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Simple sequence repeat (SSR)-based diversity analysis of groundnut (Arachis hypogaea L.) germplasm resistant to bacterial wilt

Published online by Cambridge University Press:  01 April 2007

E. S. Mace ,
W. Yuejin ,
L. Boshou ,
H. Upadhyaya ,
S. Chandra  and
J. H. Crouch
E. S. Mace*
Affiliation:
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, A.P. 502 324, India
W. Yuejin
Affiliation:
Institute of Crop Germplasm Resource, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, P.R. China
L. Boshou
Affiliation:
Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, Hubei 430062, P.R. China
H. Upadhyaya
Affiliation:
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, A.P. 502 324, India
S. Chandra
Affiliation:
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, A.P. 502 324, India
J. H. Crouch
Affiliation:
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, A.P. 502 324, India
*
*Corresponding author (present address): Hermitage Research Station, 604 Yangan Road, Warwick, Qld 4370, Australia. E-mail: [email protected]
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Abstract

Groundnut is one of the most important oilseed crops in the world. Bacterial wilt, caused by Ralstonia solanacearum E. F. Smith, is one of the major biotic constraints to groundnut production particularly in South-East Asia and East Africa. Several sources of resistance to bacterial wilt have been identified through field screening of groundnut germplasm. The aim of the present study was to quantify the genetic diversity among selected bacterial wilt-resistant lines, in comparison with the levels of variation observable within the cultivated A. hypogaea gene pool. Thirty-two SSR markers were used to assess the degree of molecular polymorphism between 46 selected genotypes revealing 107 alleles, of which 101 (99.4%) were polymorphic with gene diversity scores ranging from 0.103 to 0.669, averaging 0.386. Cluster and multidimensional scaling analysis revealed two distinct groups within the germplasm broadly corresponding to the two subspecies (hypogaea and fastigiata) of A. hypogaea. However, accessions of varieties peruviana and aequatoriana grouped together with the varieties from subsp. hypogaea, rather than grouping with the other varieties of subsp. fastigiata. Analysis of molecular variance (AMOVA) revealed that 15% of the total observed variation was accounted for by disease response groups. This analysis will be useful in the selection of parental genotypes for mapping populations and breeding programmes attempting to broaden the genetic base of future groundnut cultivars. In particular, this opens up significant opportunities for the development of intraspecific mapping populations that will be highly relevant to modern groundnut breeding programmes.

Keywords

bacterial wiltgenetic diversitygroundnutSSRs
Type
Research Article
Information
Plant Genetic Resources , Volume 5 , Issue 1 , April 2007 , pp. 27 - 36
Copyright
Copyright © NIAB 2007

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References

Belaj, A, Satovic, Z, Cipriani, G, Baldoni, L, Testolin, R, Rallo, L and Trujillo, I (2003) Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theoretical and Applied Genetics 107: 736–744.CrossRefGoogle ScholarPubMed
Broun, P and Tanksley, SD (1996) Characterization and genetic mapping of simple repeat sequences in the tomato genome. Molecular and General Genetics 250: 39–49.CrossRefGoogle ScholarPubMed
Buddenhagen, I and Kelman, A (1964) Biological and physiological aspects of bacterial wilt caused by Pseudomonas solanacearum. Annual Review of Phytopathology 2: 203–230.CrossRefGoogle Scholar
Burow, MD, Simpson, CE, Starr, JL and Paterson, AH (2001) Transmission genetics of chromatin from a synthetic amphiploid in cultivated peanut (A. hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 159: 823–837.CrossRefGoogle Scholar
Chen, X, Temnykh, S, Xu, Y, Cho, YG and McCouch, SR (1997) Development of a microsatellite framework map providing genome wide coverage in rice (Oryza sativa L.). Theoretical and Applied Genetics 95: 553–567.CrossRefGoogle Scholar
Dwivedi, SL, Gurtu, S, Chandra, S, Yuejin, W and Nigam, SN (2001) Assessment of genetic diversity among selected groundnut germplasm I: RAPD analysis. Plant Breeding 120: 345–349.CrossRefGoogle Scholar
Dwivedi, SL, Crouch, JH, Nigam, SN, Ferguson, ME and Paterson, AH (2003) Molecular breeding of groundnut for enhanced productivity and food security in the semi-arid tropics: opportunities and challenges. Advances in Agronomy 80: 153–221.CrossRefGoogle Scholar
Excoffier, L, Smouse, PE and Quattro, JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.CrossRefGoogle ScholarPubMed
Fahima, T, Röder, MS, Grama, A and Nevo, E (1998) Microsatellite DNA polymorphism divergence in Triticum dicoccoides accessions highly resistant to yellow rust. Theoretical and Applied Genetics 96: 187–195.CrossRefGoogle Scholar
Ferguson, ME, Bramel, J and Chandra, S (2004a) Gene diversity among botanical varieties in peanut (Arachis hypogaea L.). Crop Science 44: 1847–1854.CrossRefGoogle Scholar
Ferguson, ME, Burow, MD, Schultz, SR, Bramel, PJ, Paterson, AH, Kresovich, S and Mitchell, S (2004b) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theoretical and Applied Genetics 108: 1064–1070.CrossRefGoogle ScholarPubMed
Gianfranceschi, L, Seglias, N, Tarchini, R, Komjanc, M and Gessler, C (1998) Simple sequence repeats for the genetic analysis of apple. Theoretical and Applied Genetics 96: 1069–1076.CrossRefGoogle Scholar
Halward, T, Stalker, HT, Larue, EA and Kochert, G (1991) Genetic variation detectable with molecular markers among unadapted germplasm resources of cultivated peanut and related wild species. Genome 34: 1013–1020.CrossRefGoogle Scholar
Halward, T, Stalker, HT, Larue, EA and Kochert, G (1992) Use of single-primer DNA amplification in genetic studies of peanut (Arachis hypogaea L.). Plant Molecular Biology 18: 315–325.CrossRefGoogle ScholarPubMed
Hayward, AC (1964) Characteristics of Pseudomonas solanacerarum. Journal of Applied Bacteriology 27: 265–277.CrossRefGoogle Scholar
Hayward, AC (1990) Diagnosis, distribution and status of groundnut bacterial wilt. ACIAR Proceedings 31: 12–17.Google Scholar
Hayward, AC (1991) Biology and epidemiology of bacterial wilt caused by Pseudomonas solanacerarum. Annual Review of Phytopathology 29: 65–87.CrossRefGoogle Scholar
He, G and Prakash, C (1997) Identification of polymorphic DNA markers in cultivated peanut (Arachis hypogaea L.). Euphytica 97: 143–149.CrossRefGoogle Scholar
He, G and Prakash, C (2001) Evaluation of genetic relationships among botanical varieties of cultivated peanut (Arachis hypogaea L) using AFLP markers. Genetic Resources and Crop Evolution 48: 347–352.CrossRefGoogle Scholar
He, G, Meng, R, Newman, M, Gao, G, Pittman, RN and Prakash, CS (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biology 3: 3–9.CrossRefGoogle ScholarPubMed
He, G, Meng, R, Gao, H, Guo, B, Gao, G, Newman, M, Pittman, RN and Prakash, CS (2005) Simple sequence repeat markers for botanical varieties of cultivated peanut (Arachis hypogaea L.). Euphytica 142: 131–136.CrossRefGoogle Scholar
He, LY, Sequeria, L and Kelman, A (1983) Characteristics of strains of Pseudomonas solanacearum from China. Plant Diseases 67: 1357–1361.CrossRefGoogle Scholar
Hopkins, MS, Casa, AM, Wang, T, Mitchell, SE, Dean, RE, Kochert, GD and Kresovich, S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Science 39: 1243–1247.CrossRefGoogle Scholar
Jaccard, P (1908) Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 44: 223–270.Google Scholar
Kochert, G, Halward, T, Branch, WD and Simpson, CE (1991) RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theoretical and Applied Genetics 81: 565–570.CrossRefGoogle ScholarPubMed
Kolodny, GM (1984) An improved method for increasing the resolution and sensitivity of silver staining of nucleic acid bands in polyacrylamide gels. Analytical Biochemistry 138: 66–67.CrossRefGoogle ScholarPubMed
Krapovickas, A and Gregory, WC (1994) Taxonomia del genero Arachis (Leguminosae). Bonplandia 8: 1–186.CrossRefGoogle Scholar
Kruskal, JB and Wish, M (1978) Multidimensional Scaling. Newbury Park, CA: Sage.CrossRefGoogle Scholar
Künzel, G and Waugh, R (2002) Integration of microsatellite markers into the translocation-based physical RFLP map of barley chromosome 3H. Theoretical and Applied Genetics 105: 660–665.CrossRefGoogle ScholarPubMed
Liang, XQ (1998) Present status of groundnut bacterial wilt in south China. In: Pande, S, Liao, BS, Hong, NX, Johansen, C and Gowda, CLL (eds) Groundnut Bacterial Wilt in Asia. Proceedings of the Fourth Working Group Meeting. 11–13 May 1998. Hanoi, Vietnam: Vietnam Agricultural Science Institute, pp. 23–26.Google Scholar
Liao, B, Duan, N, Jiang, H, Liang, X and Gao, G (1998) Germplasm screening and breeding for resistance to bacterial wilt in China. In: Pande, S, Liao, BS, Hong, NX, Johansen, C and Gowda, CLL (eds) Groundnut Bacterial Wilt in Asia. Proceedings of the Fourth Working Group Meeting. 11–13 May 1998. Hanoi, Vietnam: Vietnam Agricultural Science Institute, pp. 75–81.Google Scholar
Mace, ES, Buhariwalla, HK and Crouch, JH (2003) A high throughput DNA extraction protocol for tropical molecular breeding programs. Plant Molecular Biology Reporter 21: 459a–459h.CrossRefGoogle Scholar
Mohan, M, Nair, S, Bhagwat, A, Krishna, TG, Yano, M, Bhatia, CR and Sasaki, T (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding 3: 87–103.CrossRefGoogle Scholar
Moretzsohn, MC, Hopkins, MS, Mitchell, SE, Kresovich, S, Valls, JFM and Ferreira, ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biology 4: 11.CrossRefGoogle ScholarPubMed
Moretzsohn, MC, Leoi, L, Proite, K, Guimãres, PM, Leal-Bertioli, SCM, Gimenes, MA, Martins, WS, Valls, JFM, Grattapaglia, D and Bertoli, DJ (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theoretical and Applied Genetics 111: 1060–1071.CrossRefGoogle ScholarPubMed
Nei, M and Li, WH (1979) Mathematical model for studying genetic variation in terms of restriction end nucleases. Proceedings of the National Academy of Sciences USA 76: 5269–5273.CrossRefGoogle Scholar
Paik-Rao, OG, Smith, RL and Knauft, DA (1992) Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theoretical and Applied Genetics 84: 201–208.CrossRefGoogle Scholar
Pande, S; Liao, BS; Hong, NX; Johansen, C; Gowda, CLL, (eds) (1998) Groundnut Bacterial Wilt in Asia. Proceedings of the Fourth Working Group Meeting. 11–13 May 1998. Hanoi, Vietnam: Vietnam Agricultural Science Institute.Google Scholar
Raina, SN, Kojima, T, Ogihara, Y, Singh, KP and Devarumath, RM (2001) RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome 44: 763–772.CrossRefGoogle ScholarPubMed
Röder, MS, Korzun, V, Wendehake, K, Plaschke, J, Tixier, M-H, Leroy, P and Ganal, MW (1998) A microsatellite map of wheat. Genetics 149: 2007–2023.CrossRefGoogle ScholarPubMed
Rohlf, FJ (2001) Numerical Taxonomy and Multivariate Analysis System. New York: Applied Biostatistics.Google Scholar
Schneider, S, Roessli, D and Excoffier, L (2000) Arlequin: A Software for Population Genetics Data Analysis. version 2.000. Geneva: Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva.Google Scholar
Simpson, CE (1991) Pathways for introgression of pest resistance into Arachis hypogaea L. Peanut Science 18: 22–26.CrossRefGoogle Scholar
Simpson, CE, Nelson, SC, Starr, JL, Woodard, KE and Smith, OD (1993) Registration of TxAG-6 and TxAG-7 peanut germplasm lines. Crop Science 33: 1418.CrossRefGoogle Scholar
Singh, AK, Mehan, VK and Nigam, SN (1997) Sources of Resistance to Groundnut Fungal and Bacterial Diseases, an Update and Appraisal. ICRISAT Bulletin No. 50. Patancheru, India: ICRISAT.Google Scholar
Singh, AK, Smartt, J, Simpson, CE and Raina, SN (1998) Genetic variation vis-à-vis molecular polymorphism in groundnut, Arachis hypogaea L. Genetic Resources and Crop Evolution 45: 119–126.CrossRefGoogle Scholar
Smartt, J and Simmonds, NW (1995) Evolution of Crop Plants. Harlow: Longman Scientific and Technical.Google Scholar
Sokal, RR and Michener, CD (1958) A statistical method for evaluating systematic relationships. University of Kansas Scientific Bulletin 38: 1409–1438.Google Scholar
Subramanian, V, Gurtu, S, Nageswara Rao, RC and Nigam, SN (2000) Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome 43: 656–660.CrossRefGoogle ScholarPubMed
Tallury, SP, Hilu, KW, Milla, SR, Friend, SA, Alsaghir, M, Stalker, HT and Quandt, D (2005) Genomic affinities in Arachis section Arachis (Fabaceae): molecular and cytogenetic evidence. Theoretical and Applied Genetics 111: 1229–1237.CrossRefGoogle ScholarPubMed
Upadhyaya, HD, Ferguson, ME and Bramel, PJ (2001) Status of the Arachis germplasm collection at ICRISAT. Peanut Science 28: 89–96.CrossRefGoogle Scholar
Upadhyaya, HD, Ortiz, R, Bramel, PJ and Singh, S (2003) Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genetic Resources and Crop Evolution 50: 139–148.CrossRefGoogle Scholar
Weir, BS (1990) Genetic Data Analysis. Methods for Discrete Genetic Data. Sunderland, MA: Sinauer Associates.Google Scholar
Zhebentyayaeva, TN, Reighard, GL, Gorina, V and Abbott, AG (2003) Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm. Theoretical and Applied Genetics 106: 435–444.CrossRefGoogle Scholar