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

Supplementary figure 2d

Multiple alignment of psbM-trnD region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB)

Supplementary figure 2c

Multiple alignment of trnL-F region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB)

Supplementary figure 1

Multiple alignment of ITS region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB

Supplementary figure 2b

Multiple alignment of rps16 region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB)

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Not AvailableA large portion of unused crop residues is burnt in the fields primarily to clear the left-over straw and stub bles after the combine harvest. Studies have reported several ill effects of crop-residue burning on soil orga nic carbon and fertility, including reduction in produc tivity in the long term, environmental pollution and human health. It also produces greenhouse gases causing global warming. Rice and wheat produce large amounts of residue in India. Non-availability of labour, the high cost of residue removal from the field and the increasing use of combines in harvesting the crops are the main reasons for burning crop residues in the fields. Rice straw is unsuitable animal feed due to its high silica con tent and wheat straw for due to its hard stem and diffi culty chewing in unchopped form. Using supplements like urea and is feeding straw sprayed with urea impro ves its nutritive value and intake. We have developed a mechanized baler equipped with a urea spraying system for spraying urea during baling operations on crop resi dues (paddy or wheat straw) to enhance their nutritional value. The developed system was evaluated in combine a harvested wheat residue field and nutritional analysis was performed. The crude protein in untreated wheat straw increased from 3.68% to 10.10% after urea treatment. The metabolizable energy was also found to improve by 3% compared to untreated straw. Thus, urea-treated bales have potential use in dairy farming.Not Availabl

Usage pattern of chemicals, biologicals and veterinary medicinal products in Indian aquaculture

The use of chemicals, biologicals and veterinary medicinal products (VMPs) helps in healthy and sustainable fish production. Information on the use of these products is essential for assessing farming practices, potential human health and environmental risks. A questionnaire-based nationwide survey covering aquaculture farms (n = 2936) producing carps, tilapia, pangasius and rainbow trout in freshwater and shrimp in brackishwater estimated the use of 52 different types of inputs which included disinfectants (597 g t−1), probiotics (2.28 kg t−1), environmental modifiers (22.82 kg t−1), nutritional supplements (1.96 kg t−1), natural anti-infective agents (293 g t−1), herbicide and piscicides (844 g t−1), antibiotics (2 mg PCU−1), antifungal (4 mg PCU−1), and antiparasitic (14 mg PCU−1) agents. The bulk of these inputs was used for soil and water quality improvement and had low environmental and human safety concerns. The multivariate analysis revealed significant variation in the frequency and quantity of compounds use among farm groups. Redundancy analysis revealed a significant association between the number of products used and stocking density. The survey also showed a considerable influence of education and farming experience on the usage pattern of aquaculture inputs. Results of the study indicated greater reliance of farmers on the use of disinfectants for biosecurity, nutritional supplements for enhanced growth and environmental modifiers for maintaining soil and water quality in culture systems. Though there was no use of restricted antibiotics and antiparasitic agents, the development and implementation of standard regulatory guidelines are essential for safe and effective use of inputs for sustainable aquaculture

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Not AvailableThe use of chemicals, biologicals and veterinary medicinal products (VMPs) helps in healthy and sustainable fish production. Information on the use of these products is essential for assessing farming practices, potential human health and environmental risks. A questionnaire-based nationwide survey covering aquaculture farms (n = 2936) producing carps, tilapia, pangasius and rainbow trout in freshwater and shrimp in brackishwater estimated the use of 52 different types of inputs which included disinfectants (597 g t−1), probiotics (2.28 kg t−1), environmental modifiers (22.82 kg t−1), nutritional supplements (1.96 kg t−1), natural anti-infective agents (293 g t−1), herbicide and piscicides (844 g t−1), antibiotics (2 mg PCU−1), antifungal (4 mg PCU−1), and antiparasitic (14 mg PCU−1) agents. The bulk of these inputs was used for soil and water quality improvement and had low environmental and human safety concerns. The multivariate analysis revealed significant variation in the frequency and quantity of compounds use among farm groups. Redundancy analysis revealed a significant association between the number of products used and stocking density. The survey also showed a considerable influence of education and farming experience on the usage pattern of aquaculture inputs. Results of the study indicated greater reliance of farmers on the use of disinfectants for biosecurity, nutritional supplements for enhanced growth and environmental modifiers for maintaining soil and water quality in culture systems. Though there was no use of restricted antibiotics and antiparasitic agents, the development and implementation of standard regulatory guidelines are essential for safe and effective use of inputs for sustainable aquaculture.Indian Council of Agriculture Researc