Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics (original) (raw)

Abstract

Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37-61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a "generic" pine map and serving as a foundation for studies on genome organization and evolution.

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Selected References

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  1. Andersson L., Archibald A., Ashburner M., Audun S., Barendse W., Bitgood J., Bottema C., Broad T., Brown S., Burt D. Comparative genome organization of vertebrates. The First International Workshop on Comparative Genome Organization. Mamm Genome. 1996 Oct;7(10):717–734. doi: 10.1007/s003359900222. [DOI] [PubMed] [Google Scholar]
  2. Devey M. E., Delfino-Mix A., Kinloch B. B., Jr, Neale D. B. Random amplified polymorphic DNA markers tightly linked to a gene for resistance to white pine blister rust in sugar pine. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2066–2070. doi: 10.1073/pnas.92.6.2066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Gale M. D., Devos K. M. Comparative genetics in the grasses. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1971–1974. doi: 10.1073/pnas.95.5.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Groover A., Devey M., Fiddler T., Lee J., Megraw R., Mitchel-Olds T., Sherman B., Vujcic S., Williams C., Neale D. Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics. 1994 Dec;138(4):1293–1300. doi: 10.1093/genetics/138.4.1293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kellogg E. A. Relationships of cereal crops and other grasses. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2005–2010. doi: 10.1073/pnas.95.5.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lagercrantz U., Lydiate D. J. Comparative genome mapping in Brassica. Genetics. 1996 Dec;144(4):1903–1910. doi: 10.1093/genetics/144.4.1903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lander E. S., Green P., Abrahamson J., Barlow A., Daly M. J., Lincoln S. E., Newberg L. A., Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987 Oct;1(2):174–181. doi: 10.1016/0888-7543(87)90010-3. [DOI] [PubMed] [Google Scholar]
  8. Lincoln S. E., Lander E. S. Systematic detection of errors in genetic linkage data. Genomics. 1992 Nov;14(3):604–610. doi: 10.1016/s0888-7543(05)80158-2. [DOI] [PubMed] [Google Scholar]
  9. Lyons L. A., Laughlin T. F., Copeland N. G., Jenkins N. A., Womack J. E., O'Brien S. J. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat Genet. 1997 Jan;15(1):47–56. doi: 10.1038/ng0197-47. [DOI] [PubMed] [Google Scholar]
  10. Moore G., Devos K. M., Wang Z., Gale M. D. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995 Jul 1;5(7):737–739. doi: 10.1016/s0960-9822(95)00148-5. [DOI] [PubMed] [Google Scholar]
  11. Remington D. L., Whetten R. W., Liu B. H., O'Malley D. M. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet. 1999 Jun;98(8):1279–1292. doi: 10.1007/s001220051194. [DOI] [PubMed] [Google Scholar]