Functional Genomics Lab


Research Overview

1.    Deciphering plant-fungal interaction through functional genomics and transcriptomics

Plants are exposed to a wide variety of biotic and abiotic stresses. To survive under these challenges, plants have developed elaborate signal transduction mechanisms to counter act against the external signals and establish cellular responses. Plant fungal interaction is highly complex due to their differential recognizing abilities and varied resistant mechanisms. Our group is trying to study the molecular and biochemical mechanisms associated with host fungal interaction and characterize the genes controlling signaling modules as well as plant R-genes to get better insights about the organization, function and modulation of defense response. Techniques involve next generation sequencing (Illumina seq & PacBio Seq), microarray analysis, gene cloning and genetic transformation.

2.    Delineation of non-coding networks in the molecular interaction between plants and fungal phytopathogen

The whole genome tilling and RNA-Seq analysis has revealed that pervasive transcription is a widespread feature of all eukaryotic genomes. Recent evidences indicate that a significant portion of these un-annotated transcripts called the ‘dark matter’ are actually non-coding RNAs with important role in a wide range of biological processes. However, the repertoire and functions of ncRNAs (microRNAs and long non-coding RNAs) largely remains unexplored with respect to defense against phytopathogens. Our group is trying to use modern functional genomics tools to explore the role of specific non-coding RNAs and their associated networks in host mediated pathogen defense and pathogen mediated immunosuppressant.

3.    Development of molecular markers and marker assisted selection towards disease resistance in plants

Resistance responses to plant pathogens are the focus of intensive research in the recent times as current technologies offer the possibility of using molecular markers to identify disease resistance loci and their subsequent use in molecular breeding approaches. Our group is also involved in the development of specific PCR based and sequence based markers linked to resistant traits in important vegetable plants and their subsequent utilization which could be a priority in breeding programs in order to increase productivity and economic potential of the crop.

Faculties Associated: 

  • Dr. Raj Kumar Joshi, Assistant Professor
  • Prof. S Nayak, Prof. & Head

Research Scientists / Scholars Associated:

  • Dr. Rukmini Mishra
  • Subodh Kumar Chand
  • Jatindra Nath Mohanty

Publications:

  1. Mishra R, Mohanty JN, Chand SK, Joshi RK (2017) Can-miRn37a mediated suppression of ethylene response factors enhances the resistance of chilli against anthracnose pathogen Colletotrichum truncatum L. Plant Science 257:9-21(SCI impact factor- 3.56).
  2. Chand SK, Nanda S, Mishra R, Joshi RK (2017) Multiple garlic (Allium sativum L.) microRNAs regulate the immunity against the basal rot fungus Fusarium oxysporum f. sp. cepae. Plant Science 257:9-21(SCI impact factor- 3.56).
  3. Mohanty JN, Nayak S, Jha S, Joshi RK (2017) Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.) Voigt. Gene 626: 395-406. (SCI impact factor- 2.32).
  4. Mishra R, Nanda S, Rout E, Chand SK, Mohanty JN, Joshi RK (2017) Differential expression of defense genes in chilli pepper infected with anthracnose pathogen Colletotrichum truncatum. Physiological and Molecular Plant Pathology. 97: 1-10. (SCI impact factor- 1.49).
  5. Sinha P, Nanda S, Joshi RK, Panda PC (2017) Development of a sequence-tagged site (STS) marker for sex identification in the dioecious rattan species Calamus guruba Buch.-Ham. Molecular Breeding. 37: 22. (SCI impact factor-2.108)
  6. Joshi RK, Megha S, Basu U, Rahman MH and Kav NNV (2016). Genome wide identification and functional prediction of long non coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus. PLoS ONE. 11:e0158784. (SCI impact factor- 3.06).
  7. Joshi RK, Megha S, Rahman MH, Basu U and Kav NNV (2016). A global study of transcriptome dynamics in canola (Brassica napus L.) responsive to Sclerotinia sclerotiorum infection using RNA-Seq. Gene. 590: 57-67. (SCI impact factor- 2.32).
  8. Chand SK, Nanda S and Joshi RK (2016). Regulation of  miR394 in Response to Fusarium oxysporum f. sp. cepae (FOC) Infection in Garlic (Allium sativum L). Frontiers in Plant Science. 7:258. (SCI impact factor- 4.5).
  9. Chand SK, Nanda S, Rout, Mohanty JN, Mishra R and Joshi RK (2016). De Novo sequencing and characterization of defense transcriptome responsive to Pythium aphanidermatum infection in Curcuma longa L. Physiological and Molecular Plant Pathology. 94: 27-37. (SCI impact factor- 1.49).
  10. 10.    Nanda S, Chand SK, Mandal P, Tripathy P, Joshi RK (2016) Identification of novel source of resistance and differential response of Allium genotypes to purple blotch pathogen, Alternaria porri (Ellis) Ciferri. The Plant Pathology Journal. 36:519-527. (SCI impact factor- 1.34).
  11. Chand S, Nanda S, Rout E, Mohanty JN, Mishra R, Joshi RK (2016) Identification and characterization of microRNAs in turmeric (Curcuma longa L.) responsive to infection with the pathogenic fungus Pythium aphanidermatum. Physiological and Molecular Plant Pathology. 93: 119-128. (SCI impact factor- 1.49).
  12. Mohanty JN,  Nayak S, Jha S, Joshi RK (2016) A sequence tagged site (STS) marker encoding Copia-like retrotransposable element is associated with male specific sex expression in Momordica dioica Roxb. Scientia Horticulturae. 201: 265-270. (SCI impact factor-1.43).
  13. Nanda S, Rout E, Joshi RK (2016) Curcuma longa mitogen activated protein kinase 6 (ClMPK6) stimulates the defense response pathway and enhances the resistance to necrotrophic fungal infection. Plant Molecular Biology Reporter. DOI: 10.1007/s11105-015-0972-9. (SCI impact factor-1.78).
  14. Rout E, Nanda S, Joshi RK (2015) Molecular characterization and heterologous expression of a pathogen induced PR5 gene from garlic (Allium sativum L.) conferring enhanced resistance to necrotrophic fungi. European Journal of Plant Pathology. DOI: 10.1007/s10658-015-0772-y. (SCI impact factor-1.64).
  15.  E Rout, P Tripathy, S Nanda, S Nayak, R K Joshi (2015) Evaluation of cultivated and wild Allium accession for resistance to Fusarium oxysporum f.sp cepae. Proc. Natl. Acad. Sci. INDIA. Doi: 10.1007/s40011-015-0506-0 (SCI impact factor- 0.396).
  16. B K Bhowmick, S Nanda, S Nayak, S Jha and R K Joshi (2014) An APETALA3 MADS-box linked SCAR marker associated with male specific sex expression in Coccinia grandis (L.). Scientia Horticulturae 176:85-90. (SCI impact factor- 1.504).
  17. S Nanda, S Nayak and R K Joshi (2014) Molecular characterization and differential regulation of MAP kinase genes in turmeric (Curcuma longa L.) in response to diverse environmental cues and signal substances. Biologia Plantarum (Doi: 10.1007/s10535-014-0429-2) (SCOPUS, SCI impact factor- 1.69).
  18. E Rout, S Nanda, S Nayak and R K Joshi (2014) Molecular characterization of NBS encoding resistance genes and induction analysis of a putative candidate gene linked to Fusarium basal rot resistance in Allium sativum. Physiological and Molecular Plant Pathology. 85:15-24 (SCOPUS, SCI impact factor- 1.94).
  19. B Kar, S Nayak and R K Joshi (2014) Development and evaluation of STS diagnostic marker to track turmeric (Curcuma longa L.) resistance against rhizome rot caused by Pythium aphanidermatum. Australasian Plant Pathology. 43:167-175 (SCOPUS, SCI impact factor-1.0).
  20. 20.    B Kar, S Nanda, P.K Naik, S Nayak and R K Joshi (2013) Molecular characterization and functional analysis of CzR1, a coiled-coil-nucleotide-binding-site-leucine-rich repeat R-gene from Curcuma zedoaria Loeb. That confers resistance to Pythium aphanidermatumPhysiological and Molecular Plant Pathology. 83:59-68. (SCOPUS, SCI impact factor- 1.94).
  21. B Kar, S Nayak and R K Joshi (2013) Molecular cloning, characterization and transcriptional variability study of resistance gene candidates from wild Curcuma spp. for resistance against Pythium aphanidermatum. Plant Omics Journal. 6(1):86-94. (SCOPUS, SCI impact factor- 1.79)
  22. S Nanda, B Kar, S Nayak, S Jha and R K Joshi (2013) Development of an ISSR based STS marker for sex identification in pointed gourd (Trichosanthes dioica Roxb.). Scientia Horticulturae. 150:11-15. (SCOPUS, SCI impact factor- 1.46).
  23. R K Joshi, B Kar, S Mohanty, E Subudhi and S Nayak (2012) Molecular cloning, characterization and expression analysis of resistance gene candidates in Kaempferia galanga L. Molecular Biotechnology. 50(3):200-210. (SCOPUS) (SCI impact factor- 2.262)
  24. R K Joshi, S Mohanty, B Kar and S Nayak (2012) Assessment of genetic diversity in Zingiberaceae through nucleotide binding site (NBS) based motif directed profiling. Biochemical Genetics.50:642-656. (SCOPUS) (SCI impact factor- 1.0)
  25. R K Joshi and S Nayak (2012) Perspectives of genomic diversification and molecular recombination towards R-gene evolution in plants. Physiology and Molecular Biology of Plants. DOI: 10.1007/s12298-012-0138-2. (SCOPUS) (SCI impact factor- 1.34)

Submissions in the NCBI database:

  1. SK Chand, J Mohanty, R Mishra, RK Joshi (2018) Defense transcriptomes of Allium cepa post infection with Alternaria porrii (PRJNA420926).
  2. R Mishra, R K Joshi (2016) Two small RNAome libraries of Capsicum annuum post inoculation with Colletotrichum truncatum to the sequence read archive (SRA) (Accession no. SRX1770970, SRX1770971).
  3. JN Mohanty, S Nayak, S Jha, RK Joshi (2016) Two RNAseq transcriptome libraries of Coccinia grandis floral buds to the sequence read archive (SRA) (Accession no. SRX1770849, SRX1770875).
  4. R K Joshi, S Megha, M H Rahman, U Basu, Nat NV Kav (2015) 12 defense transcriptome libraries of Brassica napus post inoculation with Sclerotinia sclerotiorum to the sequence read archive (SRA) (Accession no. SRX956927-SRX956938).
  5. Chand S, Satyabrata Nanda, Ellojita Rout, Sanghamitra Nayak, R K Joshi (2015) Two RNAseq defense transcriptome libraries of Curcuma longa post inoculation with Pythium aphanidermatum to the sequence read archive (SRA) (Accession no. SRX857364, SRX857365).
  6. JN Mohanty, R K Joshi (2018) Seventeen sequences for Momordica dioica MADS-box  genes, complete cds (Accession no.MG491289- MG491305).
  7. R Mishra, JN Mohanty, R.K.Joshi (2017) Eight gene sequences for anthracnose resistance specific markers from Capsicum annuum (Accession no.MF581010-MF581017).
  8. S. K. Chand, S. Nanda, R.K.Joshi (2017) Four sequences for purple blotch resistance specific sequence tagged site markers (Accession no.KY775605-KY775608).
  9. S. K. Chand, S. Nanda, R.K.Joshi (2017) Six sequences for Allium cepa purple blotch resistance specific markers (Accession no.KY750712-KY750712).
  10. P. Sinha, S. Nanda, P.C.Panda, R K.Joshi (2016) Thirteen sequences for Calamus guruba male specific sex marker, genomic sequences (Accession no.KX374658-KX374670).
  11. J N Mohanty, S Nayak, R K Joshi (2016) Momordica dioica retrotransposon copia-like protein gene MdRe1, complete sequence. (Accession no. KU052576).
  12. J N Mohanty, S Nayak, R K Joshi (2016) Five sequences for Momordica dioeca male sex specific molecular markers, genomic sequences (Accession no. KU052571-KU052575).
  13. J N Mohanty, S Nayak, R K Joshi (2015) Ten sequences for Momordica dioeca male sex specific molecular markers, genomic sequences (Accession no.KT887170-KT887179).
  14. E Rout, S Nanda, and Nayak S, R K Joshi (2015) Allium sativum pathogenesis related protein 5 (AsPR-5), complete cds (Accession no. KP782043).
  15. S Nanda, E Rout and Nayak S, R K Joshi (2015) Curcuma longa mitogen activated protein kinase 6 (ClMPK6), complete cds (Accession no. KP782042).
  16. B Bhowmick, S Nanda, S Jha and Nayak S, R K Joshi (2014) 11 sequences for Coccinia indica sex specific molecular markers (Accession no. KF933354-KF933364).
  17. S Nanda, E Rout and Nayak S, R K Joshi (2013) Four sequences for Curcuma longa mitogen activated protein kinase genes, complete cds (Accession no. KC907274-KC907277).
  18. B Kar, S Nanda, Nayak S R K Joshi (2013) Curcuma zedoaria CzR1 cc-NBS-LRR R-protein gene, complete cds (Accession no. JX912230).
  19. E Rout, S Nanda, Pareek S, R K Joshi (2013) 23 sequences for Vigna aconitifolia CC-NBS-LRR disease resistance protein gene (Accession no. KF438052-KF438074).
  20. E Rout, S Nanda and Nayak S, R K Joshi (2013) 28 sequences for non-TIR-NBS-LRR disease resistance protein gene from Allium sativum, partial cds (Accession no. KF373046-KF373073).
  21. B Kar, Nayak S, R K Joshi (2013) Six sequences for rhizome rot resistance specific and STS diagnostic markers  from Curcuma longa (Accession no. KF603881-KF603886).
  22. S Nanda, B Kar, S Jha and Nayak S, R K Joshi (2013) Six sequences for Trichoxanthes dioeca male specific sex marker. (Accession no. JX678996-JX679001).
  23. R K Joshi, Kar B, Mohanty S, Subudhi E and Nayak S (2011). 21 sequences for CC-NBS-LRR resistance gene candidates from three wild species of turmeric, Curcuma aromatica, Curcuma angustifolia and Curcuma zedoaria (Accession no. JN426969-JN426989).
  24. R K Joshi, Kar B, Mohanty S, Subudhi E and Nayak S (2010). 14 sequences for NBS-LRR resistance like protein sequences from Kaempferia galanga (Accession no. HQ650147-HQ650160).
  25. R K Joshi, Mohanty S, Subudhi E and Nayak S (2010). Five sequences for NBS-LRR resistance gene analogs from Curcuma longa cv Surama, partial cds (Accession no. HM117001-HM117005).

Projects


Title of Project


1. Development of sequenced characterized amplified region (SCAR) markers and marker assisted selection towards purple blotch resistance in onion (Allium sepa L.)

2. Rapid development of NGS based SNP markers and marker-assisted selection towards purple blotch resistance in Onion (Allium cepa L.)

3. Evaluation of cytogenetic diversity in some genera of Cucurbitaceae and characterization of sex-linked genes in Coccinia through SCAR marker approach

PI name


Dr. R. K Joshi

 

 

 

Dr. R. K Joshi

 

 

Dr. S.Nayak

Funding Agency


DBT, Govt. of India

 

 

 

SERB, DST, Govt. of India

 

 

DBT, Govt. of India