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Genetic diversity analysis of rice varieties (Oryza sativa L.) based on morphological, pedigree and DNA polymorphism data

  • Jorge Luis Fuentes (a1), Maria Teresa Cornide (a2), Alba Alvarez (a1), Enrique Suarez (a3) and Ernesto Borges (a3)...

Abstract

The diversity within 20 rice varieties used as progenitors in Cuban rice breeding programmes was analysed with respect to agro-morphological traits, pedigree and DNA markers. Eleven agro-morphological traits were scored, and phenotypic (Euclidian) distances between the rice varieties were calculated. Sixty random amplified polymorphism DNA (RAPD) and 115 amplified fragment length polymorphism (AFLP) bands served to determine Dice's distance estimates. Cluster analyses were performed based on genetic distance matrices using the unweighted pair-group method of arithmetical means (UPGMA) as the clustering method. This analysis showed five phenotypic, six genealogical, five RAPD and six AFLP diversity groups. Genetic diversity estimates based on RAPD data, but not on AFLP, efficiently represented the genetic parentage and phenotypic diversity between rice varieties. Combined diversity estimates allowed the identification of 11 different genetic pools and permitted a more effective separation of the progenitor set than those obtained solely by phenotypic and genealogical information. The results of this study stress the necessity to diversify rice parental stocks for further breeding purposes.

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Corresponding author

*Corresponding author: E-mail: fuentes@ceaden.edu.cu

References

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Almanza-Pizón, MI, Khairallah, M, Fox, PN and Warburton, ML (2003) Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions. Euphytica 130: 7786.
Arteche, J, Fuentes, JL, Cornide, MT and Borges, E (2005) Crop Genetic Diversity (CROPDIVER): software to optimize the varietal structure composition and the assisted progenitor recommendation based on their genetic diversity. Cultivos Tropicales 26: (3) 4550.
Autrique, E, Nachit, MN, Monneveux, P, Tanksley, SD and Sorrells, ME (1996) Genetic diversity in durum wheat based on RFLP, morphological traits and coefficient of parentage. Crop Science 36: 735742.
Barbosa-Neto, JF, Sorrells, ME and Cisar, G (1996) Prediction of heterosis in wheat using coefficient of parentage and RFLP-based estimates of genetic relationship. Genome 39: 11421149.
Barrett, BA, Kidwell, KK and Fox, PN (1998) Comparison of AFLP and pedigree-based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Science 38: 13481355.
Bernardo, R (1994) Prediction of maize single-cross performance using RFLPs and information from related hybrids. Crop Science 34: 2025.
Bernardo, R, Romero-Severson, J, Zeigle, J, Hauser, J, Hookstra, JG and Doerge, RW (2000) Parental contribution and coefficient of coancestry among maize inbreds: pedigree, RFLP and SSR data. Theoretical and Applied Genetics 100: 552556.
Bohn, M, Utz, HF and Melchinger, AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Science 39: 268275.
Cao, D and Oard, JH (1997) Pedigree RAPD analysis of commercial U.S. rice cultivars. Crop Science 37: 16301635.
Cornide, MT, Leonard, H, Canales, E, Mesa, J, Calvo, D and Ortiz, R (1999) Genetic diversity among a group of sugarcane varieties and its relationship to family performance. Cultivos Tropicales 20: 6368.
Dice, LR (1945) Measures of the amount of ecologic association between species. Ecology 26: 297302.
Dreisigacker, S, Zhang, P, Warburtun, ML, Van Ginkel, M, Hoisington, D, Bohn, M and Melchinger, AE (2004) SSR and pedigree analysis of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Science 44: 381388.
Ellis, RP, McNicol, JW, Baird, E, Booth, A, Lawrence, P, Thomas, B and Powell, W (1997) The use of AFLP to examine genetic relatedness in barley. Molecular Breeding 3: 359369.
Emik, LO and Terrill, CE (1949) Systematic procedures for calculating inbreeding coefficients. Journal of Heredity 40: 5155.
Ernst, CA, Mason, M, Gupta, M and Thompson, SA (2001) Utilization of SSR markers to determine genetic similarity and heterotic associations in Zea mays (abstract) In: Proceedings of the Plant & Animal Genome IX Conference,San Diego, CA.
Ford-Lloyd, BV, Newbury, HJ, Jackson, MT and Virk, PS (2001) Genetic basis for co-adaptive gene complexes in rice ( Oryza sativa L.) landraces. Heredity 87: 530536.
Fuentes, JL, Tohme, J, Escobar, F, Álvarez, A, Gallego, G, Duque, MC, Ferrer, M, Deus, JE Suáand, rez, E (1999) Analysis of genetic diversity in Cuban rice varieties using AFLP, RAPD and isozyme markers. Euphytica 109: 107115.
Gutiérrez, OA, Basu, S, Saha, S, Jenkins, JN, Shoemaker, DB, Cheatham, CL and McCarty, JC (2002) Genetic distance among selected cotton genotypes and its relationship with F 2 performance. Crop Science 42: 18411847.
Jaccard, A (1974) The Genetic Structure of Populations New York Springer-Verlag translated by D.B. Charles Worth
Lee, M, Godshalk, EB, Lamkey, KR and Woodman, WW (1989) Association of restriction fragment length polymorphism among maize inbreds with agronomic performance of their crosses. Crop Science 29: 10671071.
Lima, MLA, Garcia, AAF, Oliveira, KM, Matsuoka, S, de Arizono, H, de Souza, CL and Souza, AP (2002) Análisis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane ( Saccharum spp.). Theoretical and Applied Genetics 104: 3038.
Lübberstedt, T, Melchinger, AE, DuBle, C, Vuylsteke, M and Kuiper, M (2000) Relationships among early European maize inbreds IV. Genetic diversity revealed with AFLP markers and comparison with RFLP, RAPD, and pedigree data. Crop Science 40: 792797.
Mackill, DJ (1995) Classifying japonica rice cultivars with RAPD markers. Crop Science 35: 889894.
Malécot, G (1948) Les mathématiques de l'hérédité Paris: Masson et Cie.
Melchinger, AE, Lee, M, Lamkey, KR, Hallauer, AR and Woodman, WL (1990) Genetic diversity for restriction fragment length polymorphism and heterosis for two diallel sets of maize inbreds. Theoretical and Applied Genetics 80: 488496.
Mohammadi, SA and Prasanna, BM (2003) Analysis of genetic diversity in crop plants. Salient statistical tools and considerations. Crop Science 43: 12351248.
Mosser, H and Lee, M (1994) RFLP variation and genealogical distance, multivariate distance, heterosis, and genetic variance in oats. Theoretical and Applied Genetics 87: 947956.
Pearson, K (1920) Note on the history of correlation. Biometrika 13: 2545.
Redoña, ED, Moreno, LS, de la Cruz, IA and Ordoñez, SA (2001) Heterosis and parental molecular divergence in rice (abstract). In: Proceedings of the Plant & Animal Genome IX Conference,San Diego, CA
Rohlf, FJ (1997) NTSYS-pc. Numerical Taxonomy and Multivariate Analysis System, version 2.0. New York: Department of Ecology and Evolution, State University of New York.
SAS Institute (1989) SAS/STAT User Guide, version 6.09. Cary, NC: SAS Institute.
Schut, JW, Qi, X and Stam, P (1997) Association between relationship measures based on AFLP markers, pedigree data and morphological trait in barley. Theoretical and Applied Genetics 95: 11611168.
Smith, OS, Smith, JSC, Bowen, SL, Tenborg, RA and Wall, SJ (1990) Similarities among a group of elite maize inbreds as measured by pedigree, F1 grain yield, heterosis, and RFLPs. Theoretical and Applied Genetics 80: 833840.
INGER-IRRI (1996) Standard Evaluation System for Rice, 4th edn Manila, Philippines: INGER-IRRI.
Tabanao, DA, Sebastian, LS and Bernardo, RN (2001) Estimation of coancestry in rice using microsatellite DNA profiles (abstract). In: Proceedings of the Plant & Animal Genome IX Conference,San Diego, CA.
Virk, PS, Ford-Lloyd, BV, Jackson, MT, Pooni, HS, Clemeno, TP and Newbury, J (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76: 296304.
Xiao, J, Li, J, Yuan, L, McCouch, SR and Tanksley, SD (1996) Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theoretical and Applied Genetics 92: 637643.
Zhang, Q, Zhou, ZQ, Xu Yang, GP, Liu, CGKD, Saghai, and, Maroof, MA (1996) Molecular marker heterozygosity and hybrid performance in indica and japonica rice. Theoretical and Applied Genetics 93: 2181224.
Zheng, K, Qian, H, Shen, B, Zhuang, J, Lin, H and Lu, J (1994) RFLP-based phylogenetic analysis of wide compatibility varieties in Oryza sativa L. Theoretical and Applied Genetics 88: 6569.

Keywords

Genetic diversity analysis of rice varieties (Oryza sativa L.) based on morphological, pedigree and DNA polymorphism data

  • Jorge Luis Fuentes (a1), Maria Teresa Cornide (a2), Alba Alvarez (a1), Enrique Suarez (a3) and Ernesto Borges (a3)...

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