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Nuclear and cytoplasmic microsatellite markers for the species of the Dilatata group of Paspalum (Poaceae)

Published online by Cambridge University Press:  01 April 2007

Pablo Speranza  and
Marcos Malosetti
Pablo Speranza*
Affiliation:
Facultad de Agronomía, Universidad de la República, Av. E. Garzón 780, Montevideo, 12900, Uruguay
Marcos Malosetti
Affiliation:
Facultad de Agronomía, Universidad de la República, Av. E. Garzón 780, Montevideo, 12900, Uruguay Laboratory of Plant Breeding, Wageningen University, PO Box 386, 6700AJ Wageningen, The Netherlands
*
*Corresponding author. E-mail: [email protected]
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Abstract

The Dilatata group of Paspalum is a polyploid complex native to the grasslands of temperate South America. A pentaploid apomictic biotype of P. dilatatum is a widely recognized forage grass; however, the complex includes apomictic tetra- and hexaploids along with sexual allotetraploids (P. urvillei, P. dasypleurum, P. dilatatum ssp. flavescens, and biotypes Virasoro and Vacaria of P. dilatatum) which are suspected to be hybrids between different combinations of biotypes. Fifteen primer pairs for nuclear microsatellite loci were developed from a (CA)n-enriched genomic library. A single, low stutter, robust two-step PCR profile was used for all the primer pairs. Twelve primer pairs were analysed for their variability and transferability among all the sexual biotypes of the Dilatata group and the common apomictic pentaploid. Six primer pairs amplified more than one locus, and sequence and segregation evidence suggest that the additional bands correspond to homeologous loci. No close linkage was found among the 16 loci amplified in the tetraploids. One variable chloroplast microsatellite is also reported. All loci were successfully amplified from most members of the Dilatata group and variability was recorded for all the biotypes analysed. The set of loci reported here provide highly variable markers for intra-biotypic population studies, biotype-specific markers for the analysis of hybrid apomicts and a biotype-specific chloroplast marker.

Keywords

apomixischloroplast microsatellitesmicrosatellites (SSR)Paspalum dilatatumPaspalum urvilleipolyploidy
Type
Research Article
Information
Plant Genetic Resources , Volume 5 , Issue 1 , April 2007 , pp. 14 - 26
Copyright
Copyright © NIAB 2007

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References

Amos, W, Sawcer, SJ, Feakes, RW and Rubinsztein, DC (1996) Microsatellites show mutational bias and heterozygote instability. Nature Genetics 13: 390–391.CrossRefGoogle ScholarPubMed
Bashaw, EC and Forbes, I Jr (1958) Chromosome numbers and microsporogenesis in Dallisgrass Paspalum dilatatum Poir. Agronomy Journal 50: 441–445.CrossRefGoogle Scholar
Bashaw, EC and Holt, EC (1958) Megasporogenesis, embryo sac development and embryogenesis in Dallisgrass, Paspalum dilatatum Poir. Agronomy Journal 50: 753–756.CrossRefGoogle Scholar
Boutin-Garnache, I, Raposo, M, Raymond, M and Deschepper, CF (2001) M13-Tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques 31: 24–26.Google Scholar
Burson, BL (1979) Cytogenetics of Paspalum urvillei × P. intermedium and P. dilatatum × P. paniculatum hybrids. Crop Science 19: 534–538.CrossRefGoogle Scholar
Burson, BL (1983) Phylogenetic investigations of Paspalum dilatatum and related species. In: Proceedings of the XIV International Grasslands Congress. Boulder, CO: Westview Press, pp. 170–173.Google Scholar
Burson, BL (1991a) Genome relationships between tetraploid and hexaploid biotypes of dallisgrass, Paspalum dilatatum. Botanical Gazzette 152: 219–223.CrossRefGoogle Scholar
Burson, BL (1991b) Homology of chromosomes of the X genomes in common Uruguayan dallisgrass, Paspalum dilatatum. Genome 34: 950–953.CrossRefGoogle Scholar
Burson, BL (1992) Cytology and reproductive behavior of hybrids between Paspalum urvillei and two hexaploid P. dilatatum biotypes. Genome 35: 1002–1006.CrossRefGoogle Scholar
Burson, BL, Lee, H and Bennett, EC (1973) Genome relations between tetraploid Paspalum dilatatum and four diploid Paspalum species. Crop Science 13: 139–143.CrossRefGoogle Scholar
Caponio, I and Quarín, CL (1990) Intra- and interspecific hybridization between dallisgrass and vaseygrass. Crop Science 30: 362–364.CrossRefGoogle Scholar
Casa, AM, Mitchel, SE, Lopes, CR and Valls, JFM (2002) RAPD analysis reveals genetic variability among sexual and apomictic Paspalum dilatatum Poiret biotypes. Journal of Heredity 93: 300–302.CrossRefGoogle ScholarPubMed
Chen, X, Cho, YG and McCouch, SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Molecular Genetics and Genomics 268: 331–343.CrossRefGoogle ScholarPubMed
Ellegren, H, Primmer, CR and Sheldon, BC (1995) Microsatellite ‘evolution’: directionality or bias? Nature Genetics 11: 360–362.CrossRefGoogle ScholarPubMed
Elsik, CG and Williams, CG (2001) Families of clustered microsatellites in a conifer genome. Molecular Genetics and Genomics 265: 535–542.CrossRefGoogle Scholar
Ernst, JA, Branch, C, Clarck, AM and Hokit, DG (2004) Polymorphic microsatellite markers for the Florida scrub lizard (Sceloporus woodi). Molecular Ecology Notes 4: 364–365.CrossRefGoogle Scholar
Fischer, D and Bachmann, K (1998) Microsatellite enrichment in organisms with large genomes (Allium cepa L.). Biotechniques 24: 796–802.CrossRefGoogle ScholarPubMed
Hazen, SP, Leroy, P and Ward, RW (2002) AFLP in Triticum aestivum L.: patterns of genetic diversity and genome distribution. Euphytica 125: 89–102.CrossRefGoogle Scholar
Hickenbick, MCM, Flores, AIP, Cavalli-Molina, S, Weber, LH, Kersting, ACO, Costa, LS, Souza-Chies, TT and Albarus, MH (1992) Mode of reproduction and seed production in Paspalum dilatatum Poir. Virasoro biotype-Dilatata group (Gramineae). Revista Brasileira de Genética 15: 85–102.Google Scholar
Hite, JM, Eckert, KA and Cheng, KC (1996) Factors affecting fidelity of DNA synthesis during PCR amplification of d(C-A)n. D(G-T)n microsatellite repeats. Nucleic Acids Research 24: 2429–2434.CrossRefGoogle Scholar
Ishii, T and McCouch, SR (2000) Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theoretical and Applied Genetics 100: 1257–1266.CrossRefGoogle Scholar
Jakše, J and Javornik, B (2001) High throughput isolation of microsatellites in hop (Humulus lupulus L.). Plant Molecular Biology Reports 19: 217–226.CrossRefGoogle Scholar
Kandpal, RP, Kandpal, G and Weissman, SM (1994) Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. Proceedings of the National Academy of Sciences of the USA 91: 88–92.CrossRefGoogle ScholarPubMed
Kijas, JMH, Fowler, JCS, Garbett, CA and Thomas, MR (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16: 657–660.Google ScholarPubMed
Kim, HS and Ward, RW (2000) Patterns of RFLP-based genetic diversity in germplasm pools of common wheat with different geographical or breeding program origins. Euphytica 115: 197–208.CrossRefGoogle Scholar
Machado, ACC, Valls, JFM, Peñaloza, APS and dos Santos, S (2005) Novos biótipos pentaplóides do grupo Dilatata de Paspalum L. (Gramineae) no Sul do Brasil 1. Ciência Rural 35: 56–61.CrossRefGoogle Scholar
Moraes Fernandes, MIB, Barreto, IL and Salzano, FM (1968) Cytogenetic, ecologic and morphologic studies in Brazilian forms of Paspalum dilatatum. Canadian Journal of Genetics and Cytology 10: 131–138.CrossRefGoogle Scholar
Pereira, J, Sabbia, V, Fajardo, A and Speranza, PR (2000) Análisis genéticos en gramíneas nativas del género Paspalum a partir de datos isoenzimáticos y RAPD. Agrociencia 4(1): 1–11.CrossRefGoogle Scholar
Provan, J, Biss, PM, McMeel, D and Mathews, S (2004) Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Molecular Ecology Notes 4: 262–264.CrossRefGoogle Scholar
Quarín, CL and Caponio, I (1995) Cytogenetics and reproduction on P. dasypleurum and its hybrids with P. urvillei and P. dilatatum ssp. flavescens. International Journal of Plant Sciences 156: 232–235.CrossRefGoogle Scholar
Röder, MS, Plaschke, J, König, S, Börner, A, Sorrells, ME, Tanksley, SD and Ganal, MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics 246: 327–333.CrossRefGoogle ScholarPubMed
Rozen, S and Skaletsky, HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz, S and Misener, S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 365–386.Google Scholar
Schlöterer, C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109: 365–371.CrossRefGoogle Scholar
Schmidt, T and Heslop-Harrison, JS (1996) The physical and genomic organization of microsatellites in sugar beet. Proceedings of the National Academy of Sciences of the USA 93: 8761–8765.CrossRefGoogle ScholarPubMed
Sourdille, P, Tavaud, M, Charmet, G and Bernard, M (2001) Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes. Theoretical and Applied Genetics 103: 346–352.CrossRefGoogle Scholar
Speranza, P, Vaio, M and Mazzella, C (2003) Karyotypes of two cytotypes of Paspalum quadrifarium Lam. (Poaceae). An alternative technique for small chromosomes in plants. Genetics and Molecular Biology 26: 499–503.CrossRefGoogle Scholar
Symonds, VV and Lloyd, AM (2003) An analysis of microsatellite loci in Arabidopsis thaliana: mutational dynamics and application. Genetics 165: 1475–1488.CrossRefGoogle ScholarPubMed
Taberlet, P, Gelly, L, Pavtou, G and Bouvet, J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105–1109.CrossRefGoogle ScholarPubMed
Temnykh, S, Park, WD, Ayres, N, Cartinhour, S, Hauck, N, Lopovich, L, Cho, YG, Ishii, T and McCouch, SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics 100: 697–712.CrossRefGoogle Scholar
Temnykh, S, DeClerck, G, Lukashova, A, Lipovich, L, Cartinhour, S and McCouch, S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research 11: 1441–1452.CrossRefGoogle ScholarPubMed
Vaio, M, Speranza, P, Valls, JF, Guerra, M and Mazzella, C (2005) Localization of the 5S and 45S rDNA sites and cpDNA sequence analysis in species of the Quadrifaria group of Paspalum (Poaceae, Paniceae). Annals of Botany 96: 191–200.CrossRefGoogle ScholarPubMed
Valls, JFM and Pozzobon, M (1987) Variacão apresentada pelos principais grupos taxonômicos de Paspalum com interesse forrageiro no Brasil. Encontro Internacional sobre Melhoramiento Genético de Paspalum. Anais. Nova Odessa, SP, Brazil: Instituto de Zootecnia, pp. 15–21.Google Scholar
Van Ooijen, JW and Voorrips, RE (2001) JoinMap® Version 3.0: Software for the Calculation of Genetic Linkage Maps. Wageningen: Plant Research International.Google Scholar
Vigouroux, Y, Jaqueth, JS, Matsuoka, Y, Smith, OS, Beavis, WD, Smith, JSC and Doebley, J (2002) Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution 19: 1251–1260.CrossRefGoogle ScholarPubMed
Weber, JL (1990) Informativeness of human (dC-dA)n·(dG-dT)n polymorphisms. Genomics 7: 524–530.CrossRefGoogle ScholarPubMed