Niranjan Baisakh

Baisakh, Niranjan
Title Associate Professor
Department School of Plant, Environmental and Soil Sciences
Address 1 214 M.B. Sturgis Hall
Baton Rouge, LA 70803
Phone 225-578-1300
Fax 225-578-1403

Ph. D. (Botany-Plant Biotechnology), 2000, Utkal University, India, Research conducted at the International Rice Research institute (IRRI), Philippines, and Central Rice Research Institute (CRRI), India

M. S. in Agriculture (Plant Breeding and Genetics), 1993, Orissa University of Agriculture and Technology (OUAT), India

B. S. (Agriculture), 1990, OUAT, India

Associate Professor, July 2015 - present, LSU AgCenter
Assistant Professor, February 2013 - June 2015, LSU AgCenter
Assistant Professor-Research, May 2008 - January 2013, LSU AgCenter
Postdoctoral Researcher, July 2004 - June 2007, LSU AgCenter
Project Scientist (Postdoctoral fellow), January 2000 - June 2004, IRRI, Philippines
Visiting Scientist, September 2001, Institute of Molecular Agrobiology (now Temasek Life Science Laboratory), Singapore
Research Scholar, November 1997 - December 1999, IRRI, Philippines
Research Scholar, May 1995 - October 1997, CRRI, India

Teaching Experience

I teach a graduate level course ‘Special Topics in Plant Breeding’ (AGRO 7073), which is intended to orient the students of the potential of genetics and plant breeding in crop improvement through discussion of latest journal publications on contemporary research.

Plant (a)biotic stress
Molecular biology
Functional genomics
Genetic engineering
Tissue culture and dihaploid breeding

Research in my group uses a holistic approach, integrating molecular biology and functional genomics tools, with an overarching goal of improving agronomic traits of interest in field crops. Inexorable climate change would only exacerbate the biotic and abiotic stressors that negatively impact the growth and productivity of field crops. Members within primary, secondary and tertiary gene pool of crops vary with their ability to adapt to these stresses through physiological and biochemical adjustments. Strategies to develop climate-resilient designer crops depend on our depth of knowledge of plant’s responses to the stressors at tissue, cellular and molecular levels. Our research program involves basic molecular biology investigations in rice and Arabidopsis models to understand and identify the interplay of molecular genetic networks that regulate plant's tolerance/resistance under abiotic stresses, such as drought and salt. The knowledge generated from the basic research program is being translated to devise genetic tools that would complement conventional breeding efforts towards developing crop varieties with improved stress tolerance.

Sugarcane, in addition to its importance as a sugar crop, is regarded as an important second generation bioenergy grass (popularly known as energy cane). Marker-assisted breeding (MAB) can speed up conventional efforts to develop improved sugarcane varieties for the Louisiana sugar industry. Identification of stable molecular markers linked to a particular trait of interest, for example sucrose content, and biotic and abiotic stress resistance, is the key to a successful MAB. Our research aims to identify specific genes/gene-networks within the genomic regions that govern desirable traits towards development of allele-specific functional markers by exploiting the natural variations in traits that exist within the primary gene pool. We have deployed molecular markers to understand the genetic structure of Louisiana sugarcane gene pool – this information is currently being used in selection of parents for the crossing program to make sure maximum diversity is maintained to increase genetic gain. Our research focus is (1) to identify clones with high sucrose content using genomic selection – this will increase the accuracy of predicting performance based on genomic breeding values of new breeding lines; and (2) to develop and deploy markers for resistance to brown rust, leaf scald, and other imminent stressors, such as cold stress through a combination of gene expression and genome/association mapping strategies.

Similar experimental approaches are being used for development of DNA-based markers associated with various agronomic traits for their implementation in breeding of improved varieties of other commodity crops, such as wheat, sweetpotato and cotton.

Refereed Journals

Mangu VR, Ratnasekera D, Yabes JC, Wing RA, Baisakh N (2019) Functional screening of genes from a halophyte wild rice relative Porteresia coarctata in Arabidopsis model identifies candidate genes involved in salt tolerance. Current Plant Biology doi:10.1016/j.cpb.2019.100107

Fickett N, Gutierrez A, Verma M, Pontif M, Hale A, Kimbeng C, Baisakh N* (2018) Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection. Genomics

Sengupta S, Mangu V, Sanchez l, Bedre R, Joshi R, Rajasekaran K, Baisakh N* (2018) An actin depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora (SaADF2) is superior to its rice homolog (OsADF2) in conferring drought and salt tolerance when constitutively overexpressed in rice. Plant Biotechnology Journal doi:10.1111/pbi.12957

Gutierrez A, Hoy JW, Kimbeng CA, Baisakh N* (2018) Identification of genomic regions controlling leaf scald resistance in sugarcane using a bi-parental mapping population and selective genotyping by sequencing. Frontiers in Plant Science 9:877

Sengupta S, Rajaseakaran K, Baisakh N* (2018) Natural and targeted isovariants of the rice actin depolymerizing factor 2 can alter its functional and regulatory binding properties. Biochemical and Biophysical Research Communications 503:1516-1523.

Avellaneda MC, Parco AP, Hoy JH, Baisakh N (2018) Putative resistance-associated genes induced in sugarcane in response to the brown rust fungus, Puccinia melanocephala and their use in genetic diversity analysis of Louisiana sugarcane clones. Plant Gene

Zahraefard S, Foroozani M, Sepehri A, Oh D-H, Wang G, Mangu V, Chen B, Baisakh N, Dassanayake M, Smith AP (2018) Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes. Journal of Experimental Botany 69:4907-4919.

Mehanathan M, Bedre R, Mangu V, Rajasekaran K, Bhatnagar D, Baisakh N* (2018) Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. Physiology and Molecular Biology of Plants

Zhang Q, Oh DH, DiTusa SF, Ramanarao MV, Baisakh N, Dassanayake M, Smith AP (2018) Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression. BMC Genomics 19:97, doi:10.1186/s12864-017-4397-8.

Solis J, Gutierrez A, Ramanarao MV, Sanchez E, Bedre R, Linscombe S, Baisakh N* (2017) Genetic mapping of quantitative trait loci for grain yield under drought in rice under controlled greenhouse conditions. Frontiers in Chemistry 5, 10.3389/fchem.2017.00129.

Parco A, Hale AL, Barbosa MCA, Hoy J, Kimbeng CA, Pontif MJ, McCord PH, Ayala T, Todd J, Baisakh N* (217) Distribution and frequency of Bru 1, a major brown rust resistance gene, in the sugarcane world collection. Plant Breeding 136: 637-651.

Pilcher W, Zandkarimi H, Arceneaux K, Harrison S, Baisakh N* (2017) Genome-wide microarray analysis leads to identification of genes in response to herbicide, metribuzin in wheat leaves. PLoS ONE 12(12): e0189639, DOI:10.1371/journal.pone.0189639.

Muthamilarasan M, Mangu V, Zandkarimi H, Prasad M, Baisakh N* (2016) Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet, and their expression in rice. Scientific Reports 6:24008. DOI: 10.1038/srep24008.

Bedre R, Mangu V, Srivastava S, Timm L, Baisakh N* (2016) Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity. BMC Genomics 17(e) DOI: 10.1186/s12864-016-3017-3.

Ebrahimi L, Fotouhifar K, Nikkhah M, Naghavi M, Baisakh N* (2016) Population genetic structure of apple scab (Venturia inaequalis (Cooke) G. Winter) in Iran. PLoS ONE 11(9):e0160737. DOI: 10.1371/journal.pone.0160737.

Solis J, Baisakh N*, Brandt S, Villordon A, La Bonte D (2016) Transcriptome profiling of beach morning glory (Ipomoea imperati) under salinity and its comparative analysis with sweetpotato. PLoS ONE 11(2):e0147398. DOI: 10.1371/journal.pone.0147398.

Bedre R, Rajasekaran K, Mangu V, Bhatnagar D, Baisakh N* (2015) Genome-wide transcriptome analysis of cotton (Gossypium hirsutum L.) identifies candidate gene signatures in response to aflatoxin producing fungus Aspergillus flavus. PLoS ONE 10(9) doi: 10.1371/journal.pone.0138025

Zandkarimi H, Bedre R, Solis J, Mangu V, Baisakh N* (2015) Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel). Molecular Biology Reports 42: 1341-1350.

Ambavaram MMR, Basu S, Krishnan A, Ramegowda V, Batlang U, Rahman L, Baisakh A, Pereira A (2014) Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. Nature Communications 0/2014; 5:5302. DOI:10.1038/ncomms6302.

Parco AS, Avellaneda MC, Hale AH, Hoy JW, Kimbeng CA, Pontif MJ, Gravois K, Baisakh N (2014) Frequency and distribution of the brown rust resistance gene Bru1 and implications for the Louisiana sugarcane breeding program. Plant Breeding 133:654-659.

Joshi R, Ramanarao MV, Lee S, Kato N, Baisakh N (2014) Ectopic expression of ADP ribosylation factor 1 (SaARF1) from smooth cordgrass (Spartina alterniflora Loisel) confers drought and salt tolerance in transgenic rice and Arabidopsis. Plant Cell, Tissue and Organ Culture 117: 17-30.

Solis J, Villordon A, Baisakh N, Labonte D, Firon N (2014) Effect of drought on storage root development and gene expression profile of sweetpotato under greenhouse and field conditions. Journal of the American Society for Horticultural Science 139: 317-324.

Khan N, Bedre R, Parco A, Bernaola L, Hale A, Kimbeng C, Pontif M, Baisakh N* (2013) Identification of cold responsive genes in sugar/energycane for their use in genetic diversity analysis and future functional marker development. Plant Science 211: 122-131.

Joshi R, Ramanarao MV, Baisakh N* (2013) Arabidopsis plants constitutively overexpressing a myo-inositol 1-phosphate synthase gene (SaINO1) from the halophyte smooth cordgrass exhibits enhanced level of tolerance to salt stress. Plant Physiology & Biochemistry 65: 61-66.

Effendy J, La Bonte D, Baisakh N* (2013) identification and expression of skinning injury responsive genes in sweetpotato. Journal of American Society of Horticultural Science 138: 1-7.

Baisakh N*, RamanaRao MV, Rajasekaran K, Subudhi P, Galbraith D, Jonda J, Vanier C, Pereira A (2012) Enhanced salt stress tolerance of rice plants expressing a vacuolar H+-ATPase subunit c1 (SaVHAc1) gene from a halophyte grass Spartina alterniflora Löisel. Plant Biotechnology Journal 10: 453-464.

Datta K, Baisakh N, Ganguly M, Krishnan S, Yamaguchi-Shinozaki K, Datta S (2012) Overexpression of Arabidopsis and rice stress inducible transcription factor confers drought and salinity tolerance to rice. Plant Biotechnology Journal 10: 579-586.

Suman A, Ali K, Arro J, Parco A, Kimbeng C, Baisakh N* (2012) Molecular diversity among members of the Saccharum complex assessed using TRAP markers based on lignin-related genes. Bioenergy Research 5: 197-204.

RamanaRao MV, Weindorf D, Breitenbeck G, Baisakh N* (2012) Differential expression of the transcripts of Spartina alterniflora Loisel (smooth cordgrass) induced in response to petroleum hydrocarbon. Molecular Biotechnology 51: 18-26.

Lee S, Rajasekaran K, Ramanarao MV, Bedre R, Bhatnagar D, Baisakh N* (2012) Identifying cotton (Gossypium hirsutum L.) genes induced in response to Aspergillus flavus infection. Physiological & Molecular Plant Pathology 80: 35-40.

Gravois K, Baisakh N, Waguespack H, Hoy J, Kimbeng C (2012) L 01-283 – Effects of Off-Types on Cane Yield, Sucrose Content and Fiber Content. Journal American Society of Sugar Cane Technologists 32: 86.

Bertrand-Garcia SE, Knott CA, Baisakh N, Subudhi P, Harrison S, Materne M, Utomo H (2012) Selection of genetically diverse sea oats lines with improved performance for coastal restoration in the northern Gulf of Mexico. Euphytica 185: 103-117.

Knott CA, Materne MD, Utomo H, Subudhi PK, Baisakh N, Harrison SA (2012) Registration of smooth cordgrass cultivars LA11-101, LA11-102, and LA11-103. Journal of Plant registrations 6: 252-258.

Knott CA, Materne MD, Subudhi PK, Baisakh N, Utomo H, Harrison SA (2012) Registration of sea oats cultivars LA12-201, LA12-202, and LA12-203. Journal of Plant registrations 6: 289-293.

Knott CA, Materne MD, Utomo H, Subudhi P, Baisakh N, Harrison SA (2012) Registration of ‘St. Bernard’, ‘Las Palomas’, and ‘Lafourche’ smooth cordgrass cultivars. Journal of Plant Registrations 7: 12-17.

Parco A, Arro JA, Patil SB , Bernaola L, Kimbeng CA, Baisakh N* (2011) Genetic diversity of commercial sugarcane cultivars of Louisiana analyzed using SSR markers. Journal of the American Society of Sugar Cane Technologists 31: 59.

Subudhi P, Baisakh N* (2011) Spartina alterniflora Loisel., a halophyte grass model to dissect salt stress tolerance. In vitro Cell Developmental Biology – Plant 47: 441-457.

Rao MVR, Behera KS, Baisakh N*, Rao GJN (2009) Transgenic indica rice cultivar ‘Swarna’ expressing a potato chymotrypsin pin2 gene shows enhanced levels of resistance to yellow stem borer. Plant Cell Tissue & Organ Culture 99: 277-285.

Baisakh N*, Subudhi PK, Parco AP, Arumuganathan K, Harrsion SA, Knott C, Materne MD (2009a) Development and interspecific transferability of genic microsatellite markers in Spartina spp with different genome sizes. Aquatic Botany 91:262-266.

Baisakh N, Subudhi P (2009b) Heat stress alters the expression of salt stress induced genes in smooth cordgrass (Spartina alterniflora L.). Plant Physiology & Biochemistry 47:232-235.

Baisakh N, Subudhi P, Varadwaj P (2008) Primary response to salt stress in a halophyte, smooth cordgrass (Spartina alterniflora Loisel). Functional & Integrative Genomics 8: 287-300.

Baisakh N, Subudhi P, Parami N (2006) cDNA-AFLP analysis reveals differential gene expression in response to salt stress in a halophyte Spartina alterniflora Loisel. Plant Science 170: 1141-1149.

* Corresponding author

Book chapters

Joshi R, Mangu VR, Bedre R, Sanchez L, Pilcher W, Zandkarimi H, Baisakh N (2015) Salt adaptation mechanisms of halophytes: improvement of salt tolerance in crop plants. In Elucidation of Abiotic Stress Signaling in Plants, 2 Girdhar Pandey (ed) Springer publ. pp. 243-279.

Batlang U, Baisakh N, Ambavaram MMR, Pereira A (2012) Phenotypic and Physiological evaluation for drought and salinity stress responses in rice. In “Rice Methods” Yinong Yang (ed), Humana Press. pp. 209-226.

Kang MS, Subudhi PK, Baisakh N, Priyadarshan PM (2007) Crop breeding methodologies: classic and modern. In “Breeding major food staples” MS Kang and PM Priyadarshan (eds), Blackwell publ. pp. 1-22.

Baisakh N, Datta SK (2007) Stem Borer Resistance: Bt Rice. In “Rice improvement in the Genomics Era” SK Datta (ed), Haworth publ. pp.139-177.

Other publications

Baisakh N*, Famoso A, Yabes J, Tabien R, Harrell D (2019) Developing Rice Varieties Suitable for Alternative Irrigation Regimes in Louisiana. Louisiana Agriculture 62: 18-19.

Baisakh N*, Avellaneda CA, Gutierrez A, Parco A, Khan N, Hoy J, Kimbeng C, Gravois K (2014) Molecular biology tools to facilitate sugarcane breeding in Louisiana. Louisiana Agriculture 57: 8-9.

Hoy JW, Baisakh N, Kimbeng CK (2013) Breeding for disease resistance: Change is coming. Sugar Journal 75: 20-23.

Harrison SA, Baisakh N, Materne MD, Knott C, Subudhi P, Utomo HS (2007) Breeding native coastal plants: use in coastal wetland reclamation and preservation. Louisiana Agriculture 50: 18-19.

Subudhi P, Baisakh N, Sahoo D, Harrison SA, Materne M, Utomo HS (2007) Sea oats micropropagation aids in coastal restoration. Louisiana Agriculture 50: 20.

Subudhi P, Baisakh N, Harrison SA, Materne MD, Utomo HS (2007) Plant genetic diversity essential for a dynamic Louisiana coast. Louisiana Agriculture 50: 21.

Utomo HS, Materne MD, Harrison SA, Subudhi P, Baisakh N (2007) Improved marsh plants and seed-based propagation. Louisiana Agriculture 50: 22-23.

Service award for serving on the Louisiana State University Inter-Institutional Biological and Recombinant DNA Safety Committee, Louisiana 2014

Teacher Merit Honor Roll, LSU Chapter of Gamma Sigma Delta, 2014

Travel Award to attend the 1st international workshop on Engineered Crops, Des Moines, IA, 2014

LSU Campus-wide first Laboratory Safety Accreditation Award 2011

Travel Award from National science Foundation to attend the 2nd Pan American congress on plants and bioenergy, San Pedro, Brazil, 2010

Tipton Team Research Award, Louisiana State University Agricultural Center, 2007

Innovate . Educate . Improve Lives

The LSU AgCenter and the LSU College of Agriculture