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Morphological and genetic diversity analysis of rice accessions (Oryza sativa L.) differing in iron toxicity tolerance

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Abstract

A major emphasis in breeding for iron toxicity tolerance in rice is to identify differences that are associated with resistance and harness them for genetic improvement. In this study, thirty accessions, including IRRI gene bank accessions, two varieties from Brazil, 8 cultivars from West Africa and 10 cultivars from Uganda were analyzed for sensitivity to iron toxicity, and genetic diversity using morphological and SSR markers. Two genotypes, IR61612-313-16-2-2-1 and Suakoko 8 showed significantly high resistance with an average score of ≤ 3.5 on 1–9 scale. The SRR markers were highly informative and showed mean polymorphism information content (pic) of 0.68. The PIC values revealed that RM10793, RM3412, RM333, RM562, RM13628, RM310, RM5749, and RM154 could be the best markers for genetic diversity estimation of these rice cultivars. Diversity at the gene level showed an average of 4.61 alleles ranging from 2 to 12 per locus. Mean gene diversity (H) value for all SSR loci for the 30 genotypes evaluated was 0.69 but was decreased to 0.53 when analysis was performed on Ugandan accessions. The low genetic diversity found among the Ugandan accessions is the evidence of a narrow genetic base, and such a scenario has a potential vulnerability for resistance break down. A low correlation was detected between the observed molecular and morphological datasets. This means that a combination of morphological traits and SSR analysis would be required when assessing genetic variation under iron toxic conditions, and could be a practical strategy for breeders when planning crosses. A distinction between the resistant and susceptible accessions in both phenotyping and SSR datasets suggests the presence of unique alleles that could be harnessed for improvement of rice against iron toxicity.

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References

  • Abifarin AO. 1988. Grain yield due to iron toxicity. WARDA Tech. Newsl. 8: 1–2

    Google Scholar 

  • Aguirre C, Alvarado R, Hinrichsen P. 2005. Identificación de cultivares y líneas de mejoramiento de arroz de Chile mediante amplificación de fragmentos polimórficos (AFLP). Agricultura Técnica 65: 356–369

    Article  Google Scholar 

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181–186

    Article  PubMed  CAS  Google Scholar 

  • Audebert A, Sahrawat KL. 2000. Mechanisms for iron toxicity tolerance in lowland rice. J. Plant Nutr. 23: 1877–1885

    Article  CAS  Google Scholar 

  • Bandopadhyay R, Sharma S, Rustgi S, Singh R, Kumar A, Balyan HS, Gupta PK. 2004. DNA polymorphism among 18 species of Triticum-Aegilops complex using wheat EST-SSRs. Plant Sci. 166: 349–356

    Article  CAS  Google Scholar 

  • Becker M, Asch F. 2005. Iron toxicity — conditions and management concepts. J. Plant Nutr. Soil Sci. 168: 558–573

    Article  CAS  Google Scholar 

  • Bligh HFJ, Blackhall NW, Edwards KJ, McClung AM. 1999. Using amplified length polymorphisms and simple sequence length polymorphisms to identify cultivars of brown and white milled rice. Crop Sci. 39: 1715–1721

    Article  CAS  Google Scholar 

  • Bruschi P, Vendramin F, Bussotti P, Grossoni GG. 2003. Morphological and molecular diversity among Italian populations of Quercus petraea (Fagaceae). Ann. Bot. 91: 707–716

    Article  PubMed  CAS  Google Scholar 

  • Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A et al. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3: 1745–1756

    Article  PubMed  CAS  Google Scholar 

  • Cho YG, Ishii T, Temnykh SV, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S. 2000. Diversity of microsatellites derived from genomic libraries and genbank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100: 713–722

    Article  CAS  Google Scholar 

  • Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ. 2001. Microsatellite markers from sugarcane (Saccharum spp.): ESTs cross transferable to Erianthus and Sorghum. Plant Sci. 160: 1115–1123

    Article  PubMed  CAS  Google Scholar 

  • Cornelious BK, Sneller CH. 2002. Yield and molecular diversity of soybean lines derived from crosses of Northern and Southern elite parents. Crop Sci. 42: 642–647

    Article  Google Scholar 

  • Cuevas-Perez FE, Guimaraes EP, Berrio LE, Gonzales DI. 1992. Genetic base of the irrigated rice in Latin America and the Caribbean. Crop Sci. 32: 1054–1059

    Article  Google Scholar 

  • Dalton CC, Iqbal K, Turner DA. 1983. Iron phosphate precipitation in Murashige and Skoog media. Physiol. Plant 57: 472–476

    Article  CAS  Google Scholar 

  • De Datta SK, Neue HU, Senadhira D, Quijano C. 1994. Success in rice improvement for poor soils. In: Proceedings of the Workshop on Adaptation of Plants to Soil Stresses, 1–4 August 1993, University of Nebraska, Lincoln, Nebraska. INTSORMIL Publication No. 94-2.Lincoln, Nebraska, USA, University of Nebraska, pp 248–268

    Google Scholar 

  • Dice LR. 1945. Measures of the amount of ecological association between species. Ecology 26: 297–302

    Article  Google Scholar 

  • Dilday RH. 1990. Contribution of ancestral lines in the development of new cultivars of rice. Crop Sci. 30: 905–911

    Article  Google Scholar 

  • Dufey I, Hakizimana P, Draye X, Lutts S, Bertin P. 2009. QTL mapping for biomass and physiological parameters linked to resistance mechanisms to ferrous iron toxicity in rice. Euphytica 167: 143–160

    Article  CAS  Google Scholar 

  • Fuentes JL, Escobar F, Alvarez A, Gallego G, Duque MC, Ferrer M, Deus JE, Tohme J. 1999. Analyses of genetic diversity in Cuban rice varieties using isozyme, RAPD and AFLP markers. Euphytica 109: 107–115

    Article  CAS  Google Scholar 

  • Garland SH, Lewin L, Abedinia M, Henry R, Blackeney A. 1999. The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.). Euphytica 108: 53–63

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ghneim T, Posso D, Perez I, Torrealba G, Pieters AJ, Martinez CP, Tohme JM. 2008. Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Electron. J. Biotechnol. 11: 1–14

    Google Scholar 

  • Giarrocco LE, Marassi MA, Salerno GL. 2007. Assessment of the genetic diversity in Argentine rice cultivars with SSR markers. Crop Sci. 47: 853–858

    Article  CAS  Google Scholar 

  • Guimaraes EP, Borrero J, Ospina-Rey Y. 1995. Genetic diversity of upland rice germplasm distributed in Latin America. Pesqui. Agropecu. Bras. 31: 187–194

    Google Scholar 

  • Gunawardena I, Virmani SS, Sumo FJ. 1982. Breeding rice for tolerance to iron toxicity. Oryza 19: 5–12

    Google Scholar 

  • Hashimoto Z, Mori N, Kawamura M, Ishii T, Yoshida S, Ikegami M, Takumi S, Nakamura C. 2004. Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers. Theor. Appl. Genet. 109: 1586–1596

    Article  PubMed  CAS  Google Scholar 

  • Hartl LD, Clark AG. 1997. Principles of population genetics (3rd edition), Snauer Associates, Inc. Publishers, Sunderland, pp 1–682

    Google Scholar 

  • Innan H, Terauchi R, Miyashita T. 1997. Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics 146: 1441–1452

    PubMed  CAS  Google Scholar 

  • IRRI. 1996. The International Rice Testing Programme Standard Evaluation System (IRTP-SES) for rice. International Rice Research Institute, Los Baños, The Philippines, 4th Ed., pp 35

    Google Scholar 

  • Jeung JU, Hwang HG, Moon HP, Jena KK. 2005. Fingerprinting temperate japonica and tropical indica rice genotypes by comparative analysis of DNA markers. Euphytica 146: 239–251

    Article  CAS  Google Scholar 

  • Jones ES, Sullivan H, Bhattramakki D, Smith JSC. 2007. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor. Appl. Genet. 115: 361–371

    Article  PubMed  CAS  Google Scholar 

  • Khush GS. 2005. What it will take to feed five billion rice consumers by 2030. Plant Mol. Biol. 59: 1–6

    Article  PubMed  CAS  Google Scholar 

  • Lin MS. 1991: Genetic base of Japonica rice varieties released in Taiwan. Euphytica 56: 43–46

    Google Scholar 

  • Kölliker R, Jones ES, Jahufer MZZ, Forster. 2001. Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.). Euphytica 121: 305–315

    Article  Google Scholar 

  • Kölliker R, Stadelmann FJ, Reidy B, Nösberger J. 1999. Genetic variability of forage grass cultivars: A comparison of Festuca pratensis Huds., Lolium perenne L. and Dactylis plomerata L. Euphytica 106: 261–270

    Article  Google Scholar 

  • Majerus V, Bertin P, Lutts S. 2007a. Effects of iron toxicity on osmotic potential, osmolytes and polyamines concentrations in the African rice (Oryza glaberrima Steud.). Plant Sci. 173: 96–105

    Article  CAS  Google Scholar 

  • Majerus V, Bertin P, Swenden V, Fortemps A, Lobréaux S, Lutts S. 2007b. Organ-dependent responses of the African rice to short-term iron toxicity: ferritin regulation and antioxidative responses. Biol. Plant.51: 303–312

    Article  CAS  Google Scholar 

  • Mantel NA. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209–220

    PubMed  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K et al. 2002. Development and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199–207

    Article  PubMed  CAS  Google Scholar 

  • Mohanty SK, Panda K. 1991. Varietal behavior of rice towards Fe toxicity. Oryza 28: 513–515

    Google Scholar 

  • Nei M. 1972. Genetic distance between populations. Am. Nat. 106: 283–292

    Article  Google Scholar 

  • Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, pp 512

    Google Scholar 

  • Olufowote JO, Xu Y, Chen X, Goto M, McCouch SR, Park WD, Beachell HM, Dilday RH. 1997. Comparative evaluation of within cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40: 370–378

    Article  PubMed  CAS  Google Scholar 

  • Onaga G, Edema R, Asea G. 2012. Tolerance of rice germplasm to iron toxicity stress and the relationship between tolerance, Fe2+, P and K content in the leaves and roots. Arch. Agron. Soil Sci. 59: 213–219

    Article  Google Scholar 

  • Panaud O, Chenayd 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

    PubMed  CAS  Google Scholar 

  • Ponnamperuma FN, Bradfield R, Peech M. 1955. Physiological disease of rice attributable to iron toxicity. Nature 175: 265

    Article  CAS  Google Scholar 

  • Rana MK, Bhat KV. 2004. A comparison of AFLP and RAPD markers for genetic diversity and cultivar identification in cotton. J. Plant Biochem. Biotech. 13: 19–24

    Article  CAS  Google Scholar 

  • Ribeiro-Carvalho CR, Guedes-Pinto H, Igrejas G, Stephenson P, Schwarzacher T, Heslop-Harrison JS. 2004. High levels of genetic diversity throughout the range of the Portuguese wheat landrace Barbela. Ann. Bot. 94: 699–705

    Article  PubMed  CAS  Google Scholar 

  • Rohlf FJ. 2000. NTSYS-pc: Numerical Taxonomy System. Ver. 2.1. Exeter Software, Setauket, NY, USA, pp 29–34

    Google Scholar 

  • Sahrawat KL. 2004. Iron toxicity in wetland rice and the role of other nutrients. J. Plant Nutr. 27: 1471–1504

    Article  CAS  Google Scholar 

  • Sahrawat KL, Diatta S, Singh BN. 2000. Reducing iron toxicity in lowland rice through an integrated use of tolerant genotypes and plant nutrient management. Oryza 37: 44–47

    Google Scholar 

  • SAS Institute. 2012. Statistical analysis software. Version 9.3. SAS Inst., Cary, NC

    Google Scholar 

  • Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF. 1998. The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol. Biol. Evol.15: 1751–1760

    Article  PubMed  CAS  Google Scholar 

  • Shabala S. 2010. Physiological and cellular aspects of phytotoxicity tolerance in plants: the role of membrane transporters and implications for crop breeding for water logging tolerance. New Physiol. Rev. 3: 1–10

    Google Scholar 

  • Shimizu A. 2009. QTL analysis of genetic tolerance to iron toxicity in rice (Oryza sativa L.) by quantification of bronzing score. J. New Seeds 10:171–179

    Article  Google Scholar 

  • Siwach P, Jain S, Saini N, Chowdhury VK, Jain RK. 2004. Allelic diversity among Basmati and non-Basmati longgrain indica rice varieties using microsatellite markers. J. Plant Biochem. Biotechnol.13: 25–32

    Article  CAS  Google Scholar 

  • Smith S, Helentjaris T. 1996. DNA fingerprinting and plant variety protection. In AH Paterson, ed, Genome Mapping in Plants, Landes Company, Texas, pp 95–110

    Google Scholar 

  • Song MT, Lee JH, Cho YS, Jeon YH, Lee SB, Ku JH, Choi SH, Hwang HG. 2002. Narrow genetic background of Korean rice germplasm as revealed by DNA fingerprinting with SSR markers and their pedigree information. Korean J. Genet. 24:397–403

    CAS  Google Scholar 

  • Temnykh S, Park WD, Aires N, Cartinhour S, Hauch N, Lipovich L, Cho YG, Ishii T, McCouch SR. 2000. Mapping and genome organization of microsatellite in rice (Oryza sativa L.). Theor. Appl. Genet. 95: 163–173

    Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A. 2003. Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordium L.). Theor. Appl. Genet. 106: 411–422

    PubMed  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR. 2007. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using micosatellite markers. Theor. Appl. Genet. 114: 559–568

    Article  PubMed  CAS  Google Scholar 

  • Van Breemen N, Moormann FR. 1978. Iron-toxic soils, in IRRI: Soils and Rice. The International Rice Research Institute, Manila, Philippines, pp 781–799

    Google Scholar 

  • Van Inghelandt D, Melchinger AE, Lebreton C, Stich B. 2010. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers, Theor. Appl. Genet. 120: 1289–1299

    Article  Google Scholar 

  • Varshney RK, Sigmund R, Borner A, Korzun V, Stein N, Sorrelles ME, Langridge P, Graner A. 2004. Interspecific transferability and comparative mapping of barley ESTSSR markers in wheat, rye and rice. Plant Sci. 68: 195–202

    Google Scholar 

  • Vignal A Milan D, SanCristobal M, Eggen A. 2002. A review of SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34: 275–305

    Article  PubMed  CAS  Google Scholar 

  • Virmani SS. 1977. Varietal tolerance of rice to iron toxicity in Liberia. Int. Rice Res. Newsl. 2: 4–5

    Google Scholar 

  • Wan JL, Zhai HQ, Wan JM, Ikehashi H. 2003. Detection and analysis of QTLs for ferrous iron toxicity tolerance in rice, Oryza sativa L. Euphytica 131: 201–206

    Article  CAS  Google Scholar 

  • Wu P, Lou A, Zhang L, Wu Y, Huang N. 2003. Molecular markers linked to genes for tolerance to ferrous toxicity. Rice Genet. Newsl. 14: 17–17

    Google Scholar 

  • Xu Y, Beachell H, McCouch SR. 2004. A marker-based approach to broadening the genetic base of rice in USA. Crop Sci. 44: 1947–1959

    Article  Google Scholar 

  • Yamanouchi M, Yoshida S. 1981. Physiological mechanisms of rice’s tolerance for iron toxicity. Paper presented at the IRRI Saturday Seminar, June 6, 1981. The International Rice Research Institute, Manila, Philippines.

    Google Scholar 

  • Yoshida S. 1981. Fundamentals of rice crop science. The International Rice Research Institute, Manila, The Philippines

    Google Scholar 

  • Yosida SI Forno DA, Cock JH, Gomez KA. 1976 Laboratory manual for physiological studies of rice. International Rice Research znstitute (IRRI) manila, phiippines

    Google Scholar 

  • Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY et al. 2003. Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor. Appl. Genet. 108: 131–140

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Zhang F, Mao D. 1998. Effect of iron plaque outside roots on nutrient uptake by rice (Oryza sativa L.): II. Zinc uptake by Fe-deficient rice. Plant Soil 202: 33–39

    Article  CAS  Google Scholar 

  • Zhang X, Zhang Y, Yan R, Han J, Hong F, Wang JH, Cao K. 2010. Genetic variation of white clover (Trifolium repens L.) collections from China detected by morphological traits, RAPD and SSR. Afr. J. Biotech. 9: 3032–304

    CAS  Google Scholar 

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Authors and Affiliations

  1. International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines

    Geoffrey Onaga, James Egdane & Ismail Abdelbagi

  2. College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda

    Richard Edema

  3. National Crop Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda

    Geoffrey Onaga

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  1. Geoffrey Onaga
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Onaga, G., Egdane, J., Edema, R. et al. Morphological and genetic diversity analysis of rice accessions (Oryza sativa L.) differing in iron toxicity tolerance. J. Crop Sci. Biotechnol. 16, 53–62 (2013). https://doi.org/10.1007/s12892-012-0104-0

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