title: Integrative analysis and expression profiling of secondary cell wall genes in C4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering.
abstract: Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Mehanathan
authors.initials: M
authors.lastname: Muthamilarasan
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Khan
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Jananee
authors.initials: J
authors.lastname: Jaishankar
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Shweta
authors.initials: S
authors.lastname: Shweta
authors.affiliation: Division of Plant-Microbe Interactions, CSIR-National Botanical Research Institute Lucknow, India.
authors.forename: Charu
authors.initials: C
authors.lastname: Lata
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
keywords: bioenergy grasses; comparative mapping; foxtail millet (Setaria italica L.); genomics; lignocellulose; secondary cell wall biosynthesis