A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae

Theoretical and Applied Genetics

Volumn 111, Issue 8, 2005, Pages 1466-1488

  Pelgas, Betty ^a   Bousquet, Jean ^a   Beauseigle, Stéphanie ^a   Isabel, Nathalie ^a,b  

^a UNIVERSITÉ LAVAL   (Canada)

^b LAURENTIAN FORESTRY CENTRE   (Canada)

Author keywords

Codominant markers; Colinearity; Comparative mapping; Consensus map; Pinaceae; Synteny

Indexed keywords

CHROMOSOMES; MOLECULAR BIOLOGY; MUTAGENESIS;

CODOMINANT MARKERS; COLINEARITY; COMPARATIVE MAPPING; CONSENSUS MAP; PINACEAE; SYNTENY;

GENE TRANSFER;

ARTICLE; CHROMOSOME MAP; COMPARATIVE STUDY; CROSS BREEDING; GENETIC MARKER; GENETICS; NUCLEIC ACID AMPLIFICATION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SPECIES DIFFERENCE; SPRUCE; SYNTENY; VARIABLE NUMBER OF TANDEM REPEAT;

CHROMOSOME MAPPING; CROSSES, GENETIC; GENETIC MARKERS; MINISATELLITE REPEATS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PICEA; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SPECIES SPECIFICITY; SYNTENY;

PICEA; PICEA MARIANA; PICEA RUBENS; PINACEAE; PSEUDOTSUGA; PSEUDOTSUGA MENZIESII;

EID: 27744554512     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-005-0068-2     Document Type: Article

References (104)

1. Acheré V, Faivre-Rampant P, Jeandroz S, Besnard G, Markussen T, Aragones A, Fladung M, Ritter E, Favre JM (2004) A saturated consensus linkage map of Picea abies including AFLP, SSR, STS, 5S rDNA and morphological markers. Theor Appl Genet 108:1602-1613
2. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324-2326
3. Beavis WD, Grant D (1991) A linkage map based on information from four F2 populations of maize (Zea mays L.). Theor Appl Genet 82:636-644
4. Besnard G, Acheré V, Faivre-Rampant P, Favre JM, Jeandroz S (2003) A set of cross-species amplifying microsatellite markers developed from DNA sequence databanks in Picea (Pinaceae). Mol Ecol Notes 3:380-383
5. Brondani RPV, Brondani C, Grattapaglia D (2002) Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol Gen Genet 267:338-347
6. Brown GR, Kadel EE III, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (P. taeda L.) for integrating pine genomics. Genetics 159:799-809
7. Bucci G, Kubisiak TL, Nance WL, Menozzi P (1997) A population consensus partial linkage map of Picea abies Karst based on RAPD markers. Theor Appl Genet 95:643-654
8. Cato SA, Corbett GE, Richardson TE (1999) Evaluation of AFLP for genetic mapping in Pinus radiata D. Don. Mol Breed 5:275-281
9. Causse M, Santoni S, Damerval C, Maurice A, Charcosset A, Deatrick J, De Vienne D (1996) A composite map of expressed sequences in maize. Genome 39:418-432
10. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Roman C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671-1685
11. Cervera MT, Storme V, Ivens B, Gusmao J, Liu B-H, Hostyn V, van Slycken J, Van Montagu M, Boerjan W (2001) Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158:787-809
12. Chagné D, Lalanne C, Madur D, Kumar S, Frigerio JM, Krier C, Decroocq S, Savouré A, Bou-Dagher-Kharrat M, Bertocchi E, Brach J, Plomion C (2002) A high density genetic map of maritime pine based on AFLPs. Ann For Sci 59:627-636
13. Chagné D, Brown G, Lalanne C, Madur D, Pot D, Neale D, Plomion C (2003) Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 12:185-195
14. Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera M-T, Vendramin GG, Garcia V, Frigerio JM, Echt C, Richardson T, Plomion C (2004) Cross species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 109:1204-1214
15. Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128:175-182
16. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289-15294
17. Costa P, Pot D, Dubos C, Frigerio J-M, Pionneau C, Bodénès C, Bertocchi E, Cervera M, Remington DL, Plomion C (2000) A genetic map of maritime pine based on AFLP, RAPD and protein markers. Theor Appl Genet 100:39-48
18. Devey ME, Fiddler TA, Liu B-H, Knapp SJ, Neale DB (1994) A RFLP linkage map for loblolly pine based on three-generation outbred pedigree. Theor Appl Genet 88:273-278
19. Devey MD, Sewell MM, Uren TL, Neale D (1999) Comparative mapping in loblolly pine and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 99:656-662
20. Devey ME, Carson SD, Nolan MF, Matheson AC, Te Riini C, Hohepa J (2004) QTL associations for density and diameter in Pinus radiata and the potential for marker-aided selection. Theor Appl Genet 108:516-524
21. Gentzbittel L, Vear F, Zhang Y-X, Bervillé A, Nicolas P (1995) Development of a consensus linkage RFLP map of cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 90:1079-1086
22. Gosselin I, Zhou Y, Bousquet J, Isabel N (2002) Megagametophyte-derived linkage maps of white spruce (Picea glauca) based on RAPD, SCAR and ESTP markers. Theor Appl Genet 104:987-997
23. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test-cross: mapping strategy and RAPD markers. Genetics 137:1121-1137
24. Guillet-Claude C, Isabel N, Pelgas B, Bousquet J (2004) The evolutionary implications of knox-Igene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence. Mol Biol Evol 21:2232-2245
25. Hackett CA, Broadfoot LB (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33-38
26. Haldane JBS (1919) The combination of linkage values, and the calculation of distances between loci of linked factors. J Genet 8:299-309
27. Hanson WD (1959) The Breakup of initial linkage blocks under selected mating systems. Genetics 44:857-868
28. Harry DE, Temesgen B, Neale D (1998) Codominant PCR-based markers of Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97:327-336
29. Hauge BM, Hanley SM, Cartinhour S, Cherry JM, Goodman HM, Koornneef M, Stam P, Chang C, Kempin C, Medrano L, Meyerowitz EM (1993). An integrated genetic/physical map of the Arabidopsis thaliana genome. Plant J 3:745-754
30. Hayashi E, Kondo T, Terada K, Kuramoto N, Goto Y, Okamura M, Kawasaki (2001) Linkage map of Japanese black pine based on AFLP and RAPD markers including markers linked to resistance against the pine needle gall midge. Theor Appl Genet 102:871-875
31. Hodgetts RB, Aleksiuk MA, Brown A, Clarke C, Macdonald E, Nadeem S, Khasa D (2001) Development of microsatellite markers for white spruce (Picea glauca) and related species. Theor Appl Genet 102:1252-1258
32. Hori K, Kobayashi T, Shimizu A, Sato K, Takeda K, Kawasaki S (2003) Efficient construction of high-density linkage map an dits application to QTL analysis in barley. Theor Appl Genet 107:806-813
33. Hulbert S, Ilott T, Legg EJ, Lincoln S, Lander E, Michelmore R (1988) Genetic analysis of the fungus Bremia lactucae, using restriction length polymorphism. Genetics 120:947-958
34. Isabel N, Beaulieu J, Bousquet J (1995) Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. Proc Natl Acad Sci USA 92:6369-6373
35. Jany JL, Bousquet J, Khasa DP (2003) Microsatellite markers for Hebeloma species developed from expressed sequence tags in the ectomycorrhizal fungus Hebeloma cylindrosporum. Mol Ecol Notes 3:659-661
36. Jermstad KD, Bassoni DL, Wheeler NC, Neale DB (1998) A sex-averaged linkage map in coastal Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) based on RFLP and RAPD markers. Theor Appl Genet 97:762-770
37. Karhu A, Dieterich JH, Savolainen O (2000) Rapid expansion of microsatellite sequences in pines. Mol Biol Evol 17:259-265
38. Knox MR, Ellis THN (2002) Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations. Genetics 162:861-873
39. Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667-678
40. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
41. Kowalski S, Lan T, Feldmann K, Paterson A (1994) Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 138:499-510
42. Krutovskii KV, Vollmer SS, Sorensen FC, Adams WT, Knapp SJ, Strauss SH (1998) RAPD genome maps of Douglas fir. J Hered 89:197-205
43. Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447-461
44. 1 family. Theor Appl Genet 90:1119-1127
45. Kumar S, Spelman RJ, Garrick DJ, Richardson TE, Lousberg M, Wilcox PL (2000) Multiple marker mapping of wood density loci in an outbred pedigree of radiata pine. Theor Appl Genet 100:926-933
46. Lan TH, DelMonte TA, Reischmann KP, Hyman J, Kowalski SP, McFerson J, Kresovich S, Paterson AH (2000) An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res 10:776-788
47. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
48. Lange K, Boehnke M (1982) How many polymorphic genes will it take to span the human genome? Am J Hum Genet 24:842-845
49. Lerceteau E, Plomion C, Andresson B (2001) AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study. Mol Breed 6:451-458
50. Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109:361-369
51. Liu B-H (1998) Statistical genomics: linkage mapping and QTL analysis. CRC Press, Boca Raton, FL
52. Livingstone K, Rieseberg L (2003) Chromosomal evolution and speciation: a recombination-based approach. New Physiol 161:107-112
53. Ma H, Moore PH, Liu Z, Kim MS, Yu Q, Fitch MM, Sekioka T, Paterson AH, Ming R (2004) High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166:419-436
54. Maliepaard C, Jansen J, Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet Res 70:237-250
55. Marques CM, Araujo JA, Ferreira JG, Whetten R, O'Malley DM, Liu B-H, Sederoff R (1998) AFLP genetic maps of Eucalyptus globulus and E. tereticornis. Theor Appl Genet 96:727-737
56. Mukai Y, Suyama Y, Tsumura Y, Kawahara T, Yoshimaru H, Hondo T, Tomaru N, Kuramoto N, Murai M (1995) A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci. Theor Appl Genet 90:835-840
57. Myburg AA, Remington DL, O'Malley DM, Sederoff RR, Whetten RW (2001) High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer. Biotech 30:348-357
58. Myburg AA, Griffin AR, Sederoff RR, Whetten RW (2003) Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach. Theor Appl Genet 107:1028-1042
59. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325-330
60. Nelson CD, Kubisiak TL, Stine M, Nance WL (1994) A genetic linkage map of longleaf pine (Pinus palustris Mill.) based on random amplified polymorphic DNAs. J Hered 85:433-439
61. Nikaido AM, Ujino T, Iwata H, Yoshimura K, Yoshimura H, Suyama Y, Murai M, Nagasaka K, Tsumura Y (2000) AFLP and CAPS linkage maps of Cryptomeria Japonica. Theor Appl Genet 100:825-831
62. Orr HA (1996) Dobzhansky, Bateson, and the genetics of speciation. Genetics 144:1331-1335
63. Paglia G, Morgante M (1998) PCR-based multiplex DNA finger-printing techniques for the analysis of conifer genomes. Mol Breed 4:173-177
64. Paglia P, Olivieri AM, Morgante M (1998) Towards second-generation STS (sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce (Picea abies K.). Mol Gen Genet 258:466-478
65. Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of Quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735-742
66. Pelgas B, Isabel N, Bousquet J (2004) Efficient screening for expressed sequence tag polymorphisms (ESTPs) by DNA pool sequencing and denaturing gradient gel electrophoresis (DGGE) in spruces. Mol Breed 3:263-279
67. Perron M, Bousquet J (1997) Natural hybridization between black spruce and red spruce. Mol Ecol 6:725-734
68. Perron M, Gordon AG, Bousquet J (1995) Species-specific RAPD fingerprints for the closely related Picea mariana and P. rubens. Theor Appl Genet 91:142-149
69. Perron M, Perry D, Andalo C, Bousquet J (2000) Evidence from sequence-tagged-site markers of a recent progenitor-derivative species pair in conifers. Proc Natl Acad Sci USA 97:11331-11336
70. Perry DJ, Bousquet J (1998a) Sequence-tagged-site (STS) markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149:1089-1098
71. Perry DJ, Bousquet J (1998b) Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theor Appl Genet 97:735-743
72. Pfeiffer A, Olivieri AM, Morgante M (1997) Identification and characterization of microsatellites in Norway spruce (Picea abies K.). Genome 40:411-419
73. Plomion C, O'Malley DM (1996) Recombination rate differences for pollen parents and seed parents in pine. Heredity 77:341-350
74. Plomion C, O'Malley DM, Durel CE (1995) Genomic analysis in maritime pine (Pinus pinaster): Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. Theor Appl Genet 90:1028-1034
75. Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379-394
76. Qi X, Stam P, Lindhout P (1998) Use of locus-specific AFLP markers to construct a high-density molecular map in barley. Theor Appl Genet 96:376-384
77. Rajora OP, Rahman MH, Dayanandan S, Mosseler A (2001) Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species. Mol Gen Genet 264:871-882
78. Remington DL, Whetten RW, Liu BH, O'Malley DM (1999) Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet 98:1279-1292
79. Rieseberg LH, Buerkle CA (2002) Genetic mapping in hybrid zones. Am Nat 159:836-850
80. Rieseberg LH, Linder CR, Seiler GJ (1995) Chromosomal and genic barriers to introgression in Helianthus. Genetics 141:1163-1171
81. Roeder GS (1997) Meiotic chromosomes: it takes two to tango. Genes Dev 11:2600-2621
82. Rouppe van der Voort JN, van Zandvoort P, van Eck HJ, Folkertsma RT, Hutten RC, Draaistra J, Gommers FJ, Jacobsen E, Helder J, Bakker J (1997) Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes. Mol Gen Genet 255:438-447
83. Rungis D, Bérubé Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K (2004) Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor Appl Genet 109:1283-1294
84. Salse J, Piégu B, Cooke R, Delseny M (2002) Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucl Acids Res 30:2316-2328
85. Salse J, Piégu B, Cooke R, Delseny M (2004) New in silico insight into the synteny between rice (Oriza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396-409
86. Schiex T, Gaspin C (1997) CARTHAGENE: constructing and joining maximum likelihood genetic maps. Proc Int Conf Intell Syst Mol Biol 5:258-67
87. Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE (2000) Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 43:41-46
88. Scotti I, Magni F, Paglia G, Morgante M (2002a) Efficient development of dinucleotide microsatellite markers in Norway spruce (Picea abies Karst.) through dot-blot selection. Theor Appl Genet 104:1035-1041
89. Scotti I, Magni F, Paglia G, Morgante M (2002b) Trinucleotide microsatellites in Norway spruce (Picea abies K.): Their features and the development of molecular markers. Theor Appl Genet 106:40-50
90. Sewell MM, Sherman BK, Neale DB (1999) A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 151:321-330
91. Shepherd M, Cross M, Dieters MJ, Henry R (2003) Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers. Theor Appl Genet 106:1409-1419
92. Sokal RR, Rohlf FJ (1998) Biometry, 4th edn. W. H. Freeman, New York
93. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 3:739-744
94. Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K, Tsumura Y (2003) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165:1551-1568
95. Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB (2001) Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664-675
96. Tsumura Y, Suyama Y, Yoshimura K, Shirato N, Mukai Y (1997) Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theor Appl Genet 94:764-772
97. Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE (1992) Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Bio/Technology 10:686-690
98. Van Ooijen JW, Voorrips RE (2001) Joinmap 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands, Website: http://www.joinmap.nl
99. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407-4414
100. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Luebberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921-935
101. Waugh R, Bonar N, Baird E, Thomas B, Graner A, Hayes P, Powell W (1997) Homology of AFLP products in three mapping populations of barley. Mol Gen Genet 255:311-321
102. Wu RL, Han YF, Hu JJ, Fang JJ, Li L, Li ML, Zeng Z-B (2000) An integrated genetic map of Populus deltoides based on amplified fragment length polymorphisms. Theor Appl Genet 100:1249-1256
103. Yin TM, Wang XR, Andersson B, Lerceteau-Köhler E (2003) Nearly complete genetic maps of Pinus sylvestris L. (Scots pine) constructed by AFLP marker analysis in a full-sib family. Theor Appl Genet 106:1075-1083
104. Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA (2004) Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor Appl Genet 109:451-463