Comparative and functional genomics analysis of starch Biosynthesis pathways in cassava (Record no. 160022)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 04164nam a22001817a 4500 |
| 082 ## - DEWEY DECIMAL CLASSIFICATION NUMBER | |
| Classification number | 660.6 |
| Item number | POO/CO |
| 100 ## - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Pooja Harshan |
| 245 ## - TITLE STATEMENT | |
| Title | Comparative and functional genomics analysis of starch Biosynthesis pathways in cassava |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT) | |
| Place of publication, distribution, etc | Vellayani |
| Name of publisher, distributor, etc | Department of Plant Biotechnology, College of Agriculture |
| Date of publication, distribution, etc | 2017 |
| 300 ## - PHYSICAL DESCRIPTION | |
| Extent | 82p. |
| 502 ## - DISSERTATION NOTE | |
| Dissertation note | BSc-MSc (Integrated) |
| 520 3# - SUMMARY, ETC. | |
| Abstract | he study entitled “Comparative and Functional Genomics Analysis of<br/>Starch biosynthesis Pathways in Cassava [Manihot esculenta Crantz.]” was<br/>carried out at the Section of Extension and Social Sciences, ICAR-Central Tuber<br/>Crops Research Institute, Sreekariyam, Thiruvananthapuram during 2016-2017.<br/>The objectives of the study were to study the starch biosynthesis pathways in<br/>cassava using data integration and also the temporal gene expression pattern<br/>during different growth stages. The knowledge on differentially expressed genes<br/>can be exploited for plant breeding programs in order to develop high starch<br/>cassava varieties.<br/>Starch related gene and protein sequences were collected from the<br/>respective databases of cassava and each of the template plants viz. Arabidopsis,<br/>Maize, Rice, Castor bean and Potato. Reciprocal Blast was performed to check for<br/>respective orthologues that corresponds to the template plants in cassava with a<br/>predetermined function. Three novel gene sequences were predicted electronically<br/>with functions similar to alpha 1, 4 glucan branching enzyme, sucrose phosphate<br/>synthase and UDP glycosyl-transferase super family.<br/>The identified gene<br/>sequences were annotated using E2P2 (Ensemble Enzyme Prediction Pipeline)<br/>software which is maintained by the Plant Metabolic Network (PMN). Protein<br/>Motif Analysis (PMA) was carried out using the MEME Suite version 4.12.0<br/>which is a package of tools for motif analyses like motif discovery, motif<br/>enrichment, motif scanning and motif comparison.<br/>Starch biosynthesis pathways in cassava include the carbon-dioxide fixation,<br/>starch and sucrose biosynthesis pathways as a whole. So in order to get a better<br/>comprehension on various pathways that regulate starch metabolism in the crop,<br/>the entire starch biosynthesis pathways were made into a single consolidated<br/>pathway. This reduces the complexity of pathway reconstruction for different<br/>pathways yielding the same end product. Pathway reconstruction becomes<br/>beneficial to the agricultural community only when some useful information on<br/>the genes that are linked to some phenotypic traits is considered in the pathway.<br/>Insights on the cis regulatory elements involved in the pathway enhance the<br/>possibility of starch production and accumulation in the roots of cassava.<br/>Promoter analysis and Transcription factor prediction was carried out in the work.<br/>The tool employed for promoter analysis is Promoter Scan maintained at BIMAS<br/>(Bioinformatics and Molecular Analysis Section), NIH. For transcription factor<br/>and transcription factor binding site prediction, PlantTFDB (Plant Transcription<br/>Factor Database) was used.<br/>Candidate gene prioritization is one among the other approaches being used<br/>in the study. Through gene prioritisation, five potential candidate genes have been<br/>found out which have a major role in revolutionising the starch biosynthesis<br/>pathway in cassava. One of the genes was a negative regulator/ suppressor of<br/>starch synthesis in cassava which made a breakthrough in the work. Finally, the<br/>output data of all the approaches were integrated together in the pathway<br/>constructed to create a better interactive pathway for visualization. Cell illustrator<br/>version 4.0 was employed for the construction of the starch biosynthesis pathway<br/>and output data integration in cassava. Hence, the starch biosynthesis pathway<br/>was not merely reconstructed but also the molecular insights into the genes and<br/>other auxiliary regulatory elements were also incorporated to create a highly<br/>interactive pathway.<br/> |
| 650 ## - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Biotechnology |
| 650 ## - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Plant Biotechnology |
| 700 ## - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Sreekumar, J (Guide) |
| 856 ## - ELECTRONIC LOCATION AND ACCESS | |
| Uniform Resource Identifier | http://krishikosh.egranth.ac.in/handle/1/5810143448 |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Item type | Theses |
| Not for loan | Collection code | Home library | Current library | Shelving location | Date acquired | Full call number | Barcode | Date last seen | Koha item type |
|---|---|---|---|---|---|---|---|---|---|
| Not For Loan | Reference Book | KAU Central Library, Thrissur | KAU Central Library, Thrissur | Theses | 12/04/2018 | 660.6 POO/CO | 174176 | 12/04/2018 | Theses |