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Comparative and functional genomics analysis of starch Biosynthesis pathways in cassava
he study entitled “Comparative and Functional Genomics Analysis of Starch biosynthesis Pathways in Cassava [Manihot esculenta Crantz.]” was carried out at the Section of Extension and Social Sciences, ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram during 2016-2017. The...
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| Format: | Ph.D Thesis |
| Publié: |
Vellayani
Department of Plant Biotechnology, College of Agriculture
2017
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| Sujets: |
| LEADER | 04200nam a22001817a 4500 | ||
|---|---|---|---|
| 082 | |a 660.6 |b POO/CO | ||
| 100 | |a Pooja Harshan | ||
| 245 | |a Comparative and functional genomics analysis of starch Biosynthesis pathways in cassava | ||
| 260 | |a Vellayani |b Department of Plant Biotechnology, College of Agriculture |c 2017 | ||
| 300 | |a 82p. | ||
| 502 | |a BSc-MSc (Integrated) | ||
| 520 | 3 | |a he study entitled “Comparative and Functional Genomics Analysis of Starch biosynthesis Pathways in Cassava [Manihot esculenta Crantz.]” was carried out at the Section of Extension and Social Sciences, ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram during 2016-2017. The objectives of the study were to study the starch biosynthesis pathways in cassava using data integration and also the temporal gene expression pattern during different growth stages. The knowledge on differentially expressed genes can be exploited for plant breeding programs in order to develop high starch cassava varieties. Starch related gene and protein sequences were collected from the respective databases of cassava and each of the template plants viz. Arabidopsis, Maize, Rice, Castor bean and Potato. Reciprocal Blast was performed to check for respective orthologues that corresponds to the template plants in cassava with a predetermined function. Three novel gene sequences were predicted electronically with functions similar to alpha 1, 4 glucan branching enzyme, sucrose phosphate synthase and UDP glycosyl-transferase super family. The identified gene sequences were annotated using E2P2 (Ensemble Enzyme Prediction Pipeline) software which is maintained by the Plant Metabolic Network (PMN). Protein Motif Analysis (PMA) was carried out using the MEME Suite version 4.12.0 which is a package of tools for motif analyses like motif discovery, motif enrichment, motif scanning and motif comparison. Starch biosynthesis pathways in cassava include the carbon-dioxide fixation, starch and sucrose biosynthesis pathways as a whole. So in order to get a better comprehension on various pathways that regulate starch metabolism in the crop, the entire starch biosynthesis pathways were made into a single consolidated pathway. This reduces the complexity of pathway reconstruction for different pathways yielding the same end product. Pathway reconstruction becomes beneficial to the agricultural community only when some useful information on the genes that are linked to some phenotypic traits is considered in the pathway. Insights on the cis regulatory elements involved in the pathway enhance the possibility of starch production and accumulation in the roots of cassava. Promoter analysis and Transcription factor prediction was carried out in the work. The tool employed for promoter analysis is Promoter Scan maintained at BIMAS (Bioinformatics and Molecular Analysis Section), NIH. For transcription factor and transcription factor binding site prediction, PlantTFDB (Plant Transcription Factor Database) was used. Candidate gene prioritization is one among the other approaches being used in the study. Through gene prioritisation, five potential candidate genes have been found out which have a major role in revolutionising the starch biosynthesis pathway in cassava. One of the genes was a negative regulator/ suppressor of starch synthesis in cassava which made a breakthrough in the work. Finally, the output data of all the approaches were integrated together in the pathway constructed to create a better interactive pathway for visualization. Cell illustrator version 4.0 was employed for the construction of the starch biosynthesis pathway and output data integration in cassava. Hence, the starch biosynthesis pathway was not merely reconstructed but also the molecular insights into the genes and other auxiliary regulatory elements were also incorporated to create a highly interactive pathway. | |
| 650 | |a Biotechnology | ||
| 650 | |a Plant Biotechnology | ||
| 700 | |a Sreekumar, J (Guide) | ||
| 942 | |2 ddc |c TH | ||
| 999 | |c 160022 |d 160022 | ||
| 952 | |0 0 |1 0 |4 0 |6 660_600000000000000_POOCO |7 1 |8 REF |9 158595 |a KAUCLV |b KAUCLV |c THESES |d 2018-04-12 |o 660.6 POO/CO |p 174176 |r 2018-04-12 |w 2018-04-12 |y TH | ||