Identification and characterization of a NBS–LRR class resistance gene analog in Pistacia atlantica subsp. Kurdica

Document Type: Original article


Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran


P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plant which grows in Kurdistan, Iran.  The identification of resistance gene analogs holds great promise for the development of resistant cultivars. A PCR approach with degenerate primers designed according to conserved NBS-LRR (nucleotide binding site-leucine rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from P. atlantica subsp. Kurdica. A DNA fragment of the expected 500-bp size was amplified. The nucleotide sequence of this amplicon was obtained through sequencing and the predicted amino acid sequence compared to the amino acid sequences of known R-genes revealed significant sequence similarity. Alignment of the deduced amino acid sequence of P. atlantica subsp. Kurdica resistance gene analog (RGA) showed strong identity, ranging from 68% to 77%, to the non-toll interleukin receptor (non-TIR) R-gene subfamily from other plants. A P-loop motif (GMMGGEGKTT), a conserved and hydrophobic motif GLPLAL, a kinase-2a motif (LLVLDDV), when replaced by IAVFDDI in PAKRGA1 and a kinase-3a (FGPGSRIII) were presented in all RGA. A phylogenetic tree, based on the deduced amino-acid sequences of PAKRGA1 and RGAs from different species indicated that they were separated in two clusters, PAKRGA1 being on cluster II. The isolated NBS analogs can be eventually used as guidelines to isolate numerous R-genes in Pistachio.


1.Daneshrad A, Aynehchi Y. Chemical studies of the oil from Pistacia nuts growing wild in Iran. Journal of the American Oil Chemists’ Society 1980;57:248-249.

2.Rezaei PF, Fouladdel S, Hassani S, Yousefbeyk F, Ghaffari SM, Amin G, et al. Induction of apoptosis and cell cycle arrest by pericarp polyphenol-rich extract of Baneh in human colon carcinoma HT29 cells. Food and Chemical Toxicology 2012;50:1054-1059.

3.Aarts MG, Lintel Hekkert Bt, Holub EB, Beynon JL, Stiekema WJ, Pereira A. Identification of R-gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana. Molecular Plant-Microbe Interactions 1998;11:251-258.

4.Ghazvini RF, Sajadian H, Hokmabadi H, Ahmad S. Effects of pistachio rootstocks on ecophysiological characteristics of commercial pistachio cultivars. Int J Agr Biol 2007;9:352-354.

5.Mirzaie-Nodoushan H, Arefi H. Variability in seed blankness in Pistacia atlantica Desf. in a natural habitat. Plant Genetic Resources Newsletter 2001:46-48.[6] Ellis J, Dodds P, Pryor T. Structure, function and evolution of plant disease resistance genes. Current opinion in plant biology 2000;3:278-284.

6.Song W-Y, Pi L-Y, Wang G-L, Gardner J, Holsten T, Ronald PC. Evolution of the rice Xa21 disease resistance gene family. The Plant Cell Online 1997;9:1279-1287.

7.Hammond-Kosack KE, Jones DA, Jones JD. Ensnaring microbes: the components of plant disease resistance. New phytologist 1996; 133:11-24.

8.Saraste M, Sibbald PR, Wittinghofer A. The P-loop-a common motif in ATP-and GTP-binding proteins. Trends in biochemical sciences 1990;15:430-434.

9.Leister D, Ballvora A, Salamini F, Gebhardt C. A PCR–based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nature genetics 1996;14:421-4299.

10.Yu YG, Buss GR, Maroof M. Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proceedings of the National Academy of Sciences 1996; 93:11751-11756.

11.Zamora MM, Castagnaro A, Ricci JD. Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries. Molecular genetics and genomics 2004;272:480-487.

12.Zhang X-C, Wu X, Findley S, Wan J, Libault M, Nguyen HT, et al. Molecular evolution of lysin motif-type receptor-like kinases in plants. Plant physiology 2007;144:623-636.

13.Cao A, Xing L, Wang X, Yang X, Wang W, Sun Y, et al. Serine/threonine kinase gene Stpk-V, a key member of powdery mildew resistance gene Pm21, confers powdery mildew resistance in wheat. Proceedings of the National Academy of Sciences 2011;108:7727-7732.

14. Joshi R, Mohanty S, Subudhi E, Nayak S. Isolation and characterization of NBS-LRR- resistance gene candidates in turmeric (Curcuma lonqa cv. surama). Genetics and Molecular Research 2010;9:1796-1806.

15.Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research 1997;25:4876-4882.

16.Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution 1987;4:406-425.

17.Deng Z, Huang S, Ling P, Chen C, Yu C, Weber C, et al. Cloning and characterization of NBS-LRR class resistance-gene candidate sequences in citrus. Theoretical and Applied Genetics 2000;101:814-822.

18.Karimi HR, Kafkas S. Genetic relationships among Pistacia species studied by SAMPL markers. Plant Systematics and Evolution 2011;297:207-212.