An integrated molecular map of yellow passion fruit based on simultaneous maximum-likelihood estimation of linkage and linkage phases

Journal of the American Society for Horticultural Science

Volumn 133, Issue 1, 2008, Pages 35-41

  Oliveira, Eder J ^a,d   Vieira, Maria Lucia C ^a   Garcia, Antonio Augusto F ^a   Munhoz, Carla F ^a   Margarido, Gabriel R A ^a   Consoli, Luciano ^a   Matta, Frederico P ^a   Moraes, Michel C ^a   Zucchi, Maria I ^b   Fungaro, Maria Helena P ^c  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b INSTITUTO AGRONÔMICO   (Brazil)

^c STATE UNIVERSITY OF LONDRINA   (Brazil)

^d EMBRAPA CERRADOS   (Brazil)

Author keywords

AFLP; Linkage map integration; Microsatellites; Multipoint distances; Outcrossing species; Passiflora edulis f. flavicarpa

Indexed keywords

PASSIFLORA EDULIS; PASSIFLORA EDULIS F. FLAVICARPA;

EID: 37849007543     PISSN: 00031062     EISSN: None     Source Type: Journal    
DOI: 10.21273/jashs.133.1.35     Document Type: Article

References (45)

1. Alonso-Blanco, C., A.J.M. Peeters, M. Koornneef, C. Lister, C. Dean, N. van den Bosh, J. Pot, and M.T.R. Kuiper. 1998. Development of an AFLP based linkage map of Ler Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J. 14:259-271.
2. 1 segregating almond progenies. J. Amer. Soc. Hort. Sci. 119:339-344.
3. Brondani, R.P.V., C. Brondani, and D. Grattapaglia. 2002. Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol. Genet. Genomics 267:338-347.
4. Carneiro, M.S., L.E.A. Camargo, A.S.G. Coelho, R. Vencovsky, R.P. Leite, Jr., N.M.C. Stenzel, and M.L.C. Vieira. 2002. RAPD-based genetic linkage maps of yellow passion fruit (Passiflora edulis Sims f. flavicarpa Deg.). Genome 45:670-678.
5. Coelho, A.S.G. 2005. TreeMap: software para construção de mapas genéticos em cruzamentos derivados de genótipos não-endogâmicos. Univ. Federal de Goiânia, Goiânia, Brazil.
6. Creste, S., A. Tulmann-Neto, and A. Figueira. 2001. Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol. Biol. Rpt. 19:299-306.
7. Cuco, S.M., M.L.C. Vieira, M. Mondin, and M.L.R. Aguiar-Perecin. 2005. Comparative karyotype analysis of three Passiflora L. species and cytogenetic characterization of somatic hybrids. Caryologia 58:220-228.
8. Dempster, A.P., N.M. Laird, and D.B. Rubin. 1977. Maximum likelihood from incomplete data via the EM algorithm. J. Royal Stat. Soc. Ser. B 39:1-38.
9. Doerge, R.W. 1996. Constructing genetic maps by rapid chain delineation. J. Agr. Genomics 2:6.
10. Doucleff, M., Y. Jin, F. Gao, S. Riaz, A.F. Krivanek, and M.A. Walker. 2004. A genetic linkage map of grape utilizing Vitis rupestris x Vitis arizonica. Theor. Appl. Genet. 109:1178-1187.
11. Fajardo, D., F. Angel, M. Grum, J. Tohme, M. Lobo, W.M. Roca, and I. Sanchez. 1998. Genetic variation analysis of the genus Passiflora L. Euphytica 101:341-347.
12. Fanizza, G., F. Lamaj, L. Costantini, R. Chaabane, and M.S. Grando. 2005. QTL analysis for fruit yield components in table grapes (Vitis vinifera). Theor. Appl. Genet. 111:658-664.
13. Fischer, B.M., I. Salakhutdinov, M. Akkurt, R. Eibach, K.J. Edwards, R. Töpfer, and E.M. Zyprian. 2004. Quantitative trait locus analysis of fungal disease resistance factors on a molecular map of grapevine. Theor. Appl. Genet. 108:501-515.
14. Garcia, A.A.F., E.A. Kido, A.N. Meza, H.M.B. Souza, L.R. Pinto, M.M. Pastina, C.S. Leite, J.A.G. da Silva, E.C. Ulian, A. Figueira, and A.P. Souza. 2006. Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor. Appl. Genet. 112:298-314.
15. Grattapaglia, D. and R. Sederoff. 1994. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137:1121-1137.
16. Hackett, C.A., B. Pande, and G.C. Bryan. 2003. Constructing linkage maps in autotetraploid species using simulated annealing. Theor. Appl. Genet. 106:1107-1115.
17. Hamwich, A., S.M. Udupa, W. Choumane, A. Sarker, F. Dreyer, C. Jung, and M. Baum. 2005. A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of Fusarium vascular wilt resistance. Theor. Appl. Genet. 110:669-677.
18. Keim, P., J.M. Schupp, S.E. Travis, K. Clayton, T. Zhu, L. Shi, A. Ferreira, and D.M. Webb. 1997. A high-density soybean genetic map based on AFLP markers. Crop Sci. 37:537-543.
19. Kenis, K. and J. Keulemans. 2005. Genetic linkage maps of two apple cultivars (Malus domestica Borkh.) based on AFLP and microsatellite markers. Mol. Breed. 15:205-219.
20. Kosambi, D.D. 1944. The estimation of map distance from recombination values. Ann. Eugen. 12:172-175.
21. Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Daly, E.E. Lincoln, and L. Newburg. 1987. Map Maker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181.
22. Lespinasse, D., G.M. Rodier, L. Grivet, A. Leconte, H. Legnate, and M. Seguin. 2000. A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite and isozymes markers. Theor. Appl. Genet. 100:127-138.
23. Lin, M., X.Y. Lou, M. Chang, and R. Wu. 2003. A general statistical framework for mapping quantitative trait loci in nonmodel systems: issue for characterizing linkage phases. Genetics 165:901-913.
24. Lopes, R., M.T.G. Lopes, M.S. Carneiro, F.P. Matta, L.E.A. Camargo, and M.L.C. Vieira. 2006. AFLP linkage analysis and mapping of resistance genes to Xanthomonas axonopodis pv. passiflorae in yellow passion fruit. Genome 49:17-29.
25. Lu, Q., Y. Cui, and R. Wu. 2004. A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genet. 5:1-14.
26. Maliepaard, C., F.H. Alston, G. van Arkel, L.M. Brown, E. Chevreau, F. Dunemann, K.M. Evans, S. Gardiner, P. Guilford, A.W. van Heusden, J. Janse, F. Laurens, J.R. Lynn, A.G. Manganaris, A.P.M. Den Nijs, N. Periam, E. Rikkerink, P. Roche, C. Ryder, S. Sansavini, H. Schmidt, S. Tartarini, J.J. Verhaegh, M. Vrielink-van Ginkel, and G.J. King. 1998. Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor. Appl. Genet. 97:60-73.
27. Maliepaard, C., J. Jansen, and J.W. van Ooijen. 1997. Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet. Res. 70:237-250.
28. Margarido, G.R.A., A.P. Souza, and A.A.F. Garcia. 2007. OneMap: software for genetic mapping in outcrossing species. Hereditas 144:78-79.
29. Moraes, M.C. 2005. Mapas de ligação e mapeamento de QTL ("quantitative trait loci") em maracujá-amarelo (Passiflora edulis Sims f. flavicarpa Deg.). Univ. of São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, Brazil. PhD Diss.
30. Moraes, M.C., I.O. Geraldi, F.P. Matta, and M.L.C. Vieira. 2005. Genetic and phenotypic parameter estimates for yield and fruit quality traits from a single wide cross in yellow passion fruit. HortScience 40:1978-1981.
31. Murray, M.G. and W.F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321-4325.
32. Oliveira, E.J., J.G. Padua, M.I. Zucchi, L.E.A. Camargo, M.H.P. Fungaro, and M.L.C. Vieira. 2005. Development and characterization of microsatellite markers from the yellow passion fruit (Passiflora edulis f. flavicarpa). Mol. Ecol. Notes 5:331-333.
33. Pugh, T., O. Fouet, A.M. Risterucci, P. Brottier, M. Abouladze, C. Deletrez, B. Courtois, D. Clement, P. Larmande, J.A.K. N'goran, and C. Lanaud. 2004. A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers. Theor. Appl. Genet. 108:1151-1161.
34. Risterucci, A.M., L. Grivet, J.A.K. N'goran, I. Pieretti, M.H. Flament, and C. Lanaud. 2000. A high-density linkage map of Theobroma cacao L. Theor. Appl. Genet. 101:948-955.
35. Ritter, E., C. Gebhardt, and F. Salamini. 1990. Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125:645-654.
36. Ritter, E. and F. Salamini. 1996. The calculation of recombination frequencies in crosses of allogamous plant species with applications to linkage mapping. Genet. Res. 67:55-65.
37. Sanchez, I., F. Angel, M. Grum, M.C. Duque, M. Lobo, J. Tohme, and W. Roca. 1999. Variability of chloroplast DNA in the genus Passiflora L. Euphytica 106:15-26.
38. Storey, J.D. and R. Tibshirani. 2003. Statistical significance for genome-wide studies. Proc. Natl. Acad. Sci. USA 5:9440-9445.
39. Testolin, R., W.G. Huang, O. Lain, R. Messina, A. Vecchione, and G. Cipriani. 2001. A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theor. Appl. Genet. 103:30-36.
40. van Ooijen, J.W. and R.E. Voorrips. 2001. JoinMap, version 3.0, software for the calculation of genetics linkage maps. Plant Research International, Wageningen, The Netherlands.
41. Vieira, M.L.C. and M.S. Carneiro. 2004. Passiflora spp. passionfruit, p. 435-453. In: R.E. Litz (ed.). Biotechnology of fruit and nut crops. CABI Publishing, Oxford, U.K.
42. Vuylsteke, M., R. Mank, R. Antonise, E. Bastiaans, M.L. Senior, C.W. Stuber, A.E. Melchinger, T. Lubberstedt, X.C. Xia, P. Stam, M. Zabeau, and M. Kuiper. 1999. Two high-density AFLP linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor. Appl. Genet. 99:921-935.
43. n polymorphisms. Genomics 7:524-530.
44. Wu, R., C.X. Ma, I. Painter, and Z.-B. Zeng. 2002. Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theor. Popul. Biol. 61:349-363.
45. Yin, T., Z. Zhang, M. Huang, M. Wang, Q. Zhuge, S. Tu, L.H. Zhu, and R. Wu. 2002. Molecular linkage maps of the Populus genome. Genome 45:541-555.