ICAR Central Research Institute for Jute and Allied Fibres CRIJAF

Kolkata, India

ICAR Central Research Institute for Jute and Allied Fibres CRIJAF

Kolkata, India
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Sarkar D.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Mahato A.K.,Indian Agricultural Research Institute | Satya P.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Kundu A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | And 20 more authors.
Genomics Data | Year: 2017

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000). © 2017


Biswas C.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Dey P.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Selvarajan R.,National Research Center for Banana | Bera A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | And 2 more authors.
Plant Disease | Year: 2016

Ramie (Boehmeria nivea) is a perennial herbaceous plant that produces strong and lustrous bast fiber. It is native to East Asia and is mainly grown in China, India, Taiwan, Philippines, Thailand, Brazil, and South Korea (Sarkar et al. 2012). In May 2013, ramie plants exhibiting yellow mosaic symptoms were noted in experimental fields of the CRIJAF research farm, Barrackpore, India. In young green leaves, vein-clearing was prominent, whereas older leaves showed complete yellowing. Plants were stunted and bushy. The incidence of the disease varied from 2 to 10%. Five symptomatic and five asymptomatic samples were collected from the field and DNA was extracted using the CATB method (Biswas et al. 2013). DNA samples were tested for begomovirus infection by PCR using universal primer pair PAL1v1978B/PAR1c715H (Rojas et al. 1993). Only the symptomatic samples showed amplification of a 1.5-kb product suggesting that plants were infected by a begomovirus. Furthermore, circular DNA was amplified by rolling circle amplification (RCA) with Illustra TempliPhi Kit (GE Healthcare, UK) according to the manufacturer’s instructions. RCA product was digested with EcoRI, BamHI, EcoRI, KpnI, Hind III, and PstI (New England Biolabs) respectively. The fragments of 2.1 kbp (with BamHI digestion) and 1.5 kbp (with KpnI digestion) were cloned and sequenced. The sequence of the 2.1-kbp fragment showed similarity with published sequences of begomovirus DNA-A component. From the 2.1-kbp sequence, a pair of primers was designed to obtain full-length DNA-A component, namely JAF1 (5′-CTTCATCGTTTCTCAGCATCAT-3′) and JAR1 (5′-CACTTGCACACGATCTCTAAGA-3′). The full-length DNA-A was 2686 bp nucleotides and encoded six putative ORFs (GenBank Accession No. KF962542). The sequence of the 1.5-kbp fragment shared similarity with DNA-B. The begomoviral circular DNA-B was amplified using the pair of primers JBF1 (5′-GTAACACCCGAAGTGCACG-3′) and JBR1 (5′-AAAGGAGAGACACCAGTCTGCC-3′) designed from the 1.5-kbp sequence. PCR yielded a full-length DNA-B sequence of 2666 bp nucleotides and encoded two putative ORFs (GenBank Accession No. KF962543). BLASTn analysis revealed that DNA-A from the ramie begomovirus isolate has 100% nucleotide sequence identity with the complete sequence of DNA-A component of Corchorus golden mosaic virus (Accession No. FJ463902). Similarly, DNA-B also has 100% identity with complete sequence of CoGMV DNA-B component (Accession No. FJ455448). Based on BLASTn analysis and sequence analysis using MEGALIGN (DNASTAR), the virus causing symptoms in ramie appears to be CoGMV, which is a New World begomovirus from the Old World infecting jute (Corchorus capsularis) (Ha et al. 2006). To our knowledge, this is the first report that CoGMV infects ramie plants. The incidence of CoGMV in ramie is relatively low, but in the future it may negatively affect the yield. © 2016 The American Phytopathological Society.


Kundu A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Chakraborty A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Mandal N.A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Das D.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | And 3 more authors.
Molecular Breeding | Year: 2015

We used RAD (restriction-site-associated DNA) sequencing to detect genome-wide SNPs and construct a dense linkage map using an intercross F2 population in jute (Corchorus olitorius). The linkage map comprising a total of 503 RAD markers in seven linkage groups spanned 358.5 cM with an average marker interval of 0.72 cM and covered 87.0 % of the genome. Genome-wide segregation distortion of the mapped loci (34.4 %) was non-random across the linkage map, with a directional bias mostly towards the female genotypes. Jute had maximum syntenic relationships with cocoa (47.5 % homology) and diploid cotton (29.2 % homology). However, synteny and collinearity were not conserved. Histological fibre content (FC; total number of fibre cell bundles in a stem cross section) was positively correlated with fibre yield (FY), plant height (PH), root weight (RW) and stem-base diameter (SBD). Broad-sense heritability estimates were high for all traits, with FC and FY showing maximum heritability (~93 %). QTL mapping based on the F2:3 phenotypes detected nine QTL across the two environments. The QTL for FC was coincident with one QTL each for FY, PH, RW and SBD on top of a single-SNP (C/T) marker at 40.2 cM on LG1, each accounting for ~7–11 % of the phenotypic variance. Two QTL linked in repulsion one each for PH and SBD, with varying degrees of overdominance, were associated with two single-SNP (C/T) markers on LG2, each accounting for ~17–18 % of the phenotypic variance. Few candidate genes were identified within the QTL regions. Our results would enable development of tools for marker-assisted selection in jute. © 2015, Springer Science+Business Media Dordrecht.


Chakraborty A.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Sarkar D.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Satya P.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Karmakar P.G.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Singh N.K.,National Research Center on Plant Biotechnology
Molecular Genetics and Genomics | Year: 2015

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136  bp, respectively, were assembled de novo, ~77–79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37–40 %) and GO (~22–28 %) classifications and mapped to 189 KEGG pathways (~19–21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers’ deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches. © 2015, Springer-Verlag Berlin Heidelberg.


Gotyal B.S.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | De R.K.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Selvaraj K.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Satpathy S.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | And 2 more authors.
Journal of Environmental Biology | Year: 2016

The pest status of yellow mite, Polyphagotarsonemus latus (Banks) has enhanced jute causing regular infestation. Improper crop management, particulary imbalanced fertilizer application encourages population build-up and outbreak of mite and other sucking pests.Field experiments were conducted to study the effect of different levels of nitrogenous fertilizer (40, 60, 80, 100 and 120 kg ha ) on infestation of P. latus in jute ( JRO-8432) in two subsequent cropping seasons. Results revealed there was significant variation on infestation of P. latus in jute crop treated with different levels of nitrogenous fertilizers. Moderate infestation (96.73 mites cm leaf) of yellow mite during peak period at 55 days after sowing (DAS) was recorded in the recommended dose (80:40:40 kg ha ) as compared to higher doses 120: 40: 40 kg ha (138.52 mites cm leaf). Although, positive correlation exists between N-fertilization and mite population, yield was maximum with highest N dose 120: 40: 40 and incremental dose of nitrogen on yield was clearly manifested on the benefit cost ratio (BCR) of different NPK dosages, which was highest (1.58) at 120: 40:40 level. It is evident from the study that although NPK had favorable effect on population establishment and it may also replenish the damage as fibre yield was maintained at higher doses instead of higher mite population. These study clearly suggested that slight manipulation in recommended doses of N fertilizer can contribute substantially in regulating the abundance of yellow mite with non-significant effect on yield enhancement in jute. © Triveni Enterprises, Lucknow (India).


Dey P.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Biswas C.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF | Karmakar P.G.,ICAR Central Research Institute for Jute and Allied Fibres CRIJAF
Physiological and Molecular Plant Pathology | Year: 2016

A RIL population of jute developed by crossing one resistant accession CIM 036 and a susceptible variety JRC 412 was used to identify novel defence related miRNAs activated upon challenged inoculation with stem rot pathogen Macrophomina phaseolina. About a total of 15.7 million reads were generated from the resistant line with the read length of 1 × 50 bp. Here, we identified nine mature novel microRNAs which passed Minimum Free Energy (MFE Kcal/mol) criteria. Target site and secondary structure were predicted and most of them showed ubiquitination and selective autophagy activity with high expression value. Five novel miRNAs viz. Candidate_41, Candidate_9, Candidate_66, Candidate_65 and Candidate_8 had free energy less than -25 kcal/mol. Known microRNAs viz. miR-845b and miR-166 superfamily are abundantly expressed with high expression value. The sequence of jute miR-845b superfamily is identical to that of Arabidopsis thaliana except at 18th position, but unlike in A. thaliana it targets the coding sequence for the P-loop motif in the mRNA sequences for disease resistance proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) motifs. In-silico analysis suggested that miR-845b and miR-166 superfamily provided NBS-LRR and ROS mediated defence and subsequently expression of novel microRNAs with selective autophagy activity enabled multi-layered defence cascade against M. phaseolina in jute. © 2016 Elsevier Ltd.


PubMed | ICAR Central Research Institute for Jute and Allied Fibres CRIJAF
Type: Journal Article | Journal: Molecular genetics and genomics : MGG | Year: 2015

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.

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