Transcriptional analysis of a delayed-flowering mutant under short-day conditions reveal genes related to photoperiodic response in tossa jute (Corchorus olitorius L.)

• Published in: Industrial crops and products Vol. 132; pp. 476 - 486
• Main Authors: Choudhary, Shashi Bhushan, Saha, Dipnarayan, Sharma, Hariom Kumar, Chowdhury, Isholeena, Kumar, A. Anil, Jambhulkar, Sanjay Kumar, Mitra, Jivan
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-06-2019
• Subjects: Bast fibre; Corchorus species; Delayed-flowering mutant; Jute; Photoperiodic genes; RNA-seq; Shoot-apex transcriptome assembly; Short-day flowering; nr; Short-day flowering; EST; Corchorus species; SD; QC; Bast fibre; EFS; min; s; RNA-seq; Shoot-apex transcriptome assembly; DAS; Delayed-flowering mutant; LD; NCBI; cDNA; NGS; WT; Photoperiodic genes; DETs; Jute
• ISSN: 0926-6690; 1872-633X
• DOI: 10.1016/j.indcrop.2019.03.001

•A gamma-irradiated mutant of jute, pfr 59 exhibited significantly delayed flowering-time phenotype in comparison to its wild-type plant JRO204.•Transcriptome from shoot apices of mutant and wild-type plant produced a merged assembly of 14050 transcripts with more than 90% aligning to the published jute genomes.•Digital gene expression analysis revealed 240 differentially expressed transcripts of which 10 transcripts showed homology to known photoperiodic genes of Arabidopsis.•Differential expression pattern of nine putative photoperiodic transcripts in leaf and shoot apex of mutant and wild-type infers their role in flowering-time regulation in jute.
Photoperiod profoundly determines reproductive and vegetative development in jute which is extremely correlated to fibre yield and quality. Yet, our understanding of how the photoperiodic genes regulate vegetative and reproductive growth in jute remain unresolved. We developed RNA-seq data from shoot apex tissues of a delayed-flowering mutant (pfr 59) and its wild-type cultivar JRO-204 grown under short-day conditions. A merged de novo transcriptome assembly of 14,050 high-quality transcripts with N50 length of 1371 base-pairs, was constructed from the filtered RNA-seq data. Digital gene expression analysis produced 240 differentially expressed transcripts (DETs) between pfr 59 and JRO-204 shoot-apex transcriptome. Comparative analysis of these DETs showed homology to 75% and 42.5% sequences from the NCBI-NR and SWISSPROT databases, respectively. We could successfully align > 93% of the 14,050 merged transcripts and >65% of the 240 DETs to the three published jute genomes with >94.8% identity. Homology search for proteins from the FLOR-ID database led to the identification of 55 transcripts (3.9%) from the transcriptome assembly and 10 transcripts (4.2) from the DETs matching to photoperiod-related proteins. Gene expression validations of nine putative photoperiod-related DETs showed their differential expression patterns in leaf and shoot apex tissues of pfr 59 and JRO-204 under short-day conditions. The present report describes an assembly of a shoot apex transcriptome and identification of photoperiod-responsive transcripts with their putative role in regulating flowering mechanism in jute under short-day conditions. This crucial information may lay a foundation to devise genetic improvement strategies, such as gene-editing, for delaying the early onset of short-day flowering.