Near-saturated and complete genetic linkage map of black spruce (Picea mariana)

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Kang, Bum Yong ^a,d   Mann, Ishminder K ^a   Major, John E ^c   Rajora, Om P ^a,b  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF NEW BRUNSWICK   (Canada)

^c NATURAL RESOURCES CANADA   (Canada)

^d EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICROSATELLITE DNA; PLANT DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BLACK SPRUCE; CHROMOSOME NUMBER; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE FREQUENCY; GENE MAPPING; GENE SEGREGATION; GENETIC LINKAGE; GENOME SIZE; HAPLOIDY; HETEROZYGOSITY; MICROSATELLITE MARKER; NONHUMAN; NORTH AMERICA; PEDIGREE; PLANT GENOME; POLYMORPHIC LOCUS; CHROMOSOME MAP; GENETIC MARKER; GENETICS; POISSON DISTRIBUTION; SPRUCE;

PICEA; PICEA MARIANA; PINACEAE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CHROMOSOME MAPPING; DNA, PLANT; GENETIC LINKAGE; GENETIC MARKERS; GENOME, PLANT; MICROSATELLITE REPEATS; PICEA; POISSON DISTRIBUTION;

EID: 77956904851     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-515     Document Type: Article

References (50)

1. Neale DB, Williams CG. Restriction fragment length polymorphism mapping in conifers and applications to forest genetics and tree improvement. Can J For Res 1991, 21:545-554.
2. Viereck LA, Johnston WF. Picea mariana (Mill.) B.S.P. - Black spruce. Conifers. Silvics of North America 1990, 1:227-237. US Dept Agric, Forest Service, Agriculture Handbook 654, Washington DC, Burns RM, Honkala BH.
3. Morgenstern EK, Wang BSP. Trends in forest depletion, seed supply, and reforestation in Canada during the past four decades. For Chron 2001, 6:1014-1021.
4. Ohri D, Khoshoo TN. Genome size in gymnosperms. Plant Sys Evol 1986, 153:119-132.
5. Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE. Single tree genetic linkage analysis in conifers using haploid DNA from megagametophytes. BioTechnology 1992, 10:686-690. 10.1038/nbt0692-686, 1368888.
6. Binelli G, Bucci G. A genetic linkage map of Picea abies Karst., based on RAPD markers, as a tool in population genetics. Theor Appl Genet 1994, 88:283-288.
7. Bucci G, Kubisiak TL, Nance WL, Menozzi P. A population consensus partial linkage map of Picea abies Karst. based on RAPD markers. Theor Appl Genet 1997, 95:643-654.
8. Paglia GP, Olivieri AM, Morgante M. Towards second generation STS (sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce (Picea abies K.). Mol Gen Genet 1998, 258:466-478. 10.1007/s004380050757, 9669328.
9. Acheré V, Faivre-Rampant P, Jeandroz S, Besnard G, Markussen T, Aragones A, Fladung M, Ritter E, Favre JM. A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5 S rDNA and morphological markers. Theor Appl Genet 2004, 108:1602-1613. 10.1007/s00122-004-1595-y, 14991106.
10. Gosselin I, Zhou Y, Bousquet J, Isabel N. Megagametophyte-derived linkage maps of white spruce (Picea glauca) based on RAPD, SCAR and ESTP markers. Theor Appl Genet 2002, 104:987-997. 10.1007/s00122-001-0823-y, 12582604.
11. Pelgas B, Beauseigle S, Acheré V, Jeandroz S, Bousquet J, Isabel N. Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae. Theor Appl Genet 2006, 113:1371-1393. 10.1007/s00122-006-0354-7, 17061103.
12. Pelgas B, Bousquet J, Beauseigle S, Isabel N. A composite linkage map from two crosses for the species complex Picea mariana X Picea rubens and analysis of synteny with other Pinaceae. Theor Appl Genet 2005, 111:1466-1488. 10.1007/s00122-005-0068-2, 16215729.
13. Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 2008, 9:21. 10.1186/1471-2164-9-21, 2246113, 18205909.
14. Liu BH. Statistical genomics: linkage mapping and QTL analysis. 1998, CRC Press, New York, NY.
15. Chakravarti A, Lasher LK, Reefer JE. A maximum-likelihood method for estimating genome length using genetic linkage data. Genetics 1991, 128:175-182. 1204446, 2060775.
16. Fishman L, Kelly AJ, Morgan E, Willis JH. A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 2001, 159:1701-1716. 1461909, 11779808.
17. Major JE, Mosseler A, Johnsen K, Rajora OP, Barsi DC, Kim K-H, Park J-M, Campbell M. Reproductive barriers and hybridity in two spruces, Picea rubens and Picea mariana, sympatric in eastern North America. Can J Bot 2005, 83:163-175.
18. Morgenstern EK. A diallel cross in black spruce Picea mariana (Mill.) B.S.P. Silvae Genet 1974, 23:67-70.
19. Boyle TJB. A diallel cross in black spruce. Genome 1987, 29:180-186.
20. Groover A, Williams CG, Devey ME, Lee JM, Neale DB. Sex-related differences in meiotic recombination frequency in Pinus taeda. J Hered 1995, 86:157-158.
21. Plomion C, O'Malley DM. Recombination rate differences for pollen parents and seed parents in pine. Heredity 1996, 77:341-350.
22. Boyle TJB, Morgenstern EK. Estimates of outcrossing rates in six populations of black spruce in central New Brunswick. Silvae Genet 1986, 35:102-106.
23. Sproulè AT, Dancik BP. The mating system of black spruce in north-central Alberta, Canada. Silvae Genet 1996, 45:159-164.
24. Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale BD. An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 1994, 88:273-278.
25. Groover A, Devey M, Fiddler T, Lee J, Megraw R, Sherman B, Vujcic S, Williams C, Neale D. Identification of quantitative trait loci iflencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 1994, 138:1293-1300. 1206264, 7896107.
26. Sewell MM, Sherman BK, Neale DB. A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 1999, 151:321-330. 1460451, 9872970.
27. Sewell MM, Davis MF, Tuskan GA, Wheeler NC, Elam CC, Bassoni DI, Neale DB. Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). II. Chemical wood properties. Theor Appl Genet 2002, 104:214-222. 10.1007/s001220100697, 12582689.
28. Chagne D, Brown GR, Lalanne C, Madur D, Pot D, Neale DB, Plomion C. Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 2003, 12:185-195.
29. Siljak-Yakovlev S, Cerbah M, Coulaud J, Stoian V, Brown SC, Zoldos V, Jelenic S, Papes D. Nuclear DNA content, base composition, heterochromatin and rDNA in Picea omorika and Picea abies. Theor Appl Genet 2002, 104:505-512. 10.1007/s001220100755, 12582725.
30. Remington DL, Whetten RW, Liu BH, O'Malley DM. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet 1999, 98:1279-1292. 10.1007/s001220051194, 12238515.
31. Hanley S, Barker A, Van Ooijen W, Aldam C, Harris L, Ahman I, Larsson S, Karp A. A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatellite markers. Theor Appl Genet 2002, 105:1087-1096. 10.1007/s00122-002-0979-0, 12582937.
32. Kinlaw CS, Neale DB. Complex gene families in pine genomes. Trends Plant Sci 1997, 2:356-359.
33. Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O. Comparing EST-based genetic maps between Pinus sylvestris and P. taeda. Theor Appl Genet 2003, 107:667-678. 10.1007/s00122-003-1312-2, 12827250.
34. Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB. Comparative mapping in the Pinaceae. Genetics 2004, 168:447-461. 10.1534/genetics.104.028381, 1448108, 15454556.
35. Scotti I, Burelli A, Cattonaro F, Chagné D, Fuller J, Hedley PE, Jansson G, Lalanne C, Madur D, Neale D, Plomion C, Powell W, Troggio M, Morgante M. Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies Karst). Tree Genet Genom 2005, 1:93-102.
36. Yin TM, Wang XR, Andersson B, Lerceteau-Kohler E. Nearly complete genetic maps of Pinus sylvestris L. (Scots pine) constructed by AFLP marker analysis in a full-sib family. Theor Appl Genet 2003, 106:1075-1083.
37. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Riider MS, Wing RA, Wu W, Young ND. High-density molecular linkage maps of the tomato and potato genomes. Genetics 1992, 132:1141-1160. 1205235, 1360934.
38. Johnsen KH, Flanagan LB, Huber DA, Major JE. Genetic variation in growth and carbon isotope discrimination in Picea mariana: analyses from a half-diallel mating design using field grown trees. Can J For Res 1999, 29:1727-1735.
39. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. AFLP: a new technique for DNA fingerprints. Nucl Acids Res 1995, 23:4407-4414. 10.1093/nar/23.21.4407, 307397, 7501463.
40. Gupta AK, Kang BY, Roy JK, Rajora OP. Large-scale development of selectively amplified polymorphic microsatellite loci (SAMPL) markers in spruce (Picea). Mol Eco Not 2005, 5:481-483.
41. Witsenboer H, Vogel J, Michelmore RW. Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.). Genome 1997, 40:923-936. 10.1139/g97-119, 18464878.
42. Rajora OP, Rahman MH, Dayanandan S, Mosseler A. Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species. Mol Gen Genet 2001, 264:871-882. 10.1007/s004380000377, 11254135.
43. Rajora OP, Mann IK, Shi Y-Z. Genetic diversity and population structure of boreal white spruce (Picea glauca) in pristine conifer-dominated and mixedwood forest stands. Can J Bot 2005, 83:1096-1105.
44. Rozen S, Skaletsky HJ. Primer 3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365-386. Humana Press, Totowa, NJ, USA, Krawetz S, Misener S.
45. Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo testcross mapping strategy and RAPD markers. Genetics 1994, 137:1121-1137. 1206059, 7982566.
46. Van Ooijen JW, Voorrips RE. JOINMAP 3.0, Software for the calculation of genetic linkage maps. 2001, Plant Research International, Wageningen, the Netherlands., http://www.plant.wageningen-ur.nl
47. Kosambi DD. The estimation of map distances from recombination values. Ann Eugen 1944, 12:172-175.
48. Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 2002, 93:77-78. 10.1093/jhered/93.1.77, 12011185.
49. Lange K, Boehnke M. How many polymorphic genes will it take to span the human genome?. Am J Hum Genet 1982, 34:842-845. 1685701, 6960692.
50. Cervera MT, Storme V, Ivens B, Gusmao J, Liu BH, Hostyn V, Slycken JV, Montagu MV, Boerjan W. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 2001, 158:787-809. 1461694, 11404342.