An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

BMC Genetics

Volumn 12, Issue , 2011, Pages

  Echt, Craig S ^a   Saha, Surya ^b,c   Krutovsky, Konstantin V ^d   Wimalanathan, Kokulapalan ^f   Erpelding, John E ^e   Liang, Chun ^f   Nelson, C D ^a  

^a USDA FOREST SERVICE   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

^c Department of Obstetrics Gynecology   (United States)

^d TEXAS A AND M UNIVERSITY   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

^f MIAMI UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA MARKER; MICROSATELLITE DNA; PROTEIN;

ARTICLE; CONTROLLED STUDY; GENE CLUSTER; GENE DUPLICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; LOBLOLLY PINE; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; PEDIGREE; PLANT BREEDING; PLANT GENOME; POPULATION GENETIC STRUCTURE; QUANTITATIVE TRAIT LOCUS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SIMPLE SEQUENCE REPEAT; UNINDEXED SEQUENCE; CHROMOSOME MAP; GENETIC MARKER; GENETICS; GENOTYPE; VARIABLE NUMBER OF TANDEM REPEAT;

PINUS TAEDA;

CHROMOSOME MAPPING; DNA, COMPLEMENTARY; GENETIC LINKAGE; GENETIC MARKERS; GENOTYPE; MINISATELLITE REPEATS; PINUS TAEDA; POLYMORPHISM, GENETIC;

EID: 79251581865     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-12-17     Document Type: Article

References (68)

1. Connor RC, Hartsell AJ. Forest area and conditions. Southern Forest Resource Assessment 2002, 357-402. USDA Forest Service, Wear DN, Gries JG. Asheville, [Southern Research Station General Technical Report, SRS-53].
2. Prestemon JP, Abt RC. Timber products supply and demand. Southern Forest Resource Assessment 2002, 357-402. USDA Forest Service, Wear DN, Gries JG. Asheville, [Southern Research Station General Technical Report, SRS-53].
3. McKeand S, Mullin T, Byram T, White T. Deployment of genetically improved loblolly and slash pine in the South. J Forestry 2003, 101:32-37.
4. Frederick WJ, Lien SJ, Courchene CE, Demartini NA, Ragauskas AJ, Iisa K. Production of ethanol from carbohydrates from loblolly pine: A technical and economic assessment. Bioresource Technol 2008, 99:5051-5057.
5. National Institute of Food and Agriculture, U.S. Department of Agriculture Agriculture and Food Research Initiative Competitive Grants Program. National Loblolly Pine Genome Sequencing (Program Area Code - A6141), Sustainable Bioenergy FY 2010 Request for Applications, Priority Area #5, National Institute of Food and Agriculture, U.S. Department of Agriculture., http://nifa.usda.gov/funding/rfas/pdfs/10_afri_bioenergy.pdf
6. International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project.
7. Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'Connor K, Prabhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: Integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J 2007, 50:1063-1078. 10.1111/j.1365-313X.2007.03112.x, 17488239.
8. Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: From genomes to interaction networks. Nat Rev Genet 2007, 8:699-710. 10.1038/nrg2144, 2811081, 17703239.
9. Devey ME, Fiddler TA, Liu B-H, Knapp SJ, Neale DB. An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 1994, 88:273-278.
10. Remington DL, Whetten RW, Liu B-H, O'Malley DM. Construction of an AFLP genetic map with nearly complete genome coverage in Pinustaeda. Theor Appl Genet 1999, 98:1279-1292. 10.1007/s001220051194, 12238515.
11. 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.
12. Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC, Megraw RA, Davis MF, Sewell MM, Tuskan GA, Neale DB. Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L). III. QTL verification and candidate gene mapping. Genetics 2003, 164:1537-1546. 1462646, 12930758.
13. Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB. Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 2001, 102:664-675.
14. Brown GR, Kadel EE, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB. Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 2001, 159:799-809. 1461821, 11606554.
15. Zhou Y, Gwaze DP, Reyes-Valdés MH, Bui T, Williams CG. No clustering for linkage map based on low-copy and undermethylated microsatellites. Genome 2003, 46:809-816. 10.1139/g03-062, 14608397.
16. Eckert AJ, Pande B, Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genom 2009, 5:225-234.
17. Islam-Faridi MN, Nelson CD, Kubisiak TL. Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L). Genome 2007, 50:241-251. 10.1139/G06-153, 17546089.
18. Chagné 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.
19. Komulainen P, Brown GR, Mikkonen M, Karhu A. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 2003, 107:667-678. 10.1007/s00122-003-1312-2, 12827250.
20. 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.
21. Pelgas B, Bousquest J, Beauseigle S, Isabel N. A composite linkage map form 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.
22. Pelgas B, Beauseigle S, Acheré V, Jeandroz S, Bousquest 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.
23. Neale DB, Krutovsky KV. Comparative genetic mapping in trees: The group of conifers in biotechnology in agriculture and forestry. In: Molecular Marker Systems 2004, 267-277. Lörz H, Wenzel G. Berlin: Springer-Verlag.
24. Ritland K, Krutovsky K, Tsumura Y, Pelgas B, Isabel N, Bousquet J. Genetic mapping in conifers. In:Genetics, Genomics and Breeding of Conifers 2011, 196-238. CRC Press Science Publishers, Plomion C, Bousquet J, Kole C. Enfield.
25. Krutovsky KV, Elsik CG, Matvienko M, Kozik A, Neale DB. Conserved ortholog sets in forest trees. Tree Genetics and Genomes 2006, 3:61-70.
26. Liewlaksaneeyanawin C, Zhuang J, Tang M, Farzaneh N, Lueng GL, Cullis C, Findlay S, Ritland CE, Bohlmann J, Ritland K. Identification of COS markers in the Pinaceae. Tree Genet Genom 2009, 5:247-255.
27. Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara MA, Cervera MT, Vendramin GG, García V, Frigerio JM, Echt C, Richardson T, Plomion C. Cross species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 2004, 109:1204-1214.
28. Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K. Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 2004, 109:361-369. 10.1007/s00122-004-1635-7, 15045175.
29. Auckland LD, Bui T, Zhou Y, Williams CG. Conifer microsatellite handbook. 2002, Raleigh Corporate Press.
30. Elsik CG, Minihan VT, Hall SE, Scarpa AM, Williams CG. Low-copy microsatellite markers for Pinus taeda L. Genome 2000, 43:550-555. 10.1139/gen-43-3-550, 10902720.
31. Elsik CG, Williams CG. Low-copy microsatellite recovery from a conifer genome. Theor Appl Genet 2001, 103:1189-1195.
32. Devey ME, Sewell MM, Uren TL, Neale DB. Comparative mapping in loblolly and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 1999, 99:656-662.
33. Zhuo D, Zhao WD, Wright FA, Yang H-Y, Wang J-P, Sears R, Baer T, Kwon D-H, Gordon D, Gibbs S, Dai D, Yang Q, Spitzner J, Krahe R, Stredney D, Stutz A, Yuan B. Assembly, annotation, and integration of UNIGENE clusters into the human genome draft. Genome Res 2001, 11:904-918. 10.1101/gr.GR-1645R, 311045, 11337484.
34. PineMap database on ConiferGDB. , http://www.conifergdb.org/pinemap/
35. Pine Genome Initiative. , http://pinegenomeinitiative.org/
36. Conifer Genome Database (ConiferGDB). , http://www.conifergdb.org/
37. Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM. A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). Plant Cell 2008, 20:2931-2945. 10.1105/tpc.108.059808, 2613673, 19017747.
38. ConiferEST Build 2.0 database. , http://www.conifergdb.org/coniferest/index.php
39. Liang C, Liu Y, Li L, Davis AC, Shen Y, Li QQ. ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics 2008, 179:83-93. 10.1534/genetics.107.085605, 2390652, 18493042.
40. Kutil BL, Williams CG. Triplet-repeat microsatellites shared among hard and soft pines. J Hered 2001, 97:327-332.
41. Kinlaw CS, Neale DB. Complex gene families in pine genomes. Trends Plant Sci 1997, 2:356-359.
42. Ostrander EA, Jong PM, Rine J, Duyk G. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Nat Acad Sci, USA 1992, 89:3419-3423.
43. Echt CS, May-Marquardt P, Hseih M, Zahorchak R. Characterization of microsatellite markers in eastern white pine. Genome 1996, 39:1102-1108. 10.1139/g96-138, 8983182.
44. University of Georgia Laboratory of Genomics and Bioinformatics Pine Project. , http://fungen.org/Projects/Pine/Pine.htm
45. INRA Pinus pinaster SSR database. , http://www.pierroton.inra.fr/genetics/SSR/index.php
46. Gramene SSRIT - Simple Sequence Repeat Identification Tool. , http://www.gramene.org/db/searches/ssrtool
47. You FM, Huo N, Gu YQ, Luo M-, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008, 9:253. 10.1186/1471-2105-9-253, 2438325, 18510760.
48. Jin L, Zhong Y, Chakraborty R. The exact numbers of possible microsatellite motifs. Am J Hum Genet 1994, 55:582-583. 1918418, 8079998.
49. Echt CS, May-Marquardt P. Survey of microsatellite DNA in pine. Genome 1997, 40:9-17. 10.1139/g97-002, 9061909.
50. Resnick R, Stein LD. STS_Pipeline1.2. 1995, Broad Institute, Cambridge., http://www.broadinstitute.org/ftp/distribution/software/STS_Pipeline1.2/
51. Peakall R, Smouse PE. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molec Ecol Notes 2006, 6:288-295.
52. Brownstein MJ, Carpten JD, Smith JR. Modulation of non-templated nucleotide addition by Taq DNA polymerase: Primer modifications that facilitate genotyping. BioTechniques 1996, 20:1004-1010.
53. Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nature Biotech 2000, 18:233-234.
54. Cato SA, Gardner RC, Kent J, Richardson TE. A rapid PCR-based method for genetically mapping ESTs. Theor Appl Genet 2001, 102:296-306.
55. Groover A, Devey M, Fiddler T, Lee J, Degraw R, Mitchel-Olds T, Sherman B, Vucic S, Williams C, Neale D. Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 1994, 138:1293-1300. 1206264, 7896107.
56. Stam P. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. The Plant Journal 1993, 3:739-744.
57. Van Ooijen JW, Voorrips RE. JoinMap 3.0, software for the calculation of genetic linkage maps. 2001, Plant Research International, Wageningen., http://www.kyazma.nl/
58. Hackett CA, Broadfoot LB. Effects of genotyping errors, missing values and segregation distortion molecular marker data on the construction of linkage maps. Heredity 2003, 90:33-38. 10.1038/sj.hdy.6800173, 12522423.
59. 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.
60. Chakravarti A, Lasher L, Reefer J. A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 1991, 128:175-182. 1204446, 2060775.
61. Lange K, Boehnke M. How many polymorphic genes will it take to span the human genome?. A J Hum Genet 1982, 34:842-845.
62. Massey FJ. The Kolmogorov-Smirnov test for goodness of fit. J Am Stat Assoc 1951, 46:68-78.
63. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2006, 34:D173-180. 10.1093/nar/gkj158, 1347520, 16381840., http://www.ncbi.nlm.nih.gov/unigene/
64. Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33:D501-D504. 10.1093/nar/gki025, 539979, 15608248.
65. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: Tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651., http://www.geneontology.org/index.shtml
66. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO H. Web Presence Working Group AmiGO: online access to ontology and annotation data. Bioinformatics 2009, 25:288-289. 10.1093/bioinformatics/btn615, 2639003, 19033274.
67. Wegrzyn JL, Lee JM, Tearse BR, Neale DB. TreeGenes: A forest tree genome database. International J Plant Genomes 2008 2008, Article ID 412875., http://dendrome.ucdavis.edu/treegenes/
68. Youens-Clark K, Faga B, Yap IV, Stein L, Ware D. CMap 1.01: A comparative mapping application for the Internet. Bioinformatics 2009, 25:3040-3042. 10.1093/bioinformatics/btp458, 2773250, 19648141.