Genetic diversity studies in endangered desert teak [Tecomella undulata (Sm) Seem] using arbitrary (RAPD), semi-arbitrary (ISSR) and sequence based (nuclear rDNA) markers
- 58 Downloads
Substantial genetic diversity exists in the natural populations of desert teak which needs to be conserved in-situ as well as ex-situ to ensure sustainable utilization and survival of this endangered tree.
Tecomella undulata (Sm) Seem (family bignoniaceae) is a medicinally important agroforestry tree yielding quality timber commercially known as desert teak. This slow growing tree found in hot arid regions of western Rajasthan is used to treat various ailments and disorders. This monotypic genus with three colour morphotypes is also used for phytoremediation of soils, biosorptive removal of inorganic salts, synthesis of silver nanoparticles, rehabilitation of lignite mine backfills and as bio-fertilizer. This multifaceted tree is heading towards extinction due to over exploitation, unscientific management and negligible plantation efforts. No initiatives have been undertaken to conserve, domesticate or genetically improve this pharmacologically important timber tree. An attempt was made to analyze the genetic variability existing in western Rajasthan, the natural hub of this species, using RAPD, ISSR and rDNA markers for the first time. The RAPD markers (69.05%) detected polymorphism more efficiently compared to ISSR (61.76%) among the 119 samples belonging to 22 populations. Likewise, average number of amplicons, polymorphic amplicons and polymorphism information content (PIC) were more for RAPD (11.25, 7.95 and 0.52, respectively) than for ISSR (10.4, 6.45 and 0.40) markers. The percent variability within and between populations varied among ISSR (64 and 36%, respectively) and RAPD (71 and 29%) markers. A positive correlation coefficient (r) of 0.402 was observed between RAPD and ISSR markers. The UPGMA dendrogram separated the samples into 13 (RAPD) and 11(ISSR) clusters with one out group each. At places, associations based on corolla colour, climatic, and geographical proximity were also recorded at subgroup levels. The single distinct amplicon (~ 650 bp) of 5.8S gene region showed a uniform nucleotide length of 163 bp for the conserved 5.8S rDNA region while length variations were for observed in ITS-1 (223 to 226) and ITS-2 (238 to 242) regions. The phylogram delineated the 23 samples into 5 major clusters. Sufficient genetic variability recorded vide this study was conserved (8.5 kg winged seed from 317 trees) under long-term storage facility to ensure availability for futuristic breeding and improvement programs.
KeywordsArid region Endangered tree Genetic diversity RAPD markers rDNA markers Rohida ISSR markers
Amplified fragment length polymorphism
Basic Local Alignment Search Tool
Cetyltrimethyl ammonium bromide
Inter Simple Sequence Repeat
Internal transcribed spacer
National Centre for Biotechnology Information
Principal coordinates analysis
Randomly Amplified Polymorphic DNA
Start codon targeted polymorphism
Authors acknowledge the research grant provided by Department of Biotechnology, Government of India, New Delhi, vide project no. BT/PR6558/PBD/16/998/2012.
Compliance with ethical standards
Conflict of interest
All the authors declare that there is no conflict of interest.
Data archiving statement
The 23 nuclear rDNA sequences of Tecomella undulata having GenBank accession numbers KX096239–KX096261 are available in public domain (sample details provided in Table 7 of this manuscript).
- Bhau BS, Negi MS, Jindal SK, Singh M, Lakshmikumaran M (2007) Assessing genetic diversity of Tecomella undulata (Sm.)—an endangered tree species using amplified fragment length polymorphism based molecular markers. Curr Sci 93:67–72Google Scholar
- Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
- Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genet 137:1121–1137Google Scholar
- Hamza NB, Habeballa RS, Abdalla IE (2009) Phylogenetic relationships within indigenous Sudanese Cassia senna (L.) using RAPD molecular markers. African J Biotechnol 8(19):4824–4829Google Scholar
- Jindal SK, Solanki KR, Kackar NL (1985) Phenology and breeding systems of rohida (Tecomella undulata (Sm.) Seem). Indian J For 8:317–320Google Scholar
- Jindal SK, Gupta AK, Kackar NL, Solanki KR (1987a) Variation of quality traits in rohida (Tecomella undulata (Sm.) Seem) in situ. In: Khurana DK, Ghosla PK (eds) IUFRO workshop proceeding. Agroforestry for rural needs vol II, Indian Society of Tree Scientists, Solan, IndiaGoogle Scholar
- Jindal SK, Kackar NL, Solanki KR (1987b) Germplasm collection and genetic variability in rohida (Tecomella undulata (Sm.) Seem) in western Rajasthan. Indian J For 10:52–55Google Scholar
- Jindal SK, Singh M, Solanki KR, Kackar NL (1992) Changes in genetic parameters and ranks of tree height over six growth years in Tecomella undulata (Sm.) Seem. Silvae Genet 41:213–216Google Scholar
- Josiah CC, George DO, Eleazar OM, Nyamu WF (2008) Genetic diversity in Kenyan populations of Acacia senegal (L.) willd revealed by combined RAPD and ISSR markers. African J Biotechnol 7(14):2333–2340Google Scholar
- Katyal SK, Daga K (2003) Removal of dyes by an adsorbent revived from Tecomella undulata in Western Rajasthan. Indian J Environ protect 23(1):37–40Google Scholar
- Kumar S, Kumar P, Agrawal DK, Choudhary AK (2011) Rehabilitation of lignite mine backfill with indigenous desert tree, Tecomella undulata in Indian arid zone. J Trop For 27:17–28Google Scholar
- Mathur N, Singh J, Bohra S, Bohra A, Mehboob VM, Vyas A (2010) Phytoremediation potential of some multipurpose tree species of Indian Thar Desert in oil contaminated soil. Adv Environ Biol 4:131–137Google Scholar
- Mohan Ch, Naresh B, Reddy MS, Kumar SM, Cherku PD (2017) Genetic similarity studies of Commiphora wightii accessions by fluorescent-labeled RAPD primers. Int J Biotech Biochem 13(1):55–66Google Scholar
- Nadkarni KM (2000) Indian materia medica popular Prakashan. Mumbai India 1:56–57Google Scholar
- Negi RS, Sharma MK, Sharma KC, Kshetrapal S, Kothari SL, Trivedi PC (2011) Genetic diversity and variations in the endangered tree (Tecomella undulata) in Rajasthan. Indian J Fundam App Life Sci 1:50–58Google Scholar
- Randhawa GS, Mukhopadhyay A (1986) Floriculture in India. Allied Publishers, MumbaiGoogle Scholar
- Rohlf F (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system version 2.2. Exeter Software Setauket, New YorkGoogle Scholar
- Srivastava KK, Srivastava HP, Kumar S (2004) Standardization of inoculum dose in Tecomella undulata seedlings. Indian Forester 130:1316–1318Google Scholar
- Trivedi S (2003) Do microsatellites have biased associations. Nucleus 46:61–76Google Scholar
- White TJ, Bruns T, Lee S, Taylor J (1990) Amplifcation and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, New York, pp 315–322Google Scholar
- Yeh FC, Yang RC, Boyle T (1997) POPGENE, the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Center. Univ. Alberta, CanadaGoogle Scholar