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

Published online by Cambridge University Press:  12 February 2007

Jorge Luis Fuentes ,
Maria Teresa Cornide ,
Alba Alvarez ,
Enrique Suarez  and
Ernesto Borges
Jorge Luis Fuentes*
Affiliation:
Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear (CEADEN), Apartado Postal 6122, calle 30, #502. e/ 5ta y 7ma, Miramar, Playa, C. Habana, Cuba
Maria Teresa Cornide
Affiliation:
Instituto de Investigaciones de la Caña de Azúcar (INICA), Carretera CAI Martínez Prieto, Marianao, Ciudad de la Habana, Cuba
Alba Alvarez
Affiliation:
Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear (CEADEN), Apartado Postal 6122, calle 30, #502. e/ 5ta y 7ma, Miramar, Playa, C. Habana, Cuba
Enrique Suarez
Affiliation:
Instituto de Investigaciones del Arroz (IIA), Bauta, La Habana, Cuba
Ernesto Borges
Affiliation:
Instituto de Investigaciones del Arroz (IIA), Bauta, La Habana, Cuba
*
*Corresponding author: E-mail: fuentes@ceaden.edu.cu
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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.

Keywords

AFLPgenealogyphenotypic descriptorsRAPD
Type
Research Article
Information
Plant Genetic Resources , Volume 3 , Issue 3 , December 2005 , pp. 353 - 359
Copyright
Copyright © NIAB 2005

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References

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: 77–86.CrossRefGoogle Scholar
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) 45–50.Google Scholar
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: 735–742.CrossRefGoogle Scholar
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: 1142–1149.CrossRefGoogle ScholarPubMed
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: 1348–1355.Google Scholar
Bernardo, R (1994) Prediction of maize single-cross performance using RFLPs and information from related hybrids. Crop Science 34: 20–25.CrossRefGoogle Scholar
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: 552–556.Google Scholar
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: 268–275.CrossRefGoogle Scholar
Cao, D and Oard, JH (1997) Pedigree RAPD analysis of commercial U.S. rice cultivars. Crop Science 37: 1630–1635.CrossRefGoogle Scholar
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: 63–68.Google Scholar
Dice, LR (1945) Measures of the amount of ecologic association between species. Ecology 26: 297–302.CrossRefGoogle Scholar
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: 381–388.CrossRefGoogle Scholar
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: 359–369.CrossRefGoogle Scholar
Emik, LO and Terrill, CE (1949) Systematic procedures for calculating inbreeding coefficients. Journal of Heredity 40: 51–55.CrossRefGoogle ScholarPubMed
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.Google Scholar
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: 530–536.CrossRefGoogle ScholarPubMed
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: 107–115.CrossRefGoogle Scholar
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: 1841–1847.CrossRefGoogle Scholar
Jaccard, A (1974) The Genetic Structure of Populations New York Springer-Verlag translated by D.B. Charles WorthGoogle Scholar
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: 1067–1071.CrossRefGoogle Scholar
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: 30–38.CrossRefGoogle Scholar
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: 792–797.CrossRefGoogle Scholar
Mackill, DJ (1995) Classifying japonica rice cultivars with RAPD markers. Crop Science 35: 889–894.CrossRefGoogle Scholar
Malécot, G (1948) Les mathématiques de l'hérédité Paris: Masson et Cie.Google Scholar
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: 488–496.CrossRefGoogle Scholar
Mohammadi, SA and Prasanna, BM (2003) Analysis of genetic diversity in crop plants. Salient statistical tools and considerations. Crop Science 43: 1235–1248.CrossRefGoogle Scholar
Mosser, H and Lee, M (1994) RFLP variation and genealogical distance, multivariate distance, heterosis, and genetic variance in oats. Theoretical and Applied Genetics 87: 947–956.CrossRefGoogle Scholar
Pearson, K (1920) Note on the history of correlation. Biometrika 13: 25–45.CrossRefGoogle Scholar
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, CAGoogle Scholar
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.Google Scholar
SAS Institute (1989) SAS/STAT User Guide, version 6.09. Cary, NC: SAS Institute.Google Scholar
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: 1161–1168.CrossRefGoogle Scholar
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: 833–840.CrossRefGoogle ScholarPubMed
INGER-IRRI (1996) Standard Evaluation System for Rice, 4th edn Manila, Philippines: INGER-IRRI.Google Scholar
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.Google Scholar
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: 296–304.CrossRefGoogle Scholar
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: 637–643.CrossRefGoogle Scholar
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: 218–1224.CrossRefGoogle ScholarPubMed
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: 65–69.CrossRefGoogle ScholarPubMed