BSc-MSc (Integrated)

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.