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Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes

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Abstract

Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise \(F_{\mathrm{ST}}\) analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice.

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References

  • Allahgholipour M. A. J. A., Alinia F., Nagamine T. and Kojima Y. 2006 Rice grain amylase and pasting properties for breeding better quality rice varieties. Plant Breed. 125, 357–362.

    Article  CAS  Google Scholar 

  • Anonymous 2004 Laboratory manual on rice grain quality procedure directorate of rice research, pp. 1–20. Directorate of Rice Research, Hyderabad.

  • Bansal U. K., Kaur H. and Saini R. G. 2006 Donors for quality characteristics in aromatic rice. Oryza 43, 197–202.

    Google Scholar 

  • Bhattacharya K. R. 1979 Tests for parboiled rice. In Proceedings workshop on Chemical aspects of rice grain quality, pp. 363. International Rice Research Institute, Los Bahos,.

  • Blakeney A. B., Welsh, L. A. and Martin M. 1992 In Proceedings of the 42nd RACI Cereal Chemistry Conference, pp. 342–346. Royal Australian Chemical Institute, Parkville.

  • Botstein D., White R. L., Skolnick M., and Davis R. W. 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brondani C., Borba T. C. O., Rangel, Paulo H. N. and Brondani R. P. V. 2006 Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers. Genet. Mol. Biol. 29, 676–684.

    Article  CAS  Google Scholar 

  • Cagampang G. B., Perez C. M. and Juliano B. O. 1973 A gel consistency test for eating quality of rice. J. Sci. Food Agric. 24, 1589–1594.

    Article  CAS  PubMed  Google Scholar 

  • Cameron D. K. and Wang Y. 2005 A better understanding of factors that affect the hardness and stickiness of long grain rice. Cerl. Chem. 82, 113–119.

    Article  CAS  Google Scholar 

  • Chakravarthi B. K. and Naravaneni R. 2006 SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa. L). Afr. J. Biotecnol. 5, 684–688.

    CAS  Google Scholar 

  • Chen Y., Wang M. and Pieter B. F. Ouwerkerk 2012 Molecular and environmental factors determining grain quality in rice. Food Energy Sec. 1, 111–132.

    Article  Google Scholar 

  • Cruz N. D. and Khush G. S. 2000 Rice grain quality evaluation procedures. In Aromatic rices (ed. R. K. Singh, U. S. Singh and G. S. Khush), vol. 3, pp. 15–28. Oxford & IBH, New Delhi.

  • Efferson J. N. 1985 Rice quality in world markets. In Grain quality and marketing, pp. 1–29. Paper presented at the International Rice Research Conference.

  • Garris A. J., Tai T. H., Coburn J., Kresovich S. and McCouch S. 2005 Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631–1638.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Golam F., Yin Y. H., Masitah A., Afnierna N., Majid N. A. and Khali N. et al. 2011 Analysis of aroma and yield component of aromatic rice in Malaysian tropical environment. Aust. \(J.\) Crop Sci. 5, 1318–1325.

  • Grist S. A., Firgaira F. A. and Morley A. A. 1993 Dinucleotide repeat polymorphisms isolated by the polymerase chain reaction. Bio. Techniq. 15, 304–309.

    CAS  Google Scholar 

  • He G. and Suzuki H. 1987 The relationship between translucency of rice grain and gelatinization of starch in the grain during cooking. J. Nutr. Sci. Vit. 33, 263–273.

    Article  CAS  Google Scholar 

  • Herrera T. G., Duque P. D., Almeida I. P., Nunez T. G., Pieters A. J., Martinez C. P. et al. 2008 Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Elect. J. Biot. 11, 3–4

    Google Scholar 

  • Huang X., Wei X., Sang T., Zhao Q., Feng Q., Zhao Y., Li C. et al. 2010 Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967.

    Article  CAS  PubMed  Google Scholar 

  • İbrahim S. M., Ramalingam A. and Subramanian M. 1990 Path analysis of rice grain yield under rainfed lowland conditions. Int. Rice Res. News Lett. 15, 11.

  • Jain S., Jain R. K. and McCouch S. R. 2004 Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor. Appl. Genet. 109, 965–977.

    Article  CAS  PubMed  Google Scholar 

  • Jalaluddin M., Nakai H. and Yamamoto T. 2007 Genetic diversity and DNA fingerprinting of some modern indica and japonica rice. SABRAO J. Breed. Genet. 39, 43–52.

    Google Scholar 

  • Khare R., Singh, A. K., Eram S. and Singh P. K. 2014 Genetic variability, association and diversity analysis in upland rice (Oryza sativa L.). SAARC J. Agri. 12, 40–51.

    Article  Google Scholar 

  • Kibanda J. M. N. and Luzi-kihupi A. 2007 Influence of genetic and genotype environment interaction on quality of rice grain. Afr. Crop Sci. J. 15, 173–182.

    Google Scholar 

  • Kumar S., Bisht I. S. and Bhatt K. V. 2010 Assessment of genetic diversity among rice (Oryza sativa L.) landrace populations under traditional production using microsatellite (SSR) markers. Elec. J. Plant Breed. 1, 474–483.

    Google Scholar 

  • Malik A. R., Muhammad S. M., Zabta K. S. and Kazuko Y. S. 2010 Genetic analysis of basmati and non-basmati Pakistan rice (Oryza sativa L.) cultivars using microsatellite markers. Pak. J. Bot. 42, 2551–2564.

    Google Scholar 

  • Marie N. N., Fousseyni C., Gezahegn G., Mounirou S., Roland B., Gustave D. et al. 2010 Morpho-agronomic and molecular characterization of Oryza glaberrima germplasm from Mali. Afr. J. Biotechol. 9, 7409–7417.

    Article  Google Scholar 

  • McCouch S. R., Chen X. and Cho Y. G. 2002 Sequence divergence of rice microsatellites in Oryza and other plant species. Mol. Genet. Genomics 268, 331–343.

    Article  PubMed  Google Scholar 

  • Meti N., Samal K. C., Bastia D. N. and Rout G. R. 2013 Genetic diversity analysis in aromatic rice genotypes using microsatellite based simple sequence repeats (SSR) marker. Afr. J. Biotechnol. 12, 4238–4250.

    Article  CAS  Google Scholar 

  • Mishra A., Kumar P., Sengar R. S., Kumar P., Singh R., Chaudhary R. et al. 2016 Assessment of diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties. J. App. Nat. Sci. 8, 69–76.

    Article  CAS  Google Scholar 

  • Mizukami H. and Takeda Y. 2000 Chewing properties of cooked rice from new characteristic rice cultivars and their relation to starch molecular structures. J. Appl. Glycosci. 47, 61–65.

    Article  CAS  Google Scholar 

  • Mohammadi S. A. and Prasanna B. M. 2003 Analysis of genetic diversity in crop plants - salient statistical tools and considerations. Crop Sci. 43, 1235–1248.

    Article  Google Scholar 

  • Murray M. G. and Tompson W. F. 1980 Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res. 8, 432–435.

    Article  Google Scholar 

  • Nachimuthu V. V., Muthurajan R., Duraialaguraja S., Sivakami R., Pandian B. A., Ponniah G. et al. 2015 Analysis of population structure and genetic diversity in rice germplasm using SSR markers: An initiative towards association mapping of agronomic traits in Oryza Sativa. Rice 8, 30.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.), Curr. Sci. 91, 1533–1536.

    CAS  Google Scholar 

  • Nagaraju J., Kathirvel M., Ramesh K. 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. Proc. Natl. Acad. Sci. USA 99, 5836–5841.

    Article  CAS  PubMed  Google Scholar 

  • 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-Starke 58, 155–160.

    Article  CAS  Google Scholar 

  • Ndjiondjop M. N., Semagn K., Sow M., Manneh B., Gouda A. C., Kpeki S. B. et al. 2018 Assessment of genetic variation and population structure of diverse rice genotypes adapted to lowland and upland ecologies in Africa using SNPs. Front. Plant Sci. 9, 446.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 Sci. 47, 879–884.

    Article  Google Scholar 

  • 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. J. Cerl. Sci. 21, 251–260.

    Article  CAS  Google Scholar 

  • Parida S. K., Dlal V., Singh A. K., Singh N. K. and Mohapatra T. 2012 SNPs in stress- responsive genes: validation, genotyping, functional relevance and population structure. BMC Genomics 13, 426.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patra B. C., Ray S., Ngangkham U. and Mohapatra T. 2016 Rice. In Genetic and genomic resources for grain cereals improvement, pp. 1–80. Elsevier, Cambridge.

    Google Scholar 

  • Perez C. M. and Juliano B. O. 1978 Modification of the simplified amylose test for milled rice. Starch 30, 424–426.

    Article  CAS  Google Scholar 

  • Pervaiz Z. H., Rabbani M. A., Pearce S. R. and Malik S. A. 2011. Determination of genetic variability of Asian rice (Oryza sativa L.) varieties using microsatellite markers. Afr. J. Biotechnol. 8, 5641–5651.

    Google Scholar 

  • Qian W., Ge S. and Hong D. Y. 2001 Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor. Appl. Genet. 102, 440–449.

    Article  CAS  Google Scholar 

  • Rahman Md. A., Haque M. E., Sikdar B., Islam Md. A. and Matin M. N. 2013 Correlation analysis of flag leaf with yield in several rice cultivars. J. Life Earth Sci. 8, 49–54.

    Article  Google Scholar 

  • Rai M. 1999 Rice germplasm evaluation and enhancement in India: issues, status, options, and future plan of action. In Proceedings of the International Symposium on Rice Germplasm Evaluation and Enhancement, Publ. no. 195, pp. 83–91. University of Arkansas, Arkansas.

  • Ram C. J., Kailash C. S., Sumit K. N. and Amrita P. 2010 DNA finger printing of promising rice (Oryza sativa L.) accessions from India using RAPD markers. Int. J. Integr. Biol. 10, 142–146.

    Google Scholar 

  • 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. J. Appl. Genet. 48, 337–345.

    Article  PubMed  Google Scholar 

  • Ramesh M., Zakiuddin S. A. and Bhattacharya K. R. 1999 Structure of rice starch and its relation to cooked-rice texture. Carbohyd. Polym. 38, 337–347.

    Article  CAS  Google Scholar 

  • Rani M. R. S. and Bhattacharay K. R. 1989 Slurry viscosity as a possible indicator of rice quality. J. Tex. Stud. 20, 139–149.

    Article  Google Scholar 

  • Saini N., Jain N., Jain S. and Jain R. K. 2004 Assessment of genetic diversity within and among basmati and non-basmati rice varieties using AFLP, ISSR and SSR markers. Euphytica 140, 133–146.

    Article  CAS  Google Scholar 

  • Samarajeewa P. K., Nitanthi R. M. and Lyanage A. S. 2004 Morphological and molecular characterization of locally collected wild rice germplasm. Ann. Sri Lanka Dept. Agri. 6, 177–186.

    Google Scholar 

  • Sarhadi W. A., Hien N. L., Zanjani M., Yosofzai W., Yoshihashi T. and Hirata Y. 2011 Comparative analyses for aroma and agronomic traits of native rice cultivars from Central Asia. J. Crop Sci. Biotechnol. 11, 17–22.

    Google Scholar 

  • Sarvestani Z. T., Pirdashti H., Sanavi S. A. M. M. and Balouchi H. 2008 Study of water effects in different growth stages on yield and yield components of different rice (Oryza sativa L.) cultivars. Pak. J. Bio. Sci. 11, 1303–1309.

    Article  Google Scholar 

  • Sharma S. K. and Goel N. 2011 Basmati rice and its future perspective. Division of Genetics, IARI, New Delhi.

    Google Scholar 

  • Shobha R. N., Pandey M. K., Prasad G. S. V. and Sudharshan I. 2006 Historical significance, grain quality features and precision breeding for improvement of export quality basmati varieties in India. Indian J. Crop Sci. 1, 29–41.

    Google Scholar 

  • 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 Chem. 81, 219–231.

    Article  CAS  Google Scholar 

  • Sivaranjani A. K. P., Pandey M. K., Sudharsan I., Gandhimani R., Madhav M. S., Sundaram S. et al. 2010 Assessment of genetic diversity among basmati and non-basmati aromatic rices of India using SSR markers. Curr. Sci. 99, 221–226.

    CAS  Google Scholar 

  • 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. J. Plant Biochem. Biotech. 13, 25–32.

    Article  CAS  Google Scholar 

  • Smith J. S. C., Chin E. C. L., Shu H., Smith O. S., Wall S. J., Senior M. L. et al. 1997 An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theor. Appl. Genet. 95, 163–173.

    Article  CAS  Google Scholar 

  • Sowbhagya C. M., Ramesh B. S. and Bhattacharya K. R. 1987 The relationship between cooked-rice texture and the physicochemical characteristics of rice. J. Cerl. Sci. 5, 287–297.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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. Int. J. Agri. Biol. 4, 341–343.

    Google Scholar 

  • Temnykh S., Rark W. D., Ayers N., Cartinhour S., Hauck N., Lipovich L. et al. 2000 Mapping and genome organization of microsatellite sequence in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 697–712.

    Article  CAS  Google Scholar 

  • Thomson M. J., SeptininJih E. M., Suwardjo F., Santoso T. J., Silitonga T. S. and McCouch S. R. 2007 Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114, 559–568.

    Article  CAS  PubMed  Google Scholar 

  • Tiwari K. K., Singh A., Pattnaik S., Sandhu M., Kaur S., Jain S., Tewari S. et al. 2015 Identification of a diverse mini-core panel of Indian rice germplasm based on genotyping using microsatellite markers. Plant Breed. 134, 164–171.

    Article  CAS  Google Scholar 

  • Umamaheswari D., Paramathma M. and Manivannan N. 2010 Molecular genetic diversity analysis in seed sources of Jatropha (Jatropha curcas L) using ISSR markers: Elect. J. Plant Breed. 1, 268–278.

    Google Scholar 

  • Vanniarajan C., Vinod K. K. and Pereira A. 2012 Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). J. Genet. 9, 9–19.

    Article  Google Scholar 

  • Virk P. S., Brian V. F. L., Jackson M. T. and Newbury J. 1995 Use of RAPD for the study of diversity within plant germplasm collections. Heredity 74, 170–179.

    Article  CAS  PubMed  Google Scholar 

  • Ward J. H. 1963 Hierarchical grouping to optimize an objective function. \(J\). Am. Stat. Assoc. 58, 236–244.

    Google Scholar 

  • Weber D. J., Rohilla R. and Singh U. S. 2000 Chemistry and biochemistry of aroma in scented rice. In Aromatic rice (ed. R. K. Singh, U. S. Singh and G. S. Khush), vol. 3, pp. 29–46. Oxford & IBH, New Delhi.

  • Wong S. C., Yiu P. H., Bong S. T. W., Lee H. H., Neoh P. N. P. and Rajan A. 2009 Analysis of sarawak bario rice diversity using microsatellite markers. Am. J. Agri Bio. Sci. 4, 298–304.

    Article  Google Scholar 

  • Yong-Jin J. P., Ju K. L. and Nam S. K. 2009 Simple sequence repeat polymorphisms for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14, 4546–4569.

    Article  Google Scholar 

  • Zhou W., Lv T., Yang Z., Wang T., Fu Y., Chen Y. et al. 2017 Morphophysiological mechanism of rice yield increase in response to optimized nitrogen management. Sci. Rep. 7, 17226.

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Authors thank Dr H. S. Gaur, Former Vice Chancellor for providing research facilities to conduct the present work in the Department of Agricultural Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, India.

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Authors and Affiliations

  1. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Anurag Mishra

  2. Department of Agricultural Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250 110, India

    Anurag Mishra, Pushpendra Kumar & Parveen Fatima

  3. Department of Molecular Biology and Genetic Engineering, Dr. Kalam Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, 813 210, India

    Md. Shamim

  4. Department of Plant Molecular Biology and Biotechnology, C. P. College of Agriculture, S. D. Agricultural University, S. K. Nagar, 385 506, India

    Kapil K. Tiwari

  5. Integral Institute of Agricultural Science and Technology, Integral University, Lucknow, 226 026, India

    Deepti Srivastava

  6. Zonal Research Station, Nagina, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250 110, India

    Rajendra Singh

  7. Directorate of Rapeseed Mustard Research, Bharatpur, 321 304, India

    Prashant Yadav

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  1. Anurag Mishra
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Mishra, A., Kumar, P., Shamim, M. et al. Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes. J Genet 98, 92 (2019). https://doi.org/10.1007/s12041-019-1131-0

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