Vol.:(0123456789) 1 3 Molecular Biology Reports https://doi.org/10.1007/s11033-018-4149-0 ORIGINAL ARTICLE Transcript profling and gene expression analysis under drought stress in Ziziphus nummularia (Burm.f.) Wright & Arn. Radha Yadav 1  · Om Prakash Verma 2  · Jasdeep Chatrath Padaria 1 Received: 19 September 2017 / Accepted: 18 January 2018 © Springer Science+Business Media B.V., part of Springer Nature 2018 Abstract Drought is one of the prime abiotic stresses responsible for limiting agricultural productivity. A number of drought respon- sive genes have been isolated and functionally characterized but these studies have been restricted to a few model plant systems. Very few drought responsive genes have been reported till date from non model drought tolerant plants. The present study aimed at identifying diferentially expressed genes from a drought tolerant, non-model plant, Ziziphus nummularia (Burm.f.) Wight & Arn. One month old seedlings of Z. nummularia were subjected to drought stress by 30% Polyethylene glycol (PEG 6000) treatment for 6, 12, 24, 48 and 72 h. A signifcant reduction in RWC and increase in proline was observed at 24 h and 48 h of treatment. Suppression subtractive hybridization (SSH) library was constructed with drought stressed seedlings after 24 h and 48 h of PEG 6000 treatment. A total of 142 and 530 unigenes from 24 h and 48 h library were iden- tifed respectively. Gene ontology studies revealed that about 9.78% and 15.07% unigenes from 24 h and 48 h SSH libraries were expressed in “response to stress”. Fifteen putative drought responsive genes identifed in SSH library were validated for drought responsive diferential expression by RT-qPCR. Signifcant changes in fold expressions were observed with time in the treated samples compared to the control. A heat map revealing the expression profle of genes was constructed by hierarchical clustering. Various genes identifed in SSH libraries can serve as a resource for marker discovery and selection of candidate genes to improve drought tolerance in other susceptible crops. Keywords Z. nummularia · SSH library · BLASTx · Unigenes · Gene ontology · RT-qPCR Introduction Drought is a meteorological event which implies the absence of rainfall for a period of time, long enough to cause mois- ture depletion in soil and plant tissues. It acts as a serious limiting factor in agricultural production by restricting the crop from reaching the genetically determined theoretical maximum yield [1]. Most of the plants are sensitive to water defcits, particularly during fowering to seed development stage. Certain plants are endowed with inherent metabolic mechanism which makes them capable of growing under drought conditions. Drought tolerance is a very complex molecular mechanism involving a number of metabolic path- ways which are controlled by interplay of various drought responsive genes. Such drought tolerant plants are good genetic resources to understand the genetic and metabolic control of their adaptation to drought. Identifcation and characterization of drought responsive genes from naturally drought tolerant plant species could be an efective approach to gain insights into the molecular mechanisms of drought tolerance. Ziziphus species belonging to Rhamnaceae family com- prises of more than two hundred species of spiny shrubs and small trees, among them 17 species are native to India [2]. To efectively defer dehydration and thereby survive in adverse conditions, Ziziphus species exhibit a combination of mecha- nisms for drought avoidance and drought tolerance like efec- tive photoprotective and stimulation of antioxidative metabolic pathways, osmotic adjustment and sensitive stomatal closure Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-018-4149-0) contains supplementary material, which is available to authorized users. * Jasdeep Chatrath Padaria jasdeep_kaur64@yahoo.co.in 1 National Research Centre on Plant Biotechnology, PUSA Campus, New Delhi 110012, India 2 Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India