Differences in Genetic Characteristics and Seed Proteomes of Oryza sativa ‘Khao Dawk Mali 105’ and Its Mutant ‘Mali Daeng’
Abstract
Rice (Oryza sativa L.) is one of the economic grains that are used as important sources of carbohydrates in the world. A fragrant cultivar ‘Khao Dawk Mali 105’ (KDML105) is the most popular rice among Thai and international traits. It is therefore, commonly implement as the main rice genetic resource for breeding program in order to improve novel properties of trait with higher productivity and better nutritional values. ‘Mali Daeng’ (MD) rice has been previously identified as KDML105 mutant, which was characterized by its red pericarp at seed coat. However, there was no previous report showing clear identification of the genetic differences between both cultivars. This present research is the first report that reveals the structural genetic differences between KDML105 and MD rice by using simple sequence repeats (SSRs) marker. On the other hand, the differences of proteomic patterns detected in grains using GeLC-MS/MS shotgun proteomics were clarified. The results showed that KDML105 and MD had different genetic characteristics. The differences could be found on the chromosome 4, 7 and 10 by using the SSRs molecular markers from 4 pairs of primers, namely RM241, RM11, RM481 and RM304. Moreover, different protein expression profiles were observed in rice seeds. Among the 342 identified proteins, the expression of proteins (3-ketoacyl carrier synthase III, UDP-glucose flavonoid 3-O-glucosyltransferase and glycosyltransferase family 61 protein) that related to biosynthesis of fatty acids, phenolic compounds (flavonoids) and antioxidant activity were increase in MD. The results suggested that both varieties had different genetic backgrounds and can be distinguished by using SSRs molecular markers and MD may have higher nutritional value than KDML105 rice and suitable for promotion of planting for rice export. Keywords: Khao Dawk Mali 105, Mali Daeng, molecular markers, SSRs, proteomicsReferences
Anders, N., Wilkinson, M.D., Lovegrove, A., Freeman, J., Tryfona, T., Pellny, T.K., Weimar, T., Mortimer, J.C., Stott, K., Baker, J.M., Defoin-Platel, M., Shewry, P.R., Dupree, P., & Mitchell, R.A. (2012). Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses. Proceedings of the National Academy of Sciences of the United States of America, 109(3), 989-993.
Bardou, P., Mariette, J., Escudié, F., Djemiel, & C., Klopp, C. (2014). jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, 15, 293-299.
Clough, R.C., Matthis, A.L., Barnum, S.R., & Jaworski, J.G. (1992). Purification and characterization of 3-ketoacyl-acyl carrier protein synthase III from spinach. A condensing enzyme utilizing acetyl-coenzyme A to initiate fatty acid synthesis. Journal of Biological Chemistry, 267(29), 20992-20998.
Deng, G.F., Xu, X.R., Zhang, Y., Li, D., Gan, R.Y., & Li, H.B. (2013). Phenolic compounds and bioactivities of pigmented rice. Critical Reviews in Food Science and Nutrition, 53(3), 296-306.
He, D., & Yang, P. (2013). Proteomics of rice seed germination. Frontiers in Plant Science, 4(246), 1-9.
Johansson, C., Samskog, J., Sundstrom, L., Wadensten, H., Bjorkesten, L., & Flensburg, J. (2006). Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics, 6, 4475-4485.
Kate-ngam S. (2003). DNA Markers in Plant Breeding. Journal of Ubon Ratchathani University, 5, 37-59. (in Thai)
Laokuldilok, T., Surawang, S., & Klinhom, J. (2013). Influence of milling time on the nutritional composition and antioxidant content of Thai rice bran. Food and Applied Bioscience Journal, 1(3), 112-130.
Lowry, O.H., Rosebrough, N.J., Farr, A.L., & Randall, R.J. (1951). Protein measurement with the folin phenol reagent. Journal of Biological Chemistry, 193, 265-275.
Mahatheeranont, S., Keawsa-ard, S., & Dumri, K. (2001). Quantification of the rice aroma compound, 2-acetyl-1-pyrroline, in uncooked Khao Dawk Mali 105 brown rice. Journal of Agricultural and Food Chemistry, 49(2), 773-779.
Maksup, S., Pongpakpian, S., Roytrakul, S., Cha-um, S., & Supaibulwatana, K. (2018). Comparative proteomics and protein profile related to phenolic compounds and antioxidant activity in germinated Oryza sativa ‘KDML105’ and Thai brown rice ‘Mali Dang’ for better nutritional value. Journal of the Science of Food and Agriculture, 98, 566-573.
Maksup, S., Roytrakul, S., & Supaibulwatana, K. (2014). Physiological and comparative proteomic analyses of Thai jasmine rice and two check cultivars in response to drought stress. Journal of Plant Interactions,
9, 43-55.
Malunga, L.N., & Beta, T. (2015). Antioxidant capacity of arabinoxylan oligosaccharide fractions prepared from wheat aleurone using Trichoderma viride or Neocallimastix patriciarum xylanase. Food chemistry,
167, 311-319.
Offen, W., Martinez-Fleites, C., Yang, M., Kiat-Lim, E., Davis, B.G., Tarling, C.A., Ford, C.M., Bowles, D.J., & Davies, G.J. (2006). Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification. The EMBO journal, 25(6), 1396-405.
Pereira-Caro, G., Cros, G., Yokota, T., & Crozier, A. (2013). Phytochemical profiles of black, red, brown, and white rice from the Camargue region of France. Journal of Agricultural and Food Chemistry, 61, 7976-7986.
Perkins, D.N., Pappin, D.J.C., Creasy, D.M., & Cottrell, J.S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3367.
Prathepha P. & Srisa-ard K. (2014). Application of InDel markers for subspecies indica-japonica rice classification in Thai rice germplasm. Thai Journal of Genetics, 7(2), 87-96. (in Thai)
Riabroy, K., Khanthong, S., Toojinda, T., & Katengam, S. (2013). Fragrance gene and molecular basis of fragrant rice. Thai Journal of Genetics, 6(2), 93-114. (in Thai)
Rice Department, Ministry of Agriculture and Cooperatives. (2016). Rice Knowledge Bank: Red Hawn Rice. Retrieved March 12, 2019, from http://www.ricethailand.go.th/rkb3/title-index.php-file=content.php&id=90.htm
Saengprajak, J. (2012). Application of DNA markers for assessment of genetic diversity and rice improvement. Khon Kaen Agriculture Journal, 40, 299-308. (in Thai)
Singh, H., Deshmukh, R.K., Singh, A., Singh, A.K., Gaikwad, K., Sharma, T.R., Mohapatra, T., & Singh, N.K. (2010). Highly variable SSR markers suitable for rice genotyping using agarose gels. Molecular Breeding, 25, 359–364.
Sumrith, J. & Thanananta, T. (2014). Identification and genetic relationship analysis of colored rice cultivars using HAT-RAPD and ISSR techniques. Thai Journal of Science and Technology, 3(2), 113-122. (in Thai)
Tan, B.C., Lim, Y.S., & Lau, S.-E. (2017). Proteomics in commercial crops: an overview. Journal of Proteomics, 169, 176-188.
Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y.G., Ishii, T., & McCouch, S.R. (2000). Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100(5), 697–712
Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., & McCouch, S. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research. 11(8), 1441-1452.
Thorsell, A., Portelius, E., Blennow, K., & Westman, B.A. (2007). Evaluation of sample fractionation using microscale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment. Rapid Communications in Mass Spectrometry, 21, 771-778.
Xu, H.-H., Liu, S.-J., Song, S.-H., Wang, R.-X., Wang, W.-Q., & Song, S.-Q. (2016). Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. Plant Physiology and Biochemistry, 103, 219-242.
Bardou, P., Mariette, J., Escudié, F., Djemiel, & C., Klopp, C. (2014). jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, 15, 293-299.
Clough, R.C., Matthis, A.L., Barnum, S.R., & Jaworski, J.G. (1992). Purification and characterization of 3-ketoacyl-acyl carrier protein synthase III from spinach. A condensing enzyme utilizing acetyl-coenzyme A to initiate fatty acid synthesis. Journal of Biological Chemistry, 267(29), 20992-20998.
Deng, G.F., Xu, X.R., Zhang, Y., Li, D., Gan, R.Y., & Li, H.B. (2013). Phenolic compounds and bioactivities of pigmented rice. Critical Reviews in Food Science and Nutrition, 53(3), 296-306.
He, D., & Yang, P. (2013). Proteomics of rice seed germination. Frontiers in Plant Science, 4(246), 1-9.
Johansson, C., Samskog, J., Sundstrom, L., Wadensten, H., Bjorkesten, L., & Flensburg, J. (2006). Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics, 6, 4475-4485.
Kate-ngam S. (2003). DNA Markers in Plant Breeding. Journal of Ubon Ratchathani University, 5, 37-59. (in Thai)
Laokuldilok, T., Surawang, S., & Klinhom, J. (2013). Influence of milling time on the nutritional composition and antioxidant content of Thai rice bran. Food and Applied Bioscience Journal, 1(3), 112-130.
Lowry, O.H., Rosebrough, N.J., Farr, A.L., & Randall, R.J. (1951). Protein measurement with the folin phenol reagent. Journal of Biological Chemistry, 193, 265-275.
Mahatheeranont, S., Keawsa-ard, S., & Dumri, K. (2001). Quantification of the rice aroma compound, 2-acetyl-1-pyrroline, in uncooked Khao Dawk Mali 105 brown rice. Journal of Agricultural and Food Chemistry, 49(2), 773-779.
Maksup, S., Pongpakpian, S., Roytrakul, S., Cha-um, S., & Supaibulwatana, K. (2018). Comparative proteomics and protein profile related to phenolic compounds and antioxidant activity in germinated Oryza sativa ‘KDML105’ and Thai brown rice ‘Mali Dang’ for better nutritional value. Journal of the Science of Food and Agriculture, 98, 566-573.
Maksup, S., Roytrakul, S., & Supaibulwatana, K. (2014). Physiological and comparative proteomic analyses of Thai jasmine rice and two check cultivars in response to drought stress. Journal of Plant Interactions,
9, 43-55.
Malunga, L.N., & Beta, T. (2015). Antioxidant capacity of arabinoxylan oligosaccharide fractions prepared from wheat aleurone using Trichoderma viride or Neocallimastix patriciarum xylanase. Food chemistry,
167, 311-319.
Offen, W., Martinez-Fleites, C., Yang, M., Kiat-Lim, E., Davis, B.G., Tarling, C.A., Ford, C.M., Bowles, D.J., & Davies, G.J. (2006). Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification. The EMBO journal, 25(6), 1396-405.
Pereira-Caro, G., Cros, G., Yokota, T., & Crozier, A. (2013). Phytochemical profiles of black, red, brown, and white rice from the Camargue region of France. Journal of Agricultural and Food Chemistry, 61, 7976-7986.
Perkins, D.N., Pappin, D.J.C., Creasy, D.M., & Cottrell, J.S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3367.
Prathepha P. & Srisa-ard K. (2014). Application of InDel markers for subspecies indica-japonica rice classification in Thai rice germplasm. Thai Journal of Genetics, 7(2), 87-96. (in Thai)
Riabroy, K., Khanthong, S., Toojinda, T., & Katengam, S. (2013). Fragrance gene and molecular basis of fragrant rice. Thai Journal of Genetics, 6(2), 93-114. (in Thai)
Rice Department, Ministry of Agriculture and Cooperatives. (2016). Rice Knowledge Bank: Red Hawn Rice. Retrieved March 12, 2019, from http://www.ricethailand.go.th/rkb3/title-index.php-file=content.php&id=90.htm
Saengprajak, J. (2012). Application of DNA markers for assessment of genetic diversity and rice improvement. Khon Kaen Agriculture Journal, 40, 299-308. (in Thai)
Singh, H., Deshmukh, R.K., Singh, A., Singh, A.K., Gaikwad, K., Sharma, T.R., Mohapatra, T., & Singh, N.K. (2010). Highly variable SSR markers suitable for rice genotyping using agarose gels. Molecular Breeding, 25, 359–364.
Sumrith, J. & Thanananta, T. (2014). Identification and genetic relationship analysis of colored rice cultivars using HAT-RAPD and ISSR techniques. Thai Journal of Science and Technology, 3(2), 113-122. (in Thai)
Tan, B.C., Lim, Y.S., & Lau, S.-E. (2017). Proteomics in commercial crops: an overview. Journal of Proteomics, 169, 176-188.
Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y.G., Ishii, T., & McCouch, S.R. (2000). Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100(5), 697–712
Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., & McCouch, S. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research. 11(8), 1441-1452.
Thorsell, A., Portelius, E., Blennow, K., & Westman, B.A. (2007). Evaluation of sample fractionation using microscale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment. Rapid Communications in Mass Spectrometry, 21, 771-778.
Xu, H.-H., Liu, S.-J., Song, S.-H., Wang, R.-X., Wang, W.-Q., & Song, S.-Q. (2016). Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. Plant Physiology and Biochemistry, 103, 219-242.
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2019-09-20
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