In Silico GENOME MINING FOR SALINITY-RELATED PATH-WAYS IN THE Citrus sinensis GENOME
Abstract
Citrus is an important horticulture genus which exclusively includes all cultivated edible citrus plants and their root-stocks. The genetic relationship and relatedness among the genus member have been extensively reported. Among other traits, the fluctuation in the salinity tolerance ability of several citrus species in relation to other relatives have been shown. The current study aimed to subject the published Citrus sinensis genome as a model to find possible salinity-related pathways and its completion ratio com-pared to some plant models (e.g. Arabidopsis thaliana). Toward a better understanding of how some citrus species can cope the high salinity stress for further application at arid and semiarid regions with a special relevant to high-calcic soil and newly reclaimed lands. The genome mining revealed that all genes of each of proline, glycine betaine (GB) and Abscisic acid (ABA) pathways were previously annotated and identified in the Citrus sinensis genome. The SOS and ROS pathway genes did not appear complete in the mining process. SNPs may occur to each of SOS1 gene which belongs to the SOS pathway and XOD gene which belongs to the ROS pathway in Citrus sinensis genome or substituted by other genes either copy or allele, thus this region has not been identified or defined in the Citrus sinensis genome yet. Thus, an in-silico study of Citrus sinensis by genome mining for the identification of active pathways which relate with salinity tolerance, the discovery and development of genes which could decrease the damaging effect of salinity on citrus plant cells needed more research and study.References
Al-Yassin, A. (2004). Influence of salinity on citrus: A review paper. Journal of Central European Agriculture, 5: 263-272.
Ashraf, M. (1994). Breeding for salinity tolerance in plants. Crit. Rev. Plant Sci., 13: 17-42.
Ashraf, M. and P. J. C. Harris (2004). Po- tential biochemical indicators of salinity tolerance in plants. Plant Sci., 166:3-16.
Murkute, A. A., Satyawati Sharma and S.K. Singh (2005). Citrus in terms of soil and water salinity: A review. Journal of Scientific & Industrial Research, 64: 393-402.
Cheng, N. H., J. K. Pittman, J. K. Zhu and K. D. Hirschi (2004). The protein kinase SOS2 activates the Arabidopsis H1/Ca antiporter CAX1 to integrate calcium transport and salt tolerance. J. Biol. Chem., 279: 2922-2926.
Chinnusamy, V., K. Schumaker and J. Zhu (2004). Molecular genetic per- spectives on cross-talk and specificity in abiotic stress signaling in plants. Journal of Experimental Botany, 55: 225-236.
de Oliveira, B. D. O., L. M. A. Nara and G. F. Eneas (2013). Comparison between the water and salt stress effects on plant growth and development. Responses of organisms to water stress, 4: 67-94.
FAO Statistics, (2017). Food and Agricul- ture Organization of the United Na- tions. http://faostat.fao.org/default.aspx.
Garcia-Sanchez, F. and J. P. Syvertsen (2006). Salinity tolerance of Cleopatra mandarin and Carrizo citrange citrus rootstocks seedlings is affected by CO2 enrichment during growth. J. Amer. Soc. Hort. Sci., 131: 4-31.
Hossain, M. S. and K. Dietz (2016). Tun- ing of Redox regulatory mechanisms, Reactive Oxygen Species and Redox homeostasis under salinity stress. Frontiers in Plant Science Journal, 7: 1-15.
Jeschke, W. D., A. D. Peuke, J. S. Pate and W. Hartung (1997). Transport, synthesis and catabolism of abscisic acid (ABA) in intact plants of castor bean (Ricinus communis L.) under phosphate deficiency andmoderate salinity. Journal of Experimental Botany, 48: 1737-1747.
Ji, H., J. M. Pardo, G. Batelli, M. J. Van Oosten, R. A. Bressan and X. Li (2013). The Salt Overly Sensitive (SOS) Pathway: Established and Emerging Roles. Molecular Plant J., 6: 275-286.
Kavi-Kishor, P. B., S. Sangam, R. N. Amrutha, P. Sri Laxmi, K. R. Naidu, K. R. S. S. Rao, S. Rao, K. J.
Reddy, P. Theriappan and N. Sreenivasulu (2005). Regulation of proline biosynthesis, degradation, uptake and transport in higher plants: Its implications in plant growth and abiotic stress tolerance Current Science, 88: 424-438.
Kumar, D., M. Al Hassan, M. A. Naranjo, V. Agrawal, M. Boscaiu and O. Vicente (2017). Effects of salinity and drought on growth, ionic rela- tions, compatible solutes and activation of antioxidant systems in oleander (Nerium oleander L.). PLoS ONE, 12: e0185017. https://doi.org/10.1371/journal.pone.0185017
Maas, E. V. (1990). Crop salt tolerance. In: Tanji K. K. (ed), Agricultural salinity assessment and management. Manuals and reports on engineering, No 71. Amer Soc Civil Engg, New York, p: 202-304.
Maas, E. V. (1993). Salinity and citriculture. Tree Physiology, 12: 195-216.
MALR Statistics, (2015). Economic Affairs Sector at the Ministry of Ag- riculture and Land Reclamation.
Popova, L. P., Z. G. Stoinova and L. T. Maslenkova (1995). Involvement of abscisic acid in photosynthetic process in Hordeum vulgare L. during salinity stress. Journal of Plant Growth Regulation, 14: 211-218.
Qiu, Q. S., Y. Guo, F. J. Quintero, J. M. Pardo, K. S. Schumaker and J. K. Zhu (2004). Regulation of vacuolar Na+/H+ exchange in Arabidopsis thaliana by the SOS pathway. J. Biol. Chem., 279: 207-215.
Rhodes, D., A. Nadolska-Orczyk and P. J. Rich (2004). Salinity, osmolytes and compatible solutes, in A. Lauchli and U. Luttge (ed.) Salinity: Environment-Plants-Molecules, Kluwer Academic Inc., New York, Boston, Dordrecht, London, Moscow, p: 181-204.
Shi, H., M. Ishitani, C. Kim and J. K. Zhu (2000). The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. Proc. Natl. Acad. Sci. USA, 97: 6896-6901.
Szabados, L. and A. Savoure (2009). Proline: a multifunctional amino acid. Trends in Plant Science, 15: 89-97.
Tuteja, N. (2007). Chapter twenty-four - mechanisms of high salinity tolerance in plants. Methods in Enzymology Journal, 428: 419-438.
WWAP (United Nations World Water Assessment Programme)/UN- Water (2018). The United Nations World Water Development Report: Nature-Based Solutions for Water. Paris, UNESCO.
Yang, Y., R. Tang, C. Jiang, B. Li1, T. Kang, H. Liu, N. Zhao, X. Ma, L. Yang, S. Chen and H. Zhang (2015). Overexpression of the PtSOS2 gene improves tolerance to salt stress in transgenic poplar plants. Plant Biotechnology Journal, 13: 962-973.
