Contents lists available at ScienceDirect Industrial Crops & Products journal homepage: www.elsevier.com/locate/indcrop Transcriptional analysis of a delayed-flowering mutant under short-day conditions reveal genes related to photoperiodic response in tossa jute (Corchorus olitorius L.) Shashi Bhushan Choudhary a, ⁎ ,1,3 , Dipnarayan Saha a,3 , Hariom Kumar Sharma a,2 , Isholeena Chowdhury a , A. Anil Kumar a , Sanjay Kumar Jambhulkar b , Jivan Mitra a a Division of Crop Improvement, Indian Council of Agricultural Research-Central Research Institute for Jute and Allied Fibers, Barrackpore, Kolkata, West Bengal, 700 121, India b Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, 400085, Mumbai, India ARTICLE INFO Keywords: Bast fibre Corchorus species Delayed-flowering mutant Jute Photoperiodic genes RNA-seq Short-day flowering Shoot-apex transcriptome assembly ABSTRACT Photoperiod profoundly determines reproductive and vegetative development in jute which is extremely cor- related 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 de- layed-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 ex- pressed 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, respec- tively. 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 iden- tification 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. 1. Introduction Mechanisms of flowering in higher plants, especially the regulation process influenced by seasonal cues, remained an age-old attraction for the biologists across the disciplines. In order to flower, plants must sense precisely, the daily duration of light or the photoperiod, which was first reported by Tournois in 1914, followed by Klebs in 1918 and later firmly established by Garner and Allard in the 1920s (Lin, 2000; Amasino, 2010). Besides photoperiod, temperature-sensing is also an integrated mechanism to determine the seasonal influence of flowering in plants (Song et al., 2013). Triggered by photo-thermo sensitivity, plants that favour flowering under long and short diurnal lengths are known as long-day (LD) and short-day (SD) plants, respectively. The phenomenon of photo-thermo sensing and flowering response, thus https://doi.org/10.1016/j.indcrop.2019.03.001 Received 29 August 2018; Received in revised form 27 February 2019; Accepted 1 March 2019 Abbreviations: DAS, Days after sowing; DETs, differentially expressed transcripts; cDNA, complementary DNA; EFS, early flowering under short-day conditions; EST, expressed sequence tag: GO gene ontology; LD, long-day; min, minutes; NCBI, National Center for Biotechnology Information; NGS, next-generation sequencing; nr, non-redundant; QC, quality check; RNA-seq, ribonucleic acid sequencing; s, seconds; SD, short-day; WT, wild-type ⁎ Corresponding author. E-mail address: shashigen@gmail.com (S.B. Choudhary). 1 Present Address: Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, Regional Station Ranchi, New Bhusur, Hatia, Jharkhand-8, India. 2 Present Address: Indian Council of Agricultural Research- Directorate of Rapeseed-Mustard Research, Sewar, Bharatpur, Rajsthana 321303, India. 3 These authors contributed equally. Industrial Crops & Products 132 (2019) 476–486 0926-6690/ © 2019 Elsevier B.V. All rights reserved. T