Drosophila Mediopunctata Microsatellites I: More Than A Hundred Polymorphic Loci Available For Genetic Studies

We describe the first 134 polymorphic microsatellites loci developed for the fly Drosophila mediopunctata. A genomic DNA library double-enriched for dinucleotides was constructed and approximately 600 unambiguous microsatellites were identified. The DNA library consisted of 60% positive clones, short-sized dinucleotides (mean = 8.7 repeats) and 73% of AC/GT combinations. A total of 177 primer pairs were designed and thirteen strains were used to achieve optimal PCR amplification conditions and allelic variability of the isolated loci. The average number of alleles per locus was 4.6 and means of observed and expected heterozygosities were 0.23 and 0.62, respectively. The discriminating power average was 0.72. These new developed markers will be applied in the study of natural population dynamics and for the construction of a molecular linkage map for the species. © Springer Science+Business Media B.V. 2009.11297307Ananina, G., Peixoto, A.A., Souza, W.N., da Silva, L.B., Klaczko, L.B., Polytene chromosome map and inversion polymorphism in Drosophila mediopunctata (2002) Mem Inst Oswaldo Cruz, 97, pp. 691-694Ananina, G., Peixoto, A.A., Bitner-Mathé, B.C., Souza, W.N., da Silva, L.B., Valente, V.L.S., Klaczko, L.B., Chromosomal inversion polymorphism in Drosophila mediopunctata: Seasonal, altitudinal, and latitudinal variation (2004) Genet Mol Biol, 27, pp. 61-69Andrade, C.A.C., Hatadani, L.M., Klaczko, L.B., Phenotypic plasticity of the aedeagus of Drosophila mediopunctata: Effect of the temperature (2005) J Therm Biol, 30, pp. 518-523Andrade, C.A.C., Vieira, R.D., Ananina, G., Klaczko, L.B., Evolution of the male genitalia: Morphological variation of the aedeagi in a natural population of Drosophila mediopunctata (2009) Genetica, 135, pp. 13-23Azeredo-Espin, A.M.L., Schroder, R.F.W., Huettel, M.D., Sheppard, W.S., Mitochondiral-DNA variation in geographic populations of Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera, Chrisomelidae) (1991) Experientia, 47, pp. 483-485Billotte, N., Lagoda, P.J.L., Risterucci, A.-M., Baurens, F.-C., Microsatellite- enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Bitner-Mathé, B.C., Peixoto, A.A., Klaczko, L.B., Morphological variation in a natural population of Drosophila mediopunctata: Altitudinal cline, temporal changes and influence of chromosome inversions (1995) Heredity, 75, pp. 54-61Carvalho, A.B., Klaczko, L.B., Autosomal suppressors of sex-ratio in Drosophila mediopunctata (1993) Heredity, 71, pp. 546-551Carvalho, A.B., Peixoto, A.A., Klaczko, L.B., Sex-ratio in Drosophila mediopunctata (1989) Heredity, 62, pp. 425-428Creste, S., Tulmann Neto, A., Figueira, A., Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining (2001) Plant Mol Biol Rep, 19, pp. 299-306Dobzhansky, T., Pavan, C., (1943) Studies on Brazilian Species of Drosophila, , Bol Facul Fil Cien Let Univ S Paulo n36 Biologia Geral n4Hatadani, L.M., Klaczko, L.B., Shape and size variation on the wing of Drosophila mediopunctata: Influence of chromosome inversions and genotype-environment interaction (2008) Genetica, 133, pp. 335-342Ihaka, R., Gentleman, R., R: A language for data analysis and graphics (1996) J Comput Graph Stat, 5, pp. 299-314Katti, M.V., Rankejar, P.K., Gupta, V.S., Differential distribution of simple sequence repeats of eukaryotic genome sequences (2001) Mol Biol Evol, 18, pp. 1161-1167Miller, M.P., (1997) Tools for Population Genetic Analyses (TFPGA) 1.3: A Windows Program for the Analysis of Allozyme and Molecular Population Genetic DataNei, M., Estimation of average heterozygosity and genetic distance from a small number of individuals (1978) Genetics, 89, pp. 583-590Raymond, M., Rousset, F., GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism (1995) J Hered, 86, pp. 248-249Rocha, F., Medeiros, H.F., Klaczko, L.B., The reaction norm for abdominal pigmentation and its curve in Drosophila mediopunctata depend on the mean phenotypic value (2008) Evolution, 63, pp. 280-287Rozen, S., Skaletsky, H.J., Primer3 on the WWW for general users and for biologist programmers (2000) Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365-386. , In: Krawetz S, Misener S (eds), Humana Press, TotowaSchug, M.D., Wtterstrand, K.A., Gaudette, M.S., Lim, R.H., Hutter, C.M., Aquadro, C.F., The distribution and frequency of microsatellite loci in Drosophila melanogaster (1998) Mol Ecol, 7, pp. 57-70Temnykh, S., Declerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., McCouch, S., Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential (2001) Genome Res, 11, pp. 1441-1452Tessier, C., David, J., This, P., Boursiquot, J.M., Charrier, A., Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L (1999) Theor Appl Genet, 98, pp. 171-177Tóth, G., Gáspari, Z., Jurka, J., Microsatellites in different eukaryotic genomes: Survey and analysis (2000) Genome Res, 10, pp. 967-981Vilela, C.R., On the Drosophila tripunctata species group (Diptera, Drosophilidae) (1992) Rev Bras Entomol, 36, pp. 197-22

A Molecular Linkage Map For Drosophila Mediopunctata Confirms Synteny With Drosophila Melanogaster And Suggests A Region That Controls The Variation In The Number Of Abdominal Spots

The classic approach to gene discovery relies on the construction of linkage maps. We report the first molecular-based linkage map for Drosophila mediopunctata, a neotropical species of the tripunctata group. Eight hundred F2 individuals were genotyped at 49 microsatellite loci, resulting in a map that is ≈450 centimorgans long. Five linkage groups were detected, and the species' chromosomes were identified through cross-references to BLASTn searches and Müller elements. Strong synteny was observed when compared with the Drosophila melanogaster chromosome arms, but little conservation in the gene order was seen. The incorporation of morphological data corresponding to the number of central abdominal spots on the map was consistent with the expected location of a genomic region responsible for the phenotype on the second chromosome. © 2011 The Royal Entomological Society.2118995Aljanabi, S.M., Martinez, I., Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques (1997) Nucleic Acids Research, 25 (22), pp. 4692-4693Ananina, G., Peixoto, A.A., Souza, W.N., Klaczko, L.B., Polytene chromosome map and inversion polymorphism in Drosophila mediopunctata (2002) Memorias do Instituto Oswaldo Cruz, 97 (5), pp. 691-694Bhutkar, A., Schaeffer, S.W., Russo, S.M., Xu, M., Smith, T.F., Gelbart, W.M., Chromosome rearrangement inferred from comparisons of 12 Drosophila genomes (2008) Genetics, 179, pp. 1657-1680Dobzhansky, T., Pavan, C., Studies on Brazilian species of Drosophila (1943) Bol Facul Fil Cien Let Univ S Paulo n36 Biologia Geral n4Feldmeyer, B., Pen, I., Beukeboom, L.W., A microsatellite marker linkage map of the housefly, Musca domestica: Evidence for male recombination (2010) Insect Mol Biol, 19, pp. 575-581Ferreira, A., Da Silva, M.F., Silva, L.C., Cruz, C.D., Estimating the effects of population size and type on the accuracy of genetic maps (2006) Genet Mol Biol, 29, pp. 187-192Frota-Pessoa, O., Revision of the tripunctata group of Drosophila with description of fifteen new species (Drosophilidae, Diptera) (1954) Arquivo Do Museu Paranaense, 10, pp. 253-304Hatadani, L.M., Baptista, J.C.R., Souza, W.N., Klaczko, L.B., Colour polymorphism in Drosophila mediopunctata: Genetic (chromosomal) analysis and nonrandom association with chromosome inversions (2004) Heredity, 93 (6), pp. 525-534. , DOI 10.1038/sj.hdy.6800544Huttunen, S., Aspi, J., Hoikkala, A., Schlotterer, C., QTL analysis of variation in male courtship song characters in Drosophila virilis (2004) Heredity, 92 (3), pp. 263-269. , DOI 10.1038/sj.hdy.6800406Kastritsis, C.D., (1966) Cytological Studies of Some Species of the Tripunctata Group of Drosophila, pp. 413-474. , Univ Texas Publs, TexasKlaczko, L.B., Evolutionary Genetics of Drosophila mediopunctata (2006) Genetica, 126, pp. 43-55Kosambi, D.D., The estimation of map distances from recombination values (1944) Ann Eugen, 12, pp. 172-175Laborda, P.R., Mori, G.M., Souza, A.P., Drosophila mediopunctata microsatellites I: More than a hundred polymorphic loci available for genetic studies (2009) Conserv Genet Resour, 1, pp. 297-307Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., MAPMAKER: An interactive computing package for constructing primary genetic linkages of experimental and natural populations (1987) Genomics, 1, pp. 174-181MacDonald, S.J., Goldstein, D.B., A quantitative genetic analysis of male sexual traits distinguishing the sibling species Drosophila simulans and D. sechellia (1999) Genetics, 153, pp. 1683-1699Margarido, G.R.A., Souza, A.P., Garcia, A.A.F., OneMap: Software for genetic mapping in outcrossing species (2007) Hereditas, 144 (3), pp. 78-79. , DOI 10.1111/j.2007.0018-0661.02000.xMollinari, M., Margarido, G.R., Vencovsky, R., Garcia, A.A.F., Evaluation of algorithms used to order markers on genetic maps (2009) Heredity, 103, pp. 494-502Müller, H.J., Bearings of the 'Drosophila' work on systematics (1940) The New Systematics, pp. 185-268. , (Huxley, J. ed.), Clarendon Press, OxfordPeixoto, A.A., Klaczko, L.B., Linkage disequilibrium analysis of chromosomal inversion polymorphisms of Drosophila (1991) Genetics, 129, pp. 773-777Pool, J.E., Aquadro, C.F., The genetic basis of adaptive pigmentation variation in Drosophila melanogaster (2007) Molecular Ecology, 16 (14), pp. 2844-2851. , DOI 10.1111/j.1365-294X.2007.03324.xSchäfer, M.A., Mazzi, D., Klappert, K., Kauranen, H., Vieira, J., Hoikkala, A., A microsatellite linkage map for Drosophila montana shows large variation in recombination rates, and a courtship song trait maps to an area of low recombination (2010) J Evol Biol, 23, pp. 518-527Staten, R., Schully, S.D., Noor, M.A.F., A microsatellite linkage map of Drosophila mojavensis (2004) BMC Genet, 5, pp. 12-19Stratikopoulos, E.E., Augustinos, A.A., Petalas, Y.G., Vrahatis, M.N., Mintzas, A., Mathiopoulos, K.D., Zacharopoulou, A., An integrated genetic and cytogenetic map for the Mediterranean fruit fly, Ceratitis capitata, based on microsatellite and morphological markers (2008) Genetica, 133 (2), pp. 147-157. , DOI 10.1007/s10709-007-9195-9Sturtevant, A.H., Novitski, E., The homologies of the chromosome elements in the genus Drosophila (1941) Genetics, 26, pp. 517-541True, J.R., Insect melanism: The molecules matter (2003) Trends in Ecology and Evolution, 18 (12), pp. 640-647. , DOI 10.1016/j.tree.2003.09.006Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., FlyBase: Enhancing Drosophila Gene Ontology annotations (2009) Nucleic Acids Res, 37, pp. D555-D559. , The FlyBase ConsortiumVoorrips, R.E., Mapchart: Software for the graphical presentation of linkage maps and QTLs (2002) Journal of Heredity, 93 (1), pp. 77-78Wittkopp, P.J., Carroll, S.B., Kopp, A., Evolution in black and white: Genetic control of pigment patterns in Drosophila (2003) Trends in Genetics, 19 (9), pp. 495-504. , DOI 10.1016/S0168-9525(03)00194-XWondji, C.S., Hunt, R.H., Pignatelli, P., Steen, K., Coetzee, M., Besansky, N., An integrated genetic and physical map for the malaria vector Anopheles funestus (2005) Genetics, 171, pp. 1779-178

Isolation And Characterization Of Microsatellite Markers In Acca Sellowiana (berg) Burret

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding.8614171419Billotte, N., Lagoda, P.J.L., Risterucci, A.M., Baurens, F.C., Microsatellite enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Creste, S., Tulmann-Neto, A., Figueira, A., Detection of single sequence repeat polymorphism in denaturing polyacrylamide sequencing gels by silver staining (2001) Plant Molecular Biology Reporter, 19, pp. 1-8Doyle, J.J., Doyle, J.L., Isolation of plant DNA from fresh tissue (1990) Focus, 12, pp. 13-15Lewis, P.O., Zaykin, D., (2001) Free Program Distributed by the Authors over the Internet, , http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php, Available from URLMattos, J.R., (1990) Goiabeira Serrana Fruteiras Nativas Do Brasil., , 2nd edn. Gráfica Ceue, Porto Alegre, BrazilMellersch, C., Sampson, J., Simplifying detection of microsatellite length polymorphisms (1993) BioTechniques, 15, pp. 582-584Nei, M., Estimation of average heterozigosity and genetic distance from a small number of individuals (1978) Genetics, 89, pp. 583-590Van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M., Shipley, P., Micro-checker: Software for identifying and correcting genotyping errors in microsatellite data (2004) Molecular Ecology Notes, 4, pp. 535-538Rozen, S., Skaletsky, H.J., Primer 3 on the WWW for general users and for biologist programmers (2000) Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365-386. , In: eds. Krawetz, S., Misener, S. pp. Humana Press, Totowa, New JerseySambrook, J., Fritsch, E.F., Maniatis, T., (1989) Molecular Cloning: A Laboratory Manual. 2nd Edn., , Cold Spring Harbor Laboratory Press, New YorkSantos, K.L., Welter, L.J., Dantas, A.C.M., Transference of microsatellite markers from Eucalyptus spp. to Acca Sellowiana and the successful use of this technique in genetic characterization (2007) Genetics and Molecular Biology, 30, pp. 73-79Thorp, G., Bieleski, R., (2002) Feijoas: Origins, Cultivation and Uses., , David Bateman and HortResearch, Palmerston North, New Zealan

Combining Ability, Genetic Divergence Among Maize Lines And Correlation With Heterosis [capacidade Combinatória, Divergência Genética Entre Linhagens De Milho E Correlação Com Heterose]

The objectives of this research were to evaluate single cross hybrids of maize (Zea mays L.) obtained from partial diallel crosses among contrasting inbred lines, to estimate the combining ability of the lines and to verify whether the genetic diversity among those lines assessed by moleculars markers is correlated with single cross hybrid heterosis Thirty-six single-crosses resulting from partial diallel and the 12 parental lines were evaluated in Campinas, State of São Paulo, in randomized block design, with tree replicates and two commercial checks. The following traits were evaluated: plant and ear height, ear weight and grain weight. Individual variance analysis of hybrids were performed, and the averages were compared by Tukey test (P<0.05). General combining ability of the lines was obtained according to Geraldi e Miranda Filho. Correlations among matrices were estimated through Mantel statistics, considering heterosis, yield and specific combining ability with genetic divergence assessed by AFLP and SSR. The hybrid PM624 × P398 exhibited outstanding yield capacity and the lines VER266 and L105 showed positive GCA for grain yield. Estimate heterosis ranged from -559 to 6.320 kg ha-1. No significant correlation was observed between heterosis, specific combination ability or grain yield with genetic distance assessed by AFLP and SSR. Therefore, no prediction of hybrids performance could be made on the basis of the genetic divergence of the parent lines.673639648BARBOSA, A.M.M., GERALDI, I.O., BENCHIMOL, L.L., GARCIA, A.A.F., SOUZA, C.L., SOUZA, A.P., Relationship of intra- and interpopulation tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers (2003) Euphytica, 130, pp. 87-99. , Netherlands, vBENCHIMOL, L.L.SOUZA JÚNIOR C.L.GARCIA, A.A.FKONO, P.M.S.MANGOLIN, C.A.BARBOSA, A.M.M.COELHO, A.S.G.SOUZA, A.P. Genetic diversity in tropical maize inbred lines: heterotic group assignment and hybrid performance determined by RFLP markers. Plant Breeding, Berlin, v.119, p.491-496, 2000BERNARDO, R., Relationship between single-cross performance and molecular marker heterozygosity (1992) Theoretical and Applied Genetics, 83, pp. 628-634. , Berlin, vCHARCOSSET, A., ESSIOUX, L., The effect of population struture on the relationship between heterosis and heterozygosity at marker loci (1994) Theoretical and Applied Genetics, 89 (2-3), pp. 336-343. , Berlin, vCOMSTOCK, R.E., ROBINSON, H.F., The components of genetic variance in populations of biparental progenies and their use in estimating the average degree of dominance. 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Biometrics (1953) Alexandria, 45, pp. 186-191GERALDI, I.O., MIRANDA FILHO, J.B., Adapted models for the analysis of combining abilty of varieties in partial diallel crosses (1988) Revista Brasileira de Genética, 11 (2), pp. 419-430. , Ribeirão Preto, vGRIFFING, J.B., A generalized treatment of the use of diallel crosses in quantitative inheritance (1956) Heredity, 10, pp. 31-50. , Harlow, vGRIFFING, J.B., Concept of general and specific combining ability in relation to diallel systems (1956) Australian Journal of Biological Science, 9, pp. 463-493. , East Melbourne, vGUIMARÃES, P.S., PATERNIANI, M.E.A.G.Z., LÜDERS, R.R., SOUZA, A.P., LABORDA, P.R., OLIVEIRA, K.M., Correlação da heterose de híbridos de milho com divergência genética entre linhagens. (2007) Pesquisa Agropecuária Brasíleira, 42 (6), pp. 811-816. , Brasília, VHALLAEUR, A.R., MIRANDA FILHO, J.B., (1995) Quantitative Genetics in Maize Breeding, , 2.ed. 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(2005) Theoretical and Applied Genetics, 111, pp. 1288-1299. , Berlin, vLANZA, L.L.B., SOUZAJR, C.L., OTTOBONI, L.M.M., VIEIRA, M.L.C., SOUZA, A.P., Genetic distance of inbred lines and prediction. of maize single-cross performance using RAPD markers (1997) Theoretical and Applied Genetics, 94 (8), pp. 1023-1030. , Berlin, vMANLY, B.F.J., (1991) Randomization and Monte Carlo Methods in Biology, , London: Chapman & Hall, 281pMANTEL, N., The detection of disease clustering and a generalized regression approach (1967) Cancer Research, 27, pp. 209-220MELCHINGER, A.E., BOPPENMAIER, J., DHILLON, B.S., POLLMER, W.G., HERRMAN, R.G., Genetic diversity for RFLPs in European maize inbreds. II. Relation to performance of hybrids within versus between heterotic groups for forage traits (1992) Theoretical and Applied Genetics, 84 (5-6), pp. 672-681. , Berlin, vMELCHINGER, A.E., LEE, M., LAMKEY, K.R., HALLAUER, A.R., WOODMAN, W.L., Genetic diversity for restriction fagment length polymorphisms and heterosis for two diallel ets of maize inbreds (1990) Theoretical and Applied Genetics, 80 (4), pp. 488-496. , Berlin, VMELO, W.M.C., PINHO, R.G.V., FERREIRA, D.F., Capacidade combinatória e divergência genética em híbridos comerciais d milho (2001) Ciência Agrotécnica, 25 (4), pp. 821-830. , Lavras, vMILLER, M.P., (1997) TFPGA - Tools For Population Genetic Analyses, 13. , Flagstaff: Northern Arizona UniversityMRANDA FILHO, J.B., GERALDI, I.O., An adapted model for th analysis of partial dialel crosses (1984) Revista Brasileira de Genética, 7 (4), pp. 677-688. , Ribeirão Preto, vMOL, R.H., LONNQUIST, J.H., VELEZ FORTUNO, J., JHNSON, E.C., The relationship of heterosis and divergence in maize (1965) Genetics, 52, pp. 139-144. , New York, v, JulyOIVEIRA, K.M., LABORDA, P.R., GARCIA, A.A.F., ZAGATTO-PATERNIANI, M.E.A.G., Souza, A.P., Evaluating genetic rlationships between tropical maize inbred lines by means of AFLP profiling (2004) Hereditas, 140, pp. 24-33. , Harlow, vINTO, R.M.C.GARCIA, A.A.F.SOUZA JÚNIOR, C.L. de. locação de linhagens de milho derivadas das populações BR-105 e BR-106 em grupos heteróticos. 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(2002) Bragantia, 61 (3), pp. 219-230. , Campinas, vSMOUSE, P.E., LONG, J.C., SOKAL, R.R., Multiple regression and correlation extensions of the Mantel test of matrix correspondence (1986) Systematic Zoology, 35, pp. 627-632. , New York, vVOS, P., HOGERS, R., BLEEKER, M., REIJANS, M., VAN DE LEE, T., HORNES, M., FRITJERS, A., ZABEU, M., AFLP: A new technique for DNA fingerprinting (1995) Nucleic Acids Research, Eynsham, 23, pp. 4407-4414SPRAGUE, G.F., TATUM, L.A., General vs. specific combining ability in single crosses of corn (1942) Journal of American Society of Agronomy, 34 (10), pp. 923-932. , Madison, vVENCOVSKY, R. Alguns aspectos teóricos e aplicados relativos a cruzamentos dialélicos de variedades. 1970. 110p. Tese (LivreDocência) - ESALQ/USP, Piracicaba, 197

Phenotypic and molecular characterization of corn hybrids released from 1980 to 2000

Genetic variability is the basis of plant breeding. In corn, a large and diverse genetic pool permits manipulation of different genotypes, but the genetic diversity of tropical germplasm has been little studied. With the objective of analyzing the amplitude of the genetic variability in 15 hybrids released in different periods by three different seed companies, phenotypic and molecular characterization was carried out in three environments and at two plant densities. The phenotypic assessment showed great similarity among the hybrids, suggesting that the breeding programs have developed genotypes with similar phenotypic traits. The dendogram of the molecular analysis showed clustering according with the different companies suggesting that each corn breeding program make use of different germoplasms. However, although the germplasm was different, it could be inferred that the selection pressure used by the breeders followed the same traits such as plant height, number of rows per ear and kernel weight among others analyzed in the present study, that contributed to the phenotypic uniformity of the genotype