reported in other plant species. Considering the extent and diversity of the observed mutant phenotypes, this population appears to be a useful resource for the forward and reverse genetic studies. This resource is available to the scientific community.

BackgroundForward genetic approaches have limited use for agronomic traits that can’t be reliably scored on a single plant basis. Thus, mutants in wheat and other crops are more useful for gene function studies by reverse genetic approach. With a long-term goal to develop a sequence-based mutation detection resource in hexaploid wheat, we conducted a feasibility study to accurately differentiate induced mutations from the homoeologs’ sequence variations present among the three wheat genomes.ResultsA reduced representation ApeKI library consisting of 21 Ethylmethane Sulfonate (EMS) induced mutants and two wild type cv. Indian plants was developed using individual barcode adapters and sequenced. A novel bioinformatics pipeline was developed to identify sequence variants using 178,464 wheat unigenes as a reference wheat transcriptome. In total, 14,130 mutational changes [Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (INDELs)] and 150,511 homoeologous sequence changes were detected. On an average, 662 SNPs (ranging from 46 to 1,330) and 10 small INDELs (ranging from 0 to 23) were identified for each of the mutants. A mutation frequency of one per 5 Kb was observed with 70 % being transitions and 30 % transversions. The pipeline was tested using the known sequence changes in the three wheat genes. Genes present in the distal regions of the chromosomes were found to be more prone to EMS compared to genes present in the proximal regions. Redefined parameters identified a total of 28,348 mutational changes (1,349/plant).ConclusionsWe conclude that sequencing based mutation detection is a valuable method to identify induced mutations at large.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2112-1) contains supplementary material, which is available to authorized users.

Phytohormone auxin plays a critical role in modulating plant architecture by creating a gradient regulated via its transporters such as ATP-binding cassette (ABC) B1. Except for Arabidopsis and maize, where it was shown to interrupt auxin transport, ABCB1's presence, structure and function in crop species is not known. Here we describe the structural and putative functional organization of ABCB1 among monocots relative to that of dicots. Identified from various plant species following specific and stringent criteria, ZmABCB1's "true" orthologs sequence identity ranged from 56-90% at the DNA and 75-91% at the predicted amino acid (aa) level. Relative to ZmABCB1, the size of genomic copies ranged from −27 to +1.5% and aa from −7.7 to +0.6%. With the average gene size being similar (5.8 kb in monocots and 5.7 kb in dicots), dicots have about triple the number of introns with an average size of 194 bp (total 1743 bp) compared to 556 bp (total 1667 bp) in monocots. The intron-exon junctions across species were however conserved. N-termini of the predicted proteins were highly variable: in monocots due to mismatches and small deletions of 1-13 aa compared to large, species-specific deletions of up to 77 aa in dicots. The species-, family-and group-specific conserved motifs were identified in the N-terminus and linker region of protein, possibly responsible for the specific functions. The near-identical conserved motifs of Nucleotide Binding Domains (NBDs) in two halves of the protein showed subtle aa changes possibly favoring ATP binding to the N-terminus. Predicted 3-D protein structures showed remarkable similarity with each other and for the residues involved in auxin binding.

Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (Onu), is a destructive disease of American elm (Ulmus americana L.). The molecular mechanisms of resistance and susceptibility against DED in American elm are still largely uncharacterized. In the present study, we performed a de novo transcriptome (RNA-sequencing; RNA-Seq) assembly of U. americana and compared the gene expression in a resistant genotype, ’Valley Forge’, and a susceptible (S) elm genotype at 0 and 96 h post-inoculation of Onu. A total of 85,863 non-redundant unigenes were identified. Compared to the previously characterized U. minor transcriptome, U. americana has 35,290 similar and 55,499 unique genes. The transcriptomic variations between ‘Valley Forge’ and ‘S’ were found primarily in the photosynthesis and primary metabolism, which were highly upregulated in the susceptible genotype irrespective of the Onu inoculation. The resistance to DED was associated with the activation of RPM1-mediated effector-triggered immunity that was demonstrated by the upregulation of genes involved in the phenylpropanoids biosynthesis and PR genes. The most significantly enriched gene ontology (GO) terms in response to Onu were response to stimulus (GO:0006950), response to stress (GO:0050896), and secondary metabolic process (GO:0008152) in both genotypes. However, only in the resistant genotype, the defense response (GO:0006952) was among the topmost significantly enriched GO terms. Our findings revealed the molecular regulations of DED resistance and susceptibility and provide a platform for marker-assisted breeding of resistant American elm genotypes.

Asthma is a common problem that affects about 20 million peoples in India and can be often under-diagnosed or misdiagnosed. It can be allergic or non-allergic though the former type is more common and prevalent. Allergic asthma can be triggered by many allergens and house dust mites (HDM) are one of the common indoor allergens. The present study emphasizes the significance of house dust mites in allergic asthmatic subjects which is based on 115 asthmatic subjects in Punjab, India. For the quantification and the estimation of total serum Immunoglobulin E and HDM specific IgE, a mixture of 14 allergens and a mixture of two mite allergens viz. Dermatophagoides pteronyssinus and D. farinae were used respectively. Total and specific IgE levels were detected on ImmunoCAP Phadia 100. A statistically significant correlation between total and HDM specific IgE levels of 115 asthmatic subjects was found as compared to control group of 30 non-allergic individuals. The specific IgE levels of 54.78% subjects against the allergen of two mite species were found to be positive. Dust samples were taken from various localities of the houses to identify the diversity of house dust mites which were responsible for allergic asthma. Five common house dust mite species viz. D. pteronyssinus Trouessart, D. farinae Hughes, D. microceras Griffiths and Cunnington, D. aureliani Fain and Euroglyphus maynei Cooreman were identified from the dust. The present study observed that total IgE levels were higher with higher specific IgE levels against the mixture of two mite allergens viz. D. pteronyssinus and D. farinae in the blood serum.  D. pteronyssinus was the most abundant and prevalent mite species followed by D. farinae. Therefore, present study concluded that HDM specific IgE levels against the mite allergen of D. pteronyssinus and D. farinae in the serum of allergic asthmatic subjects were found to be higher because of the higher prevalence of these two mites (D. pteronyssinus i.e. 69.80% and D. farinae i.e. 20.72%) in the house of allergic asthmatic subjects as compared to other identified mites.