Corchorus capsularis strain:JRC-212 and its mutant dlpf Transcriptome or Gene expression

RNA-seq based on next generation sequencing (NGS) technologies is now widely used to develop and characterize tissue-specific transcriptomes in many plant and animal species. This method is suitable for de novo assembly of short reads for gene discovery, allele mining and expression profiling in non-model organisms without a reference genome. White jute (Corchorus capsularis L., Malvaceae s. l.) is an important ligno-cellulosic bast (phloem) fibre crop. Despite diversified uses in textile and woven industries, white jute fibre, in contrast to the other allied bast fibres such as flax, hemp, kenaf and ramie, is characterized by high lignin content (ca. 15-18%) that renders it unsuitable for blending with cotton to produce finer fabrics. Thus, reducing the amount of lignin in bast fibre is one of the foremost priorities for jute quality breeding. The lignin from white jute fibres is structurally well-characterized. However, the lignin metabolic grid and its constituent genes that control bast fibre formation in jute are mostly unknown. In this project, our primary objective was to produce the first comprehensive transcriptome of bast fibre producing tissues (BFT) of white jute using short-read Illumina pair-end sequencing and de novo assembly techniques. Comparative analysis of the BFT transcriptome of a deficient lignified phloem fibre (dlpf) mutant with its wild-type cv. JRC-212 identified genes and regulatory sequences involved in metabolic pathways leading to monolignol biosynthesis and secondary cell wall formation. Some of the major genes with potential roles in these pathways were validated by qRT-PCR analysis, with comparative bast fibre development-specific expression profiling between the mutant dlpf and its wild-type. In this project, we also produced their hypocotyl transcriptomes, with an objective to study primary growth and identify novel transcripts associated with phloem fibre development. This project has provided valuable insights into molecular processes underlying bast fibre formation, which would enable development of biotechnological tools for producing low-lignin white jute cultivars with improved fibre characteristics. Functional markers (SSRs and SNPs) identified in this study would serve as useful genomic resources for genetic improvement of white jute.

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Chakraborty A, Sarkar D, Satya P, Karmakar PG, Singh NK