Assessment of diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties
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Abstract
The study investigates the genetic diversity among the Basmati rice genotypes. Selected nine Basmati rice genotypes were studied for twelve morphological traits, biochemical parameters and for molecular analysis with 11 SSR markers. Pusa Sugandha 5 and Basmati 370, showed strong aroma while other varieties showed medium aroma. Alkali spreading value were intermediate in Basmati 386, Vallabh Basmati 22 and Vallabh Basmati 24 while other varieties showed high values. Pusa Basmati 1 and Basmati 386 showed soft category of gel consistency while in rest varieties it was under medium category. Amylose percentage in grains were ranged from 18.02% (Taraori basmati) to 22.0% (Basmati370). Molecular analysis with 11 SSR markers showed 125 allels with an average number of allels 11.36 per locus. All the markers showed specific type of banding pattern along with 82 polymorphic allels in different genotypes. This study focuses on application of statistical methods and techniques in analysis of genetic diversity of the agronomic data, biochemical aspects related to quality parameters and at the molecular level using SSR markers for clustering procedure making dendrogram that helps the more accurate selection of the superior basmati genotypes for the further studies of the breeders and researchers.
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Keywords
Amylose, Aroma, ASV Basmati rice, Diversity, GC and SSR Primers
References
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Anonymous (2004). Laboratory Manual on Rice Grain Quality Procedure. Directorate of Rice Research, Rajendranagar, Hyderabad, India 1-20.
Bansal, U.K, Kaur, H., & Saini R. G. (2006). Donors for quality characteristics in aromatic rice. Oryza, 43 (3):197-202.
Bhattacharya, K.R. (1979). Tests for parboiled rice in Proc. Wkshp. Chem. Aspects of Rice Grain Quality. Int. Rice Res. Inst., Los Bahos, Laguna, Philippines p 363.
Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man usingrestriction fragment length polymorphisms. American Journal of Human Genetics, 32:314–331.
Brondani, C., Borba, T.C.O., Rangel. Paulo, H.N. and Brondani, RPV (2006). Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers. Genetics and Molecular Biology, 29 (4): 676-684.
Cameron, D.K., and Wang, Y. (2005). A better understanding of factors that affect the hardness and stickiness of longgrain rice. Cereal Chemistry, 82:113–11.
Chen,Y., Wang, M., Ouwerkerk and Pieter, B.F. (2012). Molecular and environmental factors determining grain quality in rice. Food and Energy Security, 1 (2): 111–132.
Ghneim, H.T., Duque, P.D., Almeida, I.P., Nunez, T.G., Pieters, A.J., Martinez, C.P. and Tohme, J.M. (2008). Assessment of genetic diversity Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidalaya. Research Journal of Agriculture Sciences,4 (3): 329-332.
Golam, F., Yin, Y.H., Masitah, A., Afnierna, N., Majid, N.A., Khali, N. and Osman, M. (2011). Analysis of aroma and yield component of aromatic rice in Malaysian tropical environment. Journal of Crop Science, 5 (11): 1318-1325.
Grist, S.A., Firgaira, F.A. and Morley, A.A. (1993). Dinucleotide repeat polymorphisms isolated by the polymerase chain reaction. Bio –Technology, 15: 304–309.
He, G., and Suzuki, H. (1987). The relationship between translucency of rice grain and gelatinization of starch in the grain during cooking. Journal of Nutritional Science and Vitaminology, 33:263–273.
Jalaluddin, M., Nakai, H. and Yamamoto, T. (2007). Genetic diversity and DNA fingerprinting of some modern in dica and japonica rice. SABRAO Journal of Breeding and Genetics, 39 (1): 43-52.
Kibanda, J.M.N. and Luzi-kihupi, A. (2007). Influence of genetic and genotype environment interaction on quality of rice grain. African Crop Science Journal, 15: 173–182.
Kumar, S., Bisht, I.S. and Bhatt, K.V. (2010). Assessment of genetic diversity among rice (Oryza sativa L.) landrace populationsunder traditional production using microsatellite (SSR) markers. Electronic Journal of Plant Breeding, 1: 474–483.
Lapitan, V.C., Brar, D.S., Abe,T .and Redona, E.D. (2007). Assessment of genetic diversity of Philippines rice cultivars carrying good quality traits using SSR markers. Breeding Science, 57: 263-270.
McCouch, S.R., Chen, X. and Cho, Y.G. (2002). Sequence divergence of rice microsatellites in Oryza and other plant species. Molecular Genetics and Genomics, 268, 331-343.
Mizukami, H. and Takeda, Y. (2000). Chewing properties of cooked rice from new characteristic rice cultivars and their relation to starch molecular structures. Journal of Applied Glycoscience, 47:61–65.
Murray, M.G. and Thompson, W.F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acid Research, 8: 432-435.
Nadaf, A.B., Krishnan, S. and Wakte, K.V. (2006). Histochemical and biochemical analysis of major compound (2-acetyl-1-pyrroline) in basmati and other scented rice (Oryza sativa. L.), Current Science, 91: 1533–1536.
Nagaraju, J., Kathirvel, M., Ramesh Kumar, R., Siddiq, E.A., and Hasnain S.E. (2002). Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by
using fluorescence-based ISSR-PCR and SSR markers. PNAS 99: 5836-5841.
Nakamura, Y., Sato, A. and Juliano, B.O. (2006). Short chain length distribution in debranched rice starches differing in gelatinization temperature or cooked rice hardness. Starch/St€arke 58:155–160.
Oliveira, M.M., Martins, P., Jayamani, S. and Negrao, B. (2007). Genetic relatedness of Portuguese rice accessions from diverse origins as assessed by microsatellite markers. Crop Science, 47: 879-884.
Ong, M.H., and Blanshard, J.M.V. (1995). Texture determinants in cooked, parboiled rice. I: Rice starch amylose and the fine structure of amylopectin. Journal of Cereal Science, 21:251–260.
Perez, C.M. and Juliano, B.O. (1978). Modification of the simplified amylose test for milled rice. Starch, 30:424-426.
Pervaiz, Z.H., Rabbani, M.A., Pearce, S.R. and Malik, S.A. (2009). Determination of genetic variability of Asian rice (Oryzasativa L.) varieties using microsatellite markers. African Journal of Biotechnology, 8:641-5651.
Pervaiz, ZH., Rabbani, M.A., Khaliq, I., Pearce, S.R. and Malik, S.A. (2010). Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice. Electronic Journal of Biotechnology, 13: 4-5.
Ram, S.G., Thiruvengadam, V. and Vinod, K.K. (2007). Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. Journal of Applied Genetics, 48: 337–345.
Ramesh, M., Zakiuddin, S.A., and Bhattacharya, K.R. (1999). Structure of rice starch and its relation to cookedrice texture. Carbohydrate Polymer, 38:337–347.
Randall, G., Mutters, James, and Thompson, F., (2009). Rice quality in the global market, Rice quality handbook. Chapter 1:1-22.
Rani, M.R.S., and Bhattacharay, K.R. (1989). Slurry viscosity as a possible indicator of rice quality. Journal Texture Studies, 20:139–149.
Saini, N., Jain, N., Jain, S. and Jain, R.K. (2004). Assessment of genetic diversity within and among basmati and nonbasmati rice varieties using AFLP, ISSR and SSR markers. Euphytica, 140: 133–146.
Shahidullah, S.M., Hanafi, M.M., Ashrafuzzaman, M., Ismail, M.R., and Khair, A. (2009). Genetic diversity in grain quality and nutrition of aromatic rice’s. Afrian Journal of Biotechnology, 8 (7): 1238-1246.
Singh. N., Singh. J., Kaur, L., Sodhi, N.S. and Gill, B.S. (2003). Morphological, thermal and rheological properties of starches from different botanical sources. Food Chemistry81: 219-231.
Sivaranjani, A.K.P. (2010). Assessment of genetic diversity among basmati and non-basmati aromatic rices of India using SSR markers. Current Science, 99: 221–226.
Siwach, P., Jain, S., Sain, N., Chowdhury,V.K. and Jain, R.K. (2004). Allelic diversity among Basmati and non- Basmati long-grain indica rice varieties using microsatellite markers. Journal of Plant Biochemistry and Biotechnology, 13: 25-32.
Smith, J.S.C., Chin, E.C.L., Shu, H., Smith, O.S., Wall, S.J., Senior, M.L., Mitchell, S.E., Kresovich, S. and Zeigle J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics, 95:163–173.
Sowbhagya, C.M., Ramesh, B.S. and Bhattacharya, K.R. (1987). The relationship between cooked-rice texture and the physicochemical characteristics of rice. Journal of Cereal Science, 5:287–297.
Sundaram, R.M., Naveenkumar, B., Biradar, S.K., Balachandran, S.M., Mishra,B. and Ahmed, M.I. (2008). Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica, 163: 215–224.
Tahir, M.H.N., Sadaqat, H.A. and Bashir, S. (2002). Correlation and path co-efficient analysis of morphological traits in sunflower (Helianthus annuus L.) Populations. International Journal of Agricultureand Biology 4 (3): 341-343.
Thompson, M.J., SeptininJih, E.M., Suwardjo, F., Santoso, T.J., Silitonga, T.S. and Mcouch S.R. (2007). Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theoretical and Applied Genetics, 114: 559- 568.
Vanniarajan, C., Vinod, K.K. and Pereira, A. (2012). Molecular evaluation of geneticdiversity and association studies in rice (Oryza sativa L.). Journal of Genetics, 9: 9–19.
Wang, F. (2009). Integrated KL (K-means-Laplacian) clustering: a new clustering approach by combining attribute data and pairwise relations. In proceeding of SDM 09, SIAM Press, pp. 38–48.
Anonymous (2004). Laboratory Manual on Rice Grain Quality Procedure. Directorate of Rice Research, Rajendranagar, Hyderabad, India 1-20.
Bansal, U.K, Kaur, H., & Saini R. G. (2006). Donors for quality characteristics in aromatic rice. Oryza, 43 (3):197-202.
Bhattacharya, K.R. (1979). Tests for parboiled rice in Proc. Wkshp. Chem. Aspects of Rice Grain Quality. Int. Rice Res. Inst., Los Bahos, Laguna, Philippines p 363.
Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man usingrestriction fragment length polymorphisms. American Journal of Human Genetics, 32:314–331.
Brondani, C., Borba, T.C.O., Rangel. Paulo, H.N. and Brondani, RPV (2006). Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers. Genetics and Molecular Biology, 29 (4): 676-684.
Cameron, D.K., and Wang, Y. (2005). A better understanding of factors that affect the hardness and stickiness of longgrain rice. Cereal Chemistry, 82:113–11.
Chen,Y., Wang, M., Ouwerkerk and Pieter, B.F. (2012). Molecular and environmental factors determining grain quality in rice. Food and Energy Security, 1 (2): 111–132.
Ghneim, H.T., Duque, P.D., Almeida, I.P., Nunez, T.G., Pieters, A.J., Martinez, C.P. and Tohme, J.M. (2008). Assessment of genetic diversity Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidalaya. Research Journal of Agriculture Sciences,4 (3): 329-332.
Golam, F., Yin, Y.H., Masitah, A., Afnierna, N., Majid, N.A., Khali, N. and Osman, M. (2011). Analysis of aroma and yield component of aromatic rice in Malaysian tropical environment. Journal of Crop Science, 5 (11): 1318-1325.
Grist, S.A., Firgaira, F.A. and Morley, A.A. (1993). Dinucleotide repeat polymorphisms isolated by the polymerase chain reaction. Bio –Technology, 15: 304–309.
He, G., and Suzuki, H. (1987). The relationship between translucency of rice grain and gelatinization of starch in the grain during cooking. Journal of Nutritional Science and Vitaminology, 33:263–273.
Jalaluddin, M., Nakai, H. and Yamamoto, T. (2007). Genetic diversity and DNA fingerprinting of some modern in dica and japonica rice. SABRAO Journal of Breeding and Genetics, 39 (1): 43-52.
Kibanda, J.M.N. and Luzi-kihupi, A. (2007). Influence of genetic and genotype environment interaction on quality of rice grain. African Crop Science Journal, 15: 173–182.
Kumar, S., Bisht, I.S. and Bhatt, K.V. (2010). Assessment of genetic diversity among rice (Oryza sativa L.) landrace populationsunder traditional production using microsatellite (SSR) markers. Electronic Journal of Plant Breeding, 1: 474–483.
Lapitan, V.C., Brar, D.S., Abe,T .and Redona, E.D. (2007). Assessment of genetic diversity of Philippines rice cultivars carrying good quality traits using SSR markers. Breeding Science, 57: 263-270.
McCouch, S.R., Chen, X. and Cho, Y.G. (2002). Sequence divergence of rice microsatellites in Oryza and other plant species. Molecular Genetics and Genomics, 268, 331-343.
Mizukami, H. and Takeda, Y. (2000). Chewing properties of cooked rice from new characteristic rice cultivars and their relation to starch molecular structures. Journal of Applied Glycoscience, 47:61–65.
Murray, M.G. and Thompson, W.F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acid Research, 8: 432-435.
Nadaf, A.B., Krishnan, S. and Wakte, K.V. (2006). Histochemical and biochemical analysis of major compound (2-acetyl-1-pyrroline) in basmati and other scented rice (Oryza sativa. L.), Current Science, 91: 1533–1536.
Nagaraju, J., Kathirvel, M., Ramesh Kumar, R., Siddiq, E.A., and Hasnain S.E. (2002). Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by
using fluorescence-based ISSR-PCR and SSR markers. PNAS 99: 5836-5841.
Nakamura, Y., Sato, A. and Juliano, B.O. (2006). Short chain length distribution in debranched rice starches differing in gelatinization temperature or cooked rice hardness. Starch/St€arke 58:155–160.
Oliveira, M.M., Martins, P., Jayamani, S. and Negrao, B. (2007). Genetic relatedness of Portuguese rice accessions from diverse origins as assessed by microsatellite markers. Crop Science, 47: 879-884.
Ong, M.H., and Blanshard, J.M.V. (1995). Texture determinants in cooked, parboiled rice. I: Rice starch amylose and the fine structure of amylopectin. Journal of Cereal Science, 21:251–260.
Perez, C.M. and Juliano, B.O. (1978). Modification of the simplified amylose test for milled rice. Starch, 30:424-426.
Pervaiz, Z.H., Rabbani, M.A., Pearce, S.R. and Malik, S.A. (2009). Determination of genetic variability of Asian rice (Oryzasativa L.) varieties using microsatellite markers. African Journal of Biotechnology, 8:641-5651.
Pervaiz, ZH., Rabbani, M.A., Khaliq, I., Pearce, S.R. and Malik, S.A. (2010). Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice. Electronic Journal of Biotechnology, 13: 4-5.
Ram, S.G., Thiruvengadam, V. and Vinod, K.K. (2007). Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. Journal of Applied Genetics, 48: 337–345.
Ramesh, M., Zakiuddin, S.A., and Bhattacharya, K.R. (1999). Structure of rice starch and its relation to cookedrice texture. Carbohydrate Polymer, 38:337–347.
Randall, G., Mutters, James, and Thompson, F., (2009). Rice quality in the global market, Rice quality handbook. Chapter 1:1-22.
Rani, M.R.S., and Bhattacharay, K.R. (1989). Slurry viscosity as a possible indicator of rice quality. Journal Texture Studies, 20:139–149.
Saini, N., Jain, N., Jain, S. and Jain, R.K. (2004). Assessment of genetic diversity within and among basmati and nonbasmati rice varieties using AFLP, ISSR and SSR markers. Euphytica, 140: 133–146.
Shahidullah, S.M., Hanafi, M.M., Ashrafuzzaman, M., Ismail, M.R., and Khair, A. (2009). Genetic diversity in grain quality and nutrition of aromatic rice’s. Afrian Journal of Biotechnology, 8 (7): 1238-1246.
Singh. N., Singh. J., Kaur, L., Sodhi, N.S. and Gill, B.S. (2003). Morphological, thermal and rheological properties of starches from different botanical sources. Food Chemistry81: 219-231.
Sivaranjani, A.K.P. (2010). Assessment of genetic diversity among basmati and non-basmati aromatic rices of India using SSR markers. Current Science, 99: 221–226.
Siwach, P., Jain, S., Sain, N., Chowdhury,V.K. and Jain, R.K. (2004). Allelic diversity among Basmati and non- Basmati long-grain indica rice varieties using microsatellite markers. Journal of Plant Biochemistry and Biotechnology, 13: 25-32.
Smith, J.S.C., Chin, E.C.L., Shu, H., Smith, O.S., Wall, S.J., Senior, M.L., Mitchell, S.E., Kresovich, S. and Zeigle J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics, 95:163–173.
Sowbhagya, C.M., Ramesh, B.S. and Bhattacharya, K.R. (1987). The relationship between cooked-rice texture and the physicochemical characteristics of rice. Journal of Cereal Science, 5:287–297.
Sundaram, R.M., Naveenkumar, B., Biradar, S.K., Balachandran, S.M., Mishra,B. and Ahmed, M.I. (2008). Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica, 163: 215–224.
Tahir, M.H.N., Sadaqat, H.A. and Bashir, S. (2002). Correlation and path co-efficient analysis of morphological traits in sunflower (Helianthus annuus L.) Populations. International Journal of Agricultureand Biology 4 (3): 341-343.
Thompson, M.J., SeptininJih, E.M., Suwardjo, F., Santoso, T.J., Silitonga, T.S. and Mcouch S.R. (2007). Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theoretical and Applied Genetics, 114: 559- 568.
Vanniarajan, C., Vinod, K.K. and Pereira, A. (2012). Molecular evaluation of geneticdiversity and association studies in rice (Oryza sativa L.). Journal of Genetics, 9: 9–19.
Wang, F. (2009). Integrated KL (K-means-Laplacian) clustering: a new clustering approach by combining attribute data and pairwise relations. In proceeding of SDM 09, SIAM Press, pp. 38–48.
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Assessment of diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties. (2016). Journal of Applied and Natural Science, 8(1), 69-76. https://doi.org/10.31018/jans.v8i1.749
