Dr. K.N. Nair

Chief Scientist

Research Interests

The main focus of our research is on understanding the taxonomy, phylogeny and phylogeography of plants of botanical and economic interests using morphological and molecular data.Elucidating morphological character evolution and identifying its genetic basis through molecular systematic approaches is another facet of our ongoing research. We also study genetic diversity, population genetic structure and phylogeography of important wild plant genetic resources using DNA markers.

We have been involved in molecular systematic studies on Citrus (Rutaceae), Luffa (Cucurbitaceae), and the Didymocarpus- Henckelia generic complex (Gesneriaceae) in India using DNA sequence analyses of  nrDNAITS and cpDNA genes. These studies are aimed at identifying and resolving the taxonomic complexes in the respective plant genera and also to infer the genetic as well a geographic origin of some of the species of disputed centre of origin.

Dr. K.N. Nair

Chief Scientist

Research Summary


Molecular phylogenetics of Indian Citrus

The taxonomy and phylogeny of Indian Citrus was revisited using PCR-RFLP of the trnDtrnT and rbcLORF 106, trnL-trnF intergenic spacer, Directed Amplification of Minisatellite DNA (DAMD) and nrDNA ITS analyses. Phylogenetic analyses supported the concept of Citrus medica (citron), C.reticulata (mandarin), and C. maxima (pummelo) as the basic species of the genus. There was no clear cut differentiation between subgenera Citrus and Papeda as proposed in Swingle’s Citrus classification system. These studies also supported the distinctiveness of C. indica (Indian wild orange), C. latipes (Khasipapeda) and C. hystrix (Melanesian papeda) as true species, besides elucidating the probable hybrid origin and relationships among the cultivated species/biotypes, such as C.aurantiifolia (sour lime) C. limon (lemon), C. taitensis (Indian rough lemon), C. limettioides(sweet lime), C. aurantium (including sour and sweet oranges and grapefruit), and other indigenous varieties of Indian origin: C. megaloxycarpa (sour pummelo), C. karna (karna orange), C. pseudolimon (Hill lemon), ‘Memangathur’, ‘Pummelo-lemon’ and ‘Kathairinimbu’. [Sci.Hort. 2009,119 :403-416; Genet. Resourc. Crop Evol. 2013, 60: 59-75; 1777-1800]


Genetic diversity assessment of Citrus and wild relatives

Inter simple sequence repeats (ISSR) polymorphism in Citrus indica, an endemic and threatened wild species, was examined along with three other closely related wild taxa (C. medica, C. latipes and C. sp. ‘Memangathur’) by analyzing 53 representative accessions sampled from North-east India. Significantly low level of genetic variation was detected in C. indica. Low genetic variability, heterozygosity and Shannon’s information index in C. medica, C. latipes and ‘Memangathur’ are also concerns that need to be addressed for developing appropriate strategies to conserve the genetic diversity extant in these valuable genetic resources.[Sci. Hort. 2010,123: 350-359 ]


Genetic diversity in Meropeangulata, a threatened mangrove associate species, was assessed using AFLP and ISSR markers. It is an under-utilized salt tolerant plant related to Citrus. The analysis was based on 55 individuals of M. angulata, sampled from two natural populations (Bhitarkanika Wildlife Sanctuary) and one ex situ population (Jharkhali Mangrove Ecological Garden) in India Moderate genetic diversity and a weak population structure were detected. Genetic diversity was correlated with high outcrossing rate and gene flow. Habitat fragmentation warrants adequate conservation measures for the species.[Aquatic Bot. 2015,120(B): 260-267]


Analysis of diversity amongst widely distributed and endemic Atalantia species from Western Ghats of India

The genus Atalantia is represented in India with four species and two varieties. The infra – generic classification and the species limits in Atalantia are, however, not well defined, due to the occurrence of intermediate forms. Two species,A. racemosa and A. monophylla, are widely distributed, while the third species, A. wightiiis endemic in the Western Ghats. Genetic diversity within and between populations of the above three species was estimated using two Single Primer Amplification Reaction (SPAR) methods. AMOVA analysis clearly indicates the lesser diversity among the species than within them. The UPGMA tree included all of the doubtful species in one single sub-cluster within the major cluster of A. racemosa and A. wightii, suggesting that these are probably hybrids derived from these two species. At the population level, all A. monophylla populations grouped together in a cluster that was clearly separated from all other species and populations. [Physiol. Mol. Biol. Plants 2009; 15(3) : 211-224]


Phenetic and genetic diversity in Indian Luffa (Cucurbitaceae) inferred from morphometric, ISSR and DAMD markers

Genetic variations and relationships among cultivated and wild genotypes of five taxa of Indian Luffa were examined using ISSR, DAMD markers and morphological characterization. Morphometric evaluation of 21 discrete characters in 51 representative accessions segregated the five taxa of Luffa in three main clusters: the two wild species (L. echinata, L. graveolens) in the first, and the cultivated L. aegyptiaca (smooth gourd) and L. acutangula (ridged gourd)/L. hermaphrodita (Hermaphrodite luffa) in the second and third clusters, respectively. Cumulative data analysis of 15 ISSR and seven DAMD markers revealed high percentage polymorphism (97.67 %), moderate genetic distance (0.06–0.72, avg. 0.51), and low heterozygosity and Shannon index values (H = 0.15; I = 0.22) across all the 76 genotypes assayed. A UPGMA dendrogram, based on the combined marker data, resolved the five taxa in two main clusters with high bootstrap support. The cluster analyses and PCoA plots revealed a nested grouping of the hermaphrodite luffa within the ridge gourd group. The Bayesian STRUCTURE analysis identified three genetic clusters for the five assumed taxa. Outcrossing test revealed a mixed mating system in Indian Luffa. [Genet. Resourc. Crop Evol. 2017, 64: 995-1010]


Molecular systematics of the Didymocarpus-Henckelia generic complex (Gesneriaceae) in India

Materials for preparing systematic revisions of Didymocarpus and Henckelia in India have been prepared. The revisionary account recognized 22 species and 2 varieties of Didymocarpus and 34 species of Henckeliain India. The systematic treatment included an updated nomenclature, detailed taxonomic description, notes on phytogeographic distribution, phenology, habitat, and etymology of the taxon names, accompanied with colour photographs and geo-referenced distribution maps of species collected during the course of this study. DNA sequences of 96 accessions nrDNA ITS and 67       accessions of cpDNAmatK representing 26 species of Henckelia were successfully generated from the freshly collected samples collected from different phytogeographic region of India. The molecular analyses were performed with three different data sets: a) ITS, b) matK, and c) ITS + matK with 67 accessions for which sequences of both the loci were generated successfully. MP, BI and ML trees drawn from ITS and ITS+ matKdata showed similar topologies segregating Henckelia and the out-groups in distinct clades, with most of the nodes and branches receiving moderate to high bootstrap support. However, the matK based MP, BI and ML tress could not resolve most of the Henckelia species, especially those from south India. 

Dr. K.N. Nair

Chief Scientist


– Misra S, Srivastava AK, Verma S, Pandey S, Bargali SS, Rana TS, Nair KN. 2017. Phenetic and genetic diversity in Indian Luffa (Cucurbitaceae) inferred from morphometric, ISSR and DAMD markers. Genet. Resour. Crop Evol. 64: 995-1010. DOI 10.1007/s10722-016-0420-1.

– Pandey S, Rana TS, Nair KN. 2016. Revision of the Trichosanthes tricuspidata- bracteata complex (Cucurbitaceae) in India. Rheedea 26: 83-93.

DOI:Jena SN, Verma,S, Nair KN, Srivastava AK, Mishra, S, Rana TS. 2015. Genetic diversity and population genetic structure of the mangrove lime (Merope angulata) in India revealed by AFLP and ISSR Markers. Aquatic Bot. 120 (B): 260-267; DOI DOI :10.1016/j.aquabot.2014.09.004

– Adekunle VA, Nair KN, Srivastava AK, Singh NK. 2014. Volume yield, tree species diversity and carbon hoard in protected areas of two developing countries. Forest Sci. Technol.10: 89-103. DOI 10.1080/21580103.2013.860050.

– Adekunle VA, Nair KN, Srivastava AK, Singh NK. 2013. Models and form factors for stand volume estimation in natural forest ecosystems: a case study of Katarniaghat Wildlife Sanctuary (KGWS), Bahraich District, India. J. Forestry Res. 24: 217−226. DOI 10.1007/s11676-013-0347-8.

– Kumar,S, Nair, KN. 2013. Genetic variation and phylogenetic relationships among Indian Citrus taxa revealed by DAMD-PCR markers. Genet. Resour. Crop Evol. 60: 1777-1800; DOI 10.1007/s10722-013-9954-7.

– Kumar S, Nair KN and Jena SN. 2013. Molecular differentiation in Indian Citrus L. (Rutaceae) inferred from nrDNA ITS sequence analysis. Genetic Resources and Crop Evolution 60: 59-75; DOI 10.1007/s10722-012-9814-x.

– Sribash Roy,Antariksh Tyagi,Virendra Shukla,Anil Kumar,Uma M. Singh,Lal Babu Chaudhary,Bhaskar Datt,Sumit K. Bag,Pradhyumna K. Singh, Nair KN, Tariq Husain,Rakesh Tuli. 2010. Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species. PLoS ONE,. October 2010 | Volume 5 | Issue 10 | e13674|27 Oct.

– Susheel Kumar, Satya Narayan Jena, Nair KN. 2010. ISSR polymorphism in Indian wild orange (Citrus indica Tanaka, Rutaceae) and related wild species in North-east India. Sci. Hort., 2010,123, 350-359.

– Ranade, SA, Nair KN, Srivastava A, Pushpangadan P (2009). Analysis of diversity amongst widely distributed and endemic Atalantia (Family Rutaceae) from Western Ghats of India Physiology and Molecular Biology of Plants. 15(3): 211-224.

– Jena, SN, Kumar S and Nair KN. 2009.  Molecular phylogeny in Indian Citrus L.(Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA. Sci. Hort. 119: 403-416.2009. doi10.1016/j.scienta.2008.08.030).

Dr. K.N. Nair

Chief Scientist


Dr. K.N. Nair

Chief Scientist

Research Scholars

Mr. Oluwatobi OSO, TWAS-CSIR Graduate Research Fellow

Dr. Abid S Yerimani, Research Associate

Mr. Aakash Maurya, CSIR-UGC SRF

Mr. Ranjith Layola M.R., CSIR-JRF

Ms. Savita Pandey, Project Assistant

Mr.  Kanthraj A.S., Project Assistant

Mr.  Ram Mohan, Project Assistant

Ms. Bhavya Priyadarshini Mishra, Project Assistant


Dr. K.N. Nair

Chief Scientist


Plant Diversity, Systematics & Herbarium

CSIR-National Botanical Research Institute,  Rana PratapMarg, Lucknow-226001

Phone no.: 0522-2297852, 853

Email: knnair@nbri.res.in