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IJSTR >> Volume 3- Issue 7, July 2014 Edition

International Journal of Scientific & Technology Research  
International Journal of Scientific & Technology Research

Website: http://www.ijstr.org

ISSN 2277-8616

Resequencing And Nucleotide Variation Of Sucrose Synthase (Nmsusy1) Gene In A Tropical Timber Tree Neolamarckia Macrophylla

[Full Text]



Choon-Ju Tan, Wei-Seng Ho, Shek-Ling Pang



Index Terms: Neolamarckia macrophylla, red kelampayan; resequencing, sucrose synthase (SuSy); single nucleotide polymorphism (SNP), nucleotide variation, marker-assisted selection



Abstract: Sucrose synthase (SuSy) is a key enzyme that catalyses the reversible synthesis and degradation of sucrose. It provides greater impact in regulating the photosynthetic processes and environmental stresses in plants. Thus, the nucleotide variation of partial NmSusy1 genomic DNAs (750 bp) generated through PCR amplification was examined in this study, and this followed by resequencing from 15 selected Neolamarckia macrophylla clones. The consensus sequences were aligned to detect the presence of single nucleotide polymorphisms (SNPs). In total, five SNPs were detected at nucleotide 1, 2, 34, 35 and 397. Of these, four SNPs were located at the predicted coding region while one SNP was located at the predicted non-coding region. Interestingly, one single base pair InDel polymorphism was also detected at nucleotide 17. On average, one SNP at every 150 bp was detected based on the 15 NmSusy1 sequences. There was one non-synonymous mutation detected, whereby amino acid glutamic acid (E) was replaced by arginine (R) in one of the 15 samples tested. This non-synonymous SNP might change the structural, functional or biochemical properties of the enzyme being produced and therefore possibly lead to changes in phenotypic characteristic of the trees. Overall, this study has demonstrated that resequencing is an effective technique for classifying molecular diversity or nucleotide variation in the Susy gene of N. macrophylla. Those SNPs, once validated, could potentially be used as a tool in marker-assisted selection (MAS) that enables more precise and accurate in the selection and prediction of yield or performance at the early developmental stages, such as at the seedling stage.



[1]. Winter, H. and Huber, S. C.: “Regulation of sucrose metabolism in higher plants: Localization and regulation of activity of key enzymes” Critical Reviews in Biochemistry and Molecular Biology, 35(4), 253-289, 2000.

[2]. Plaxton, W. C. and McManus, M.T.: “Control of primary metabolism in plants”, Volume 22.United State of America: Blackwell Publishing Ltd., 2006.

[3]. Ciereszko, I. and Kleczkowski, L. A.: “Glucose and mannose regulate the expression of a major sucrose synthase gene in Arabidopsis via hexokinase-dependent mechanisms” Plant Physiology and Biochemistry, 40, 907-911, 2002.

[4]. Carlson, S. J. and Chourey, P. S.: “Evidence for plasma membrane-associated forms of sucrose synthase in maize” Molecular and General Genetics, 252(3), 303-310, 1996.

[5]. Harada, T., Satoh, S., Yoshioka, T. and Ishizawa, K.: “Expression of sucrose synthase genes involved in enhanced elongation of pondweed (Potamogetondistinctus) turions under anoxia” Annals of Botany, 96, 1-2, 2005.

[6]. Haigler, C. H., Datcheva, M. I., Hogan, P. S., Salnikov, V. V., Hwang, S., Martin, K. and Delmer, D. P.: “Carbon partitioning to cellulose synthesis” Plant Molecular Biology, 47(1-2), 29-51, 2001.

[7]. Jayashree, B., Pradeep, R., Kumar, A. and Gopal, B.: “Correlation between the sucrose synthase protein subfamilies, variations in structure and expression in stress-derived expressed sequence tag datasets” Journal of Proteomics and Bioinformatics, 1, 408-423, 2008.

[8]. Krisnawati, H., Kallio, M. and Kanninen, M.: “Anthocephalus cadamba Miq. Ecology, silviculture and productivity” Indonesia: CIFOR, 2011.

[9]. Doyle, J.J. and Doyle, J.L.: “Isolation of plant DNA from fresh tissue” Focus, 12: 13-15, 1990.

[10]. Ho, W.S., Pang, S.L. and Julaihi, A.: “Identification and analysis of expressed sequence tags present in xylem tissues of kelampayan (Neolamarckia cadamba (Roxb.) Bosser)” Physiology and Molecular Biology of Plants, published online, 2014, DOI 10.1007/s12298-014-0230-x.

[11]. Grover, C.E., Yu, Y.S., Wing, R.A., Paterson, A.H. and Wendel, J.F.: “A phylogenetic analysis of indel dynamics in the cotton genus” Molecular Biology and Evolution, 25(7), 1415-28, 2008.

[12]. Zhang, H.Y., He, H., Chen, L.B., Li, L., Liang, M.Z., Wang, X.F., Liu, X.G., He, G.M., Chen, R.S., Ma, L.G. and Deng, X.W.: “A genome-wide transcription analysis reveals a close correlation of promoter INDEL” Molecular Plant, 1(5), 720-731, 2008.

[13]. Plantegenet, S., Weber, J., Goldstein, D.R., Zeller, G., Nussbaumer, C., Thomas, J., Weigel, D., Harshman, K., and Hardtke, C.S.: “Comprehensive analysis of Arabidopsis expression level polymorphism with simple inheritance” Molecular System Biology, 5, 542, 2009.

[14]. Garg, K., Green, P. and Nickerson, A.: “Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags” Genome Research, 9, 1087-1092, 1999.

[15]. Zhang, Z., Miteva, M. A., Wang, L. and Alexov, E.: “Analyzing effects of naturally occurring missense mutations” Computational and Mathematical Methods in Medicine, 1-15, 2012.

[16]. Turnpenny, P. and Ellard, S.: “Emery’s elements of medical genetics” Philadelphia: Churchill Livingstone, 2012.

[17]. Kanazin, V., Talbert, V., See, D., DeCamp, F., Nevo, E. and Blake, T.: “Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare)” Plant Mol. Biol., 48: 529-537, 2002.

[18]. Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A. and Cestaro, A.: “A high quality draft consensus sequence of the genome of a heterozygous grapevine variety” PLoS ONE, 2, 2007.

[19]. Ho, W.S., Pang, S.L. Lau, P. and Ismail, J.: “Sequence variation in the cellulose synthase (SpCesA1) gene from Shorea parvifolia ssp. parvifolia mother trees” Journal of Tropical Agricultural Science, 34(2), 323-329, 2011.

[20]. Tchin, B.L., Ho, W.S., Pang, S.L. and Ismail, J.: “Gene-associated single nucleotide polymorphism (SNP) in cinnamate 4-hydroxylase (C4H) and cinnamyl alcohol dehydrogenase (CAD) genes from Acacia mangium superbulk trees” Biotechnology, 10(4): 303-315, 2011.

[21]. Tchin, B.L., Ho, W.S., Pang, S.L. and Ismail, J.: “Association Genetics of the cinnamyl alcohol dehydrogenase (CAD) and cinnamate 4-hydroxylase (C4H) genes with basic wood density in Neolamarckia cadamba” Biotechnology, 11(6), 307-317, 2012.

[22]. Tiong, S.Y., Ho, W.S., Pang, S.L. and Ismail, J.: “Nucleotide diversity and association genetics of xyloglucan endotransglycosylase/ hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba” Journal of Biological Sciences, 14(4), 267-375, 2014.

[23]. Bromberg, Y. and Rost, B.: “SNAP: Predict effect of non-synonymous polymorphisms on function” Nucleic Acids Res., 35(11), 3823-3835, 2007.

[24]. Parmley, J. L. and Hurst, L.D.: “How do snynonymous mutations affect fitness?” Bioessays, 29 6), 515-519, 2007.

[25]. Rai, A. and Takabe, T.: “Abiotic stress tolerant in plants” Netherland: Springer, 2006.