title: De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty.
abstract: Vetiver, a perennial C4 grass, has long been known for its multifarious uses in perfumery, medicine and environmental protection. Two distinct vetiver morphotypes have been identified in India, i.e., A. North Indian type characterized by thick and smooth fast growing roots that produce superior quality of laevorotatory oil; and B. South Indian type with more number of thin and hairy roots that produce inferior quality of dextrorotatory oil. The two morphotypes were targeted for transcriptome analysis to understand the contribution of genetic background on oil quality and root morphology. Sample A showed enhanced activity of flavonoid and terpenoid biosynthesis related genes, i.e. ERF, MYB, bHLH, bZIP and WRKY. Interestingly, expression analysis revealed that the genes involved in sesquiterpene biosynthesis pathway were up regulated in Sample A. Moreover, some of the genes involved in mevalonate pathway of sesquiterpene biosynthesis were unique to Sample A. Our results also demonstrated several transcripts involved in root development and hormonal regulation being up regulated in Sample A. To validate gene expression results of RNA-seq data, 20 transcripts were validated by qRT-PCR experiment. The present study provided an important start point for further discovery of genes related to root oil quality in different ecotypes of vetiver.
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Debasis
authors.initials: D
authors.lastname: Chakrabarty
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Puneet Singh
authors.initials: PS
authors.lastname: Chauhan
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Abhishek Singh
authors.initials: AS
authors.lastname: Chauhan
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Yuvraj
authors.initials: Y
authors.lastname: Indoliya
authors.affiliation: Department of Botany, Lucknow University, Lucknow 226 007, India.
authors.forename: Umesh Chandra
authors.initials: UC
authors.lastname: Lavania
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Chandra Shekhar
authors.initials: CS
authors.lastname: Nautiyal
mesh_terms: D005419:Flavonoids / Q000096:biosynthesis / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D006109:Poaceae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D012717:Sesquiterpenes / Q000737:chemistry / Q000378:metabolism; D013729:Terpenes / Q000737:chemistry / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005419:Flavonoids; D010940:Plant Proteins; D012717:Sesquiterpenes; D013729:Terpenes; D012313:RNA