Identification and expression profiling of genes involved in lignin biosynthesis in rice
Student name: Ms Kalpna
Guide: Dr Anandita Singh
Year of completion: 2014
Host Organisation: The Energy and Resource Institute (TERI), New Delhi
Supervisor (Host Organisation): Dr Swatismita Dhar
Abstract: Rhizoctonia solani is known to infect a wide variety of rice plants and cause sheath blight disease
in rice. The lignin biosynthesis pathway genes have been reported to have role in providing
defense against sheath blight disease in rice. In this study, six genes (HCT, 4CL, CCoAOMT,
COMT, CCR and CAD) of lignin biosynthesis pathway are analyzed. The isoforms of the same
six genes in Arabidopsis thaliana are also identified which served as a reference genome in this
study. The putative isoforms of the six genes for both Oryza sativa and isoforms for Arabidopsis
thaliana are identified from various databases and existing literature survey. The putative
isoforms of all the genes are validated by various studies which included protein sequence
alignment of all the isoforms, signature motif analysis using EXPASY PROSITE Scan followed by
conserved domain study using EMBL Pfam SMART and by literature studies. The unrooted
neighbor-joining trees for all the six genes families of rice and Arabidopsis thailana were also
constructed to depict the relationship among the various isoforms of a particular gene family.
The pathogenicity test of the fungus Rhizoctonia solani on the rice plants varieties give the
estimate of the fungus pathogenicity and level of resistance to the disease in two Oryza sativa
varieties Tetep and PB1. The isoforms were also aligned with the already reported quantitative
trait loci’s for sheath blight disease resistance in rice. The quantitative-PCR primers were also
designed on the cDNA sequences of all isoforms belonging to the gene families.RNA were
isolated from the tissue collected at different time points after the challenge assay, followed by
cDNA preparation. Further the expression analysis data collection of each gene isoform can
provide valuable information about the role of each gene isoform in defense against sheath blight
disease of rice.
Keywords: Lignin biosynthesis genes, putative isoforms, Rhizoctonia solani, Pathogenicity test,
quantitative trait loci’s, Oryza sativa.
