Accelerating the commercialization of home-grown genetically engineered crops

Transgenic crops offer the state-of-the-art, and yet simple-to-use technologies for sustainable enhancement of agricultural productivity. During the last 20 years, several research groups in India have developed capabilities in genetic engineering of crop plant species and some of them have isolated promising genes and promoters, with potential for commercialization. However, isolated growth of researchers, limited R&D infrastructure and knowledge base available in the seed industry, and the regulatory processes involved in the release of transgenic cultivars pose serious challenges to accelerating the conversion of such leads into field crops. There is an urgent need to evolve efficient managerial approaches for developing and advancing genetically engineered cultivars into Indian agriculture. This article emphasizes the need to identify the most promising transgenics and genes available in the country, evaluate the related intellectual property issues and provide unstinted support to accelerate the process of their commercialization. An approach that would synergize public-public and public-private partnerships needs to be evolved. Initially, it may be driven by public sector through crop- and trait-specific consortia, comprising researchers and the seed industry. A few of such examples should be taken to the stage of clearance by GEAC for unregulated release of indigenously developed transgenic cultivars. These would then serve as role models and catalyse the formation of need-based teams and lasting partnerships, needed to usher Indian agriculture into a globally competitive phase of sustainable productivity

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

BACKGROUND: The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. RESULTS: Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions. CONCLUSIONS: The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers

Pathway Editing Targets for Thiamine Biofortification in Rice Grains

Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome

The psbE-F-L-J operon from chloroplast genome of Populus deltoides: Cloning, nucleotide sequence and transcript analysis

A 5-5-kbp HindIII fragment carrying psbE-F-L-J operon from the chloroplast DNA of Populus deltoides was cloned and nucleotide sequence was determined for a 1672-bp region. The coding regions showed more than 90% homology at nucleotide sequence level with plastid-encoded psbE, psbF, psbL and psbJ genes of higher plants. Pairwise alignments of psbE, psbF, psbL and psbJ coding regions of poplar with published sequences from other plants were carried out to analyse the nature of nucleotide substitutions. The 5' and 3' untranslated regions of the genes revealed high variability among different organisms both in terms of homology and the number of nucleotides. Northern hybridization data indicated that all four genes of psbE-F-L-J operon were transcribed as a single tetracistronic message which was not subjected to further processing into smaller transcripts. The transcript showed quantitative increase in mature leaves

Release of insecticidal transgenic crops and gap areas in developing approaches for more durable resistance

Transgenic cultivars expressing d-endotoxin coding genes of Bacillus thuringiensis are beinggrown globally on about 12 million hectares this year. Agriculture in India can benefit substan-tially by adopting transgenic insecticidal cultivars since, in contrast to the world average of 30%,of the total chemical pesticides used in India 75% are employed against insects. No other bio-logical approach, as safe as and yet as effective as the Bt technology is presently known to con-trol agricultural pests. The question at the center stage is to expedite the commercial release ofBt transgenics and also make a parallel effort to devise knowledge-based strategies aimed atachieving longer durability of crop resistance to insect pests. Plant breeders have encounteredsimilar situations in the past for improving crops against insects and other diseases. This articleidentifies the gap areas where research efforts are needed to develop strategies for enhancing thedurability of crop resistance

Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

<p>Abstract</p> <p>Background</p> <p>Genome-wide gene expression profiling and detailed physiological investigation were used for understanding the molecular mechanism and physiological response of <it>Gossypium herbaceum</it>, which governs the adaptability of plants in drought conditions. Recently, microarray-based gene expression analysis is commonly used to decipher genes and genetic networks controlling the traits of interest. However, the results of such an analysis are often plagued due to a limited number of genes (probe sets) on microarrays. On the other hand, pyrosequencing of a transcriptome has the potential to detect rare as well as a large number of transcripts in the samples quantitatively. We used Affymetrix microarray as well as Roche's GS-FLX transcriptome sequencing for a comparative analysis of cotton transcriptome in leaf tissues under drought conditions.</p> <p>Results</p> <p>Fourteen accessions of <it>Gossypium herbaceum </it>were subjected to mannitol stress for preliminary screening; two accessions, namely Vagad and RAHS-14, were selected as being the most tolerant and most sensitive to osmotic stress, respectively. Affymetrix cotton arrays containing 24,045 probe sets and Roche's GS-FLX transcriptome sequencing of leaf tissue were used to analyze the gene expression profiling of Vagad and RAHS-14 under drought conditions. The analysis of physiological measurements and gene expression profiling showed that Vagad has the inherent ability to sense drought at a much earlier stage and to respond to it in a much more efficient manner than does RAHS-14. Gene Ontology (GO) studies showed that the phenyl propanoid pathway, pigment biosynthesis, polyketide biosynthesis, and other secondary metabolite pathways were enriched in Vagad under control and drought conditions as compared with RAHS-14. Similarly, GO analysis of transcriptome sequencing showed that the GO terms <it>responses to various abiotic stresses </it>were significantly higher in Vagad. Among the classes of transcription factors (TFs) uniquely expressed in both accessions, RAHS-14 showed the expression of ERF and WRKY families. The unique expression of ERFs in response to drought conditions reveals that RAHS-14 responds to drought by inducing senescence. This was further supported by transcriptome analysis which revealed that RAHS-14 responds to drought by inducing many transcripts related to senescence and cell death.</p> <p>Conclusion</p> <p>The comparative genome-wide gene expression profiling study of two accessions of <it>G.herbaceum </it>under drought stress deciphers the differential patterns of gene expression, including TFs and physiologically relevant processes. Our results indicate that drought tolerance observed in Vagad is not because of a single molecular reason but is rather due to several unique mechanisms which Vagad has developed as an adaptation strategy.</p

Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

Background: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings: A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies