Morpho-agronomic and simple sequence repeat-based diversity in colored rice (Oryza sativa L.) germplasm from peninsular India

Genetic Resources and Crop Evolution

Volumn 59, Issue 2, 2012, Pages 179-189

  Gowda, S J M ^a,c   Randhawa, G J ^a   Bisht, I S ^a   Firke, P K ^a   Singh, A K ^b   Abraham, Z ^a   Dhillon, B S ^a,c  

^a NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

^b INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

^c UNIVERSITY OF HOHENHEIM   (Germany)

Author keywords

Colored rice; Genetic diversity; Germplasm accessions; Oryza sativa; SSRs

Indexed keywords

AGRONOMY; CROP YIELD; FLOWERING; GENETIC ANALYSIS; GENETIC MARKER; GENETIC RESOURCE; GENETIC VARIATION; GERMPLASM; MATURATION; MORPHOLOGY; PHYTOMASS; PRINCIPAL COMPONENT ANALYSIS; RICE; VEGETATION CLASSIFICATION;

INDIA;

ORYZA SATIVA;

EID: 84856723010     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-011-9674-9     Document Type: Article

References (49)

1. AOAC (2000) Official methods of analysis, 17 edn. Association of Official Analytical Chemists, Washington, DC.
2. Borba TCO, Brondani RPV, Rangel PHN, Brondani C (2009) Microsatellite marker-mediated analysis of the EMBRAPA rice core collection genetic diversity. Genetica 137: 293-304.
3. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of microsatellite framework map providing genome wide coverage in rice. Theor Appl Genet 95: 553-567.
4. Deepa G, Singh V, Naidu KA (2008) Nutrient composition and physicochemical properties of Indian medicinal rice-Njavara. Food Chem 106: 165-171.
5. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA mini preparation version II. Plant Mol Bio Rep 1: 19-21.
6. Dhillon BS, Singh M, Parsad R, Gupta VK, Singh BB (2004) Evaluation of plant genetic resources: Issues, advances and opportunities. In: Dhillon BS, Tyagi RK, Lal A, Saxena S (eds) Plant genetic resource management. Narosa Publishing House, New Delhi, pp 242-265.
7. Elameen A, Larsen A, Klemsdal SS, Fjellheim S, Sundheim L, Msolla S, Masumba E, Rognli OA (2010) Phenotypic diversity of plant morphological and root descriptor traits within a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania. Genet Resour Crop Evol, doi: 10. 1007/s10722-010-9585-1.
8. Frankel OH, Bennett E (eds) (1970) Genetic resources in plants-their exploration and conservation. International Biological Programme Handbook 11. Blackwell Scientific Publications, Oxford.
9. Frei M, Becker K (2005) Fatty acids and all-trans-β-carotene are correlated in differently colored rice landraces. J Sci Food Agric 85: 2380-2384.
10. Gao LZ, Zhang CH, Chang L, Jia J, Qiu Z, Dong Y (2005) Microsatellite diversity within Oryza sativa with emphasis on indica-japonica divergence. Genet Res 85: 1-14.
11. Ghalmi N, Malice M, Jacquemin JM, Ounane SM, Mekliche L, Baudoin JP (2010) Morphological and molecular diversity within Algerian cowpea (Vigna unguiculata (L.) Walp.) landraces. Genet Resour Crop Evol 57: 371-386.
12. Graham RD, Senadhira D, Beebe S, Iglesias C, Monasterio I (1999) Breeding for micronutrient density in edible portions of staple food crops: Conventional approaches. Field Crops Res 60: 57-80.
13. Gregorio GB (2002) Progress in breeding for trace minerals in staple crops. J Nutr 132: 500-502.
14. Gregorio GB, Senadhira D, Htut T, Graham RD (2000) Breeding for trace mineral density in rice. Food Nutr Bull 21: 382-386.
15. Hallauer AR, Miranda JB (1988) Quantitative genetics in maize breeding, 2nd edn. Iowa State University Press, Ames, IA.
16. IRRI (1987) Rice quality testing. GEU skill series. International Rice Research Institute, Manila, Philippines, pp 1-12.
17. Jackson MT, Loresto GC, Rao AS, Jones M, Guimaraes EP, Ng NQ (1997) Rice. In: Fuccillo D, Sears L, Stapleton P (eds) Biodiversity in trust: Conservation and use of plant genetic resources in CGIAR centers. Cambridge University Press, Cambridge.
18. Jain S, Jain R, McCouch SR (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.
19. Ji HC, Kim Y, Lee BH, Cho JW, Seo S, Yamakawa T (2007) Genetic diversity of colored rice lines based on botanical characteristics and simple sequence repeat (SSR) markers. J Fac Agr 52: 287-293.
20. Kaneda I, Yasui H, Adachi Y, Takada J, Sakurai H (2005) Determination of trace element concentrations in ancient rices (red and black rices) and a present-day rice (Koshihikari): Relationship among the trace element concentrations, species, harvest sites and rice parts. Biomed Res Trace Elements 16: 241-249.
21. Kaneda L, Kubob F, Sakurai H (2007) Relationship between trace metal concentration and antioxidative activity of ancient rice bran (red and black rice) and a present-day rice bran (Koshihikari). J Trace Elements Med Bio 21: 43-51.
22. Kumar V, Sharma S, Sharma KA, Sharma S, Bhat KV (2009) Comparative analysis of diversity based on morpho-agronomic traits and microsatellite markers in common bean. Euphytica 170: 249-262.
23. Malhotra VV, Singh VS, Singh KB (1974) Relation between geographic diversity and genetic divergence in green gram. Indian J Agric Sci 44: 815-818.
24. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
25. Matsuo T, Futsuhara Y, Kukuchi F, Yamaguchi H (1997) Science of the Rice Plant volume III. Food and Agricultural Policy Research Center, Tokyo.
26. Meera MV, Potty NN (1999) Nutritional specificity and quality properties of medicinal rice "Najavara". Oryza 36: 315-317.
27. Murty BR, Arunachalam V (1966) The nature of genetic divergence in relation to breeding system in crop plants. Indian J Genet 26: 188-189.
28. Naidu NV, Satyanarayana A (1991) Studies on genetic divergence over environments in mung bean. Indian J Genet 51: 454-460.
29. Nei M (1973) Analysis of gene diversity in sub-divided populations. PNAS 70: 3321-3323.
30. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS 76: 5269-5273.
31. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252: 597-607.
32. Paterson AH, Lan TH, Reischmann KP, Chang C, Lin SC, Burow MD, Kowalski SP, Katsar CS, DelMonte TA, Feldmann KA, Schertz KF, Wendel JF (1996) Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 14: 380-382.
33. Rahman S, Sharma MP, Suman S (2006) Nutritional and medicinal value of some indigenous rice varieties. Indian J Traditional Knowl 6: 454-458.
34. Ram SG, Thiruvengadam V, Vinod KK (2007) Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. J Appl Genet 48: 337-345.
35. Ramaiah K, Rao MBVN (1953) Rice breeding and genetics. Sci Monogr ICAR, 19, New Delhi, India.
36. Rana JC, Negi KS, Wani SA, Saxena S, Pradheep K, Kak A, Pareek SK, Sofi PA (2009) Genetic resources of rice in the Western Himalayan region of India: Current status. Genet Resour Crop Evol 56: 963-973.
37. Ravi M, Geethanjali S, Sameyafarheen F, Maheshwaran M (2003) Molecular marker based genetic diversity analysis in rice using RAPD and SSR markers. Euphytica 133: 243-252.
38. Roldan-Ruiz I, van euwijk FA, Gilliland TJ, Dubreuil P, Dillmann C, Lallemand J, De Loose M, Baril CP (2001) A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theor Appl Genet 103: 1138-1150.
39. SAS (2004) SAS for Windows Release 9. 1. SAS Institute, Inc., Cary, NC.
40. Sharma L, Prasanna BM, Ramesh B (2010) Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the North-East Himalayan region. Genetica 138: 619-631.
41. Siddiq EA, Saxena S, Malik SS (2006) Rice. In: Dhillon BS, Saxena S, Agrawal A, Tyagi RK (eds) Plant genetic resources: food grain crops. Narosa Publishing House, New Delhi, pp 27-58.
42. Solis JS, Ulloa DM, Rodriguez LA (2007) Molecular description and similarity relationships among native germplasm potatoes (Solanum tuberosum ssp. tuberosum L.) using morphological data and AFLP markers. Electron J Biotech 10: 436-443.
43. Suzuki M, Kimura T, Yamagishi K, Shinmoto H, Yamaki K (2004) Comparison of mineral contents in 8 cultivars of pigmented brown rice. J Japan Soc Food Sci Tech 51: 424-427.
44. Temnykh S, De CG, Lukashova A, Lipovich L, Catimhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice: Frequency and length variation, transposon association and genetic marker potential. Genome Res 11: 1441-1452.
45. Thomson MJ, Septiningsih E, Suwardjo F, Santoso T, Silitonga T, McCouch S (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114: 559-568.
46. Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the island of Borneo. Rice 2: 80-92.
47. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 24: 225-235.
48. Yoshida H, Tomiyama Y, Mizushina Y (2010) Lipid components, fatty acids and triacylglycerol molecular species of black and red rices. Food Chem 123: 210-215.
49. Zhang HL, Sun JL, Wang MX, Liao DQ, Zeng YW, Shen SQ, Yu P, Wang XK, Li ZC (2007) Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome 50: 72-83.