Vitae
Craig Curriculum Steinbrink Echt
U.S. Forest Service, Southern Research Station, Southern Institute of Forest Genetics 23332 Hwy 67, Saucier, Mississippi 39574 [phone] x210, [e-mail] home: [phone], mobile: [phone], [e-mail]
Academic Qualifications: Ph.D. in Genetics (1982), Biochemistry minor, at Indiana University Bloomington. PHS/NIH Genetics Training Grant Trainee. Dissertation title: An analysis of the Wx locus of maize by examination of the protein products of the waxy alleles. B.A. (1978) Biology major, cum laude, Hiram College, Hiram, Ohio. Professional history: 9 March 2003 present: Research Geneticist with US Forest Service, Southern Research Station, Saucier, Mississippi. Duties: Microsatellite marker development and conservation genetics studies of forest plant species, genome mapping and molecular breeding applications for pines. 1 March 1999 28 February 2003: Project Leader for Applications of Genomic Science Project at Forest Research (now Scion), Rotorua, New Zealand. Duties: Science leadership and administrative management for the Genomics Project; provide genomics solutions for forest tree improvement, management and sustainability. 18 October 1992 13 February 1999: Research Plant Molecular Geneticist with US Forest Service, Rhinelander, Wisconsin. Duties: Principal Investigator of the Genetic Analysis Laboratory, including microsatellite marker development, genome mapping, and population genetics of forest trees. 1 May 1990 31 October 1992: Research Assistant Professor in the Department of Plant & Soil Sciences, Montana State University Bozeman. Duties: RFLP and RAPD marker development, genome mapping, and polyploid genetic analysis in alfalfa. 1 November 1986 29 April 1990: Research Assistant Professor in the Department of Plant Pathology, University of Arizona. Duties: Study of protein expression and disease response in maize disease lesion mutants, RFLP marker development in alfalfa, guest class lecturer. 7 May 1984 30 October 1986: Research Associate in the Department of Agronomy with Dr. M.G. Neuffer, University of Missouri Columbia. Duties: Biochemical studies of disease lesion mimic mutants and photosynthetic mutants in maize.
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9 October 1982 1 May 1984: Post-Doctoral Associate in the Department of Plant Pathology, with Dr. P. Chourey, University of Florida Gainesville. Duties: Biochemical analysis of sucrose synthase isozymes in maize plants and tissue culture. Number of peer-reviewed publications: Number of patents: Professional society membership: AAAS Ecological Society of America Genetics Society of America Positions held in professional organizations: Deputy Coordinator, IUFRO Genetics Division 2.04.00 Summary of research interests: Developing DNA markers for use in molecular breeding and population genetics Genome mapping of pine species Conservation genetics of forest plant species Publications (1) Echt CS, Schwartz D (1981) Evidence for the inclusion of controlling elements within the structural gene at the waxy locus in maize. Genetics 99:275-283 (2) Schwartz D, Echt CS (1982) The effect of Ac dosage on the production of multiple forms of Wx protein by the wx-m9 controlling element mutation in maize. Mol. Gen. Genetics 187:410413 (3) Echt CS, Chourey P (1985) A comparison of sucrose synthetase isozymes from normal and shrunken maize. Plant Physiol. 79:530-536 (4) Echt CS, Polacco M, Neuffer MG (1987) A nuclear encoded chloroplast ATP synthase mutation in maize. Mol. Gen. Genetics 208:230-234 (5) McCoy TJ, Echt CS, Mancino L (1991) Segregation of molecular markers supports an allotetraploid structure for Medicago sativa x M. papillosa interspecific hybrid. Genome 34:574-575 (6) Echt CS, Erdahl L, McCoy TJ (1992) Genetic segregation of random amplified DNA in diploid cultivated alfalfa. Genome 35:84-87 24 2 (US and foreign)
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(7) Baran G, Echt CS, Bureau T, Wessler S (1992) Molecular analysis of the maize wx-B3 allele indicates that precise excision of the transposable Ac element is rare. Genetics 130:377-384 (8) McCoy TJ, Echt CS (1992) Chromosome manipulations and genetic analysis in Medicago. Plant Breeding Reviews 10:169-197 (9) McCoy TJ, Echt CS (1993) Potential of trispecies bridge crosses and RAPD markers for introgression of Medicago daghestanica Rupr. and M. pironae Vis. germplasm into alfalfa (M. sativa ). Genome 36:594-601 (10) Brummer EC, Echt CS, McCoy TJ, Kidwell KK, Osborn TC, Knapp SJ, Liu BH, Kiss GB, Csanadi G, Kalnan K Gyrgyey J, Lkrsz, Raczkevy AE, Bouton JH, Kochert G (1993) Molecular maps of alfalfa. in DNA Based Markers in Plants. eds. I. Vasil and R. Phillips. Kluwers Publ. pp 23-28. (11) Thomas JC, Wassmann CC, Echt CS, Dunn RL, Bohnert HJ, McCoy TJ (1994) Introduction and expression of an insect proteinase inhibitor in transgenic alfalfa (Medicago sativa L.). Plant Cell Reports 14:31-37 (12) Echt CS, Kidwell K, Osborn T, McCoy T (1994) Linkage mapping in diploid alfalfa. Genome 37:61-71 (13) Echt CS (1995) Meeting Report: Second International Symposium on the Applications of Biotechnology to Tree Culture, Protection and Utilization and The 1994 TAPPI R&D Biological Sciences Symposium. Plant Molecular Biology Reporter 13: 56-62. (not refereed) Also published in Dendrome Forest Tree Genome Updates, vol. 2, number 1, pp 5-8. A review of the molecular and genetic aspects of the meeting (not refereed). (14) Echt CS, May-Marquardt P, Hseih M, Zahorchak R (1996) Characterization of microsatellite markers in eastern white pine. Genome 39:1102-1108 (15) Echt CS (1996) Types, Uses and Interpretation of Molecular Markers in Forest Genetics. Proceedings of Forest Tree Genome Workshop, Institute of Forest Genetics, Placerville, CA. July 29-August 1, 1996. (Tech transfer) (16) Wu H, Echt CS, Popp M, Davis J (1997) Molecular cloning, structure and expression of an elicitor-inducible chitinase gene from pine trees. Plant Mol Biol 33:979-987 (17) Echt CS, May-Marquardt P (1997) Survey of microsatellite DNA in pine. Genome 40:9-17. (18) Echt CS, Nelson CD (1997) Linkage mapping and genome length in eastern white pine (Pinus strobus L). Theor Appl Genet 94:1031-1037. (19) Echt CS (1997) Use of molecular genetic markers in forest management. in Communicating the Role of Silviculture in Managing the National Forests, Proceedings of the National Silviculture Workshop. May 19-22 Warren, PA Northeastern Forest Experiment Station. General Technical Report NE-238.
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(20) Echt CS, DeVerno L, Anzidei M, Vendramin GG (1998) Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Molecular Ecology 7:307-316. (21) Lefort F, Echt CS, Streiff R, Vendramin GG (1998) Microsatellite sequences: a new generation of molecular markers for forest genetics. Forest Genetics 6: 5-10. (22) Vendramin GG, Anzidei M, Echt CS, Madaghiele A, Sperisen C, Ziegenhagen B (1998) Chloroplast microsatellite approach for the study of diversity in conifers. In Strategies for Improvement of Forest Tree Species. ed. G.C. Douglas. COFORD, National Council for Forest Research and Development, Dublin. pp 83-92. (23) Echt C (1998) Use of microsatellite markers in management of conifer forest species. In Strategies for Improvement of Forest Tree Species. ed. G.C. Douglas. ISBN 1 902696 02 6, COFORD, National Council for Forest Research and Development, Dublin. pp 75-82. (24) Echt C, Vendramin GG, Nelson CD, May-Marquardt P (1999) Microsatellite DNA as shared genetics markers among conifer species. Can J For Res 29: 365-371. (25) Kumar S, Echt C, Wilcox PL, Richardson TE (2004) Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theor Appl Genet 108: 292-298. (26) Chagn D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio J-M, 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. (27) Pot D, McMillan L , Echt C, Le Provost G, Cato S, Plomion C (2005) Nucleotide diversity of genes involved in wood formation in two pine species. New Phytologist 67: 101-112. (28) Cato S, McMillan L, Donaldson L, Richardson T, Echt C, Gardner R. (2006) Wood formation from the base to the crown in Pinus radiata: gradients of trachied wall thickness, wood density, radial growth rate and gene expression. Plant Molecular Biology 60: 565-581. (29) GP Gill, Wilcox PL, Whittaker D, Winz R, Bickerstaff P, Echt CE, Kent J, Humphreys MO, Elborough KM, Gardner RC (2006) A framework linkage map of perennial ryegrass based on SSR markers. Genome 49: 354-364. (30) Echt CS, Deemer D, Kubisiak T, Nelson CD. (2006) Microsatellites for Lindera species. Molecular Ecology Notes 6: 1171-1173. (31) Wilcox PL, Echt CE, Burdon RD (2007) Gene Assisted Selection: Applications of Association Genetics for Forest Tree Breeding. In: Association Mapping in Plants. Oraguzie NC, Rikkerink EHA, Gardiner SE, Nihal De Silva H. (Eds.) Springer, New York. pp 211-248. (32) Plomion C, Chagn D, Pot D, Kumar S, Wilcox PL, Burdon RD, Prat D, Peterson DG, Paiva J, Chaumeil P, Vendramin GG, Sebastiani F, Nelson CD, Echt CS, Savolainen O, Kubisiak TL, Cervera MT, de Mara N, Islam-Faridi MN (2007) The Pines. In: Genome Mapping and Molecular Breeding in Plants, Vol. 7 Forest Trees, Chitta R. Kole (Ed). Springer-Verlag, Berlin, Heidelberg. pp 29-92.
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(33) Nelson, CD, Josserand S, Echt C,Koppelman J (2006) Loblolly pine SSR Markers for Shortleaf Pine Genetics. In: Kabrick, John M.; Dey, Daniel C.; Gwaze, David, eds. Shortleaf pine restoration and ecology in the Ozarks: proceedings of a symposium; 2006 November 7-9; Springfield, MO. Gen. Tech. Rep. NRS-P-15. Newtown Square, PA: U.S. Department of Agriculture, Forest Service, Northern Research Station: 95-98. (34) Marquardt PE, Echt CS, Epperson BK and Pubanz DM (2007) Genetic structure, diversity, and inbreeding of eastern white pine under different management conditions. Canadian J Forest Research 37: 2652-2662. (35) Josserand SA, Potter KM, Echt CS, and Nelson CD (2008) Isolation and characterization of microsatellite markers for Carolina hemlock (Tsuga caroliniana). Molecular Ecology Resources 8: 1371-1374. Manuscripts under consideration S.A. Cato, D. Pot, L.K. McMillan, E.M. Hingston, P.L. Wilcox, C. Plomion, C. Echt, R.C. Gardner (2008) A 17 million-year-old balanced polymorphism in a dehydrin gene associated with abiotic stress tolerance in Pines. submitted to Molecular Biology and Evolution Patents U.S. Patent No. 6,733,965, Microsatellite DNA Markers and Uses Thereof. Inventors: Craig Echt and C. Dana Nelson. Assigned to USDA and International Paper Co. Issued May 11, 2004. New Zealand Patent No. 512941, Microsatellite DNA Markers and Uses Thereof. Inventors: Craig Echt and C. Dana Nelson. Assigned to USDA and International Paper Co. Issued January 5, 2004. Participation in Technical Conferences and Workshops Session co-chair at the 2004 IUFRO Joint Conference of Population Genetics and Genomics Working Groups: Population, Evolutionary And Ecological Genomics of Forest Trees 13-17 Sept. 2004 at the Asilomar Conference Grounds, Pacific Grove, California. Moderator of the session on Genome Scans, QTL and Association Mapping (Session 5) at the Joint Conference of IUFRO Working Groups 2.04.01 (Population, ecological and conservation genetics) and 2.04.10 (Genomics), along with the Canadian Tree Improvement Association (CTIA) held in Qubec City, August 24-29, 2008. Moderator of session at Forest Tree Genome Mapping at Plant and Animal Genome XII Conference, January 10, 2000 in San Diego, California. Chair of session at Joint Meeting of the IUFRO Working Parties S.04-07 and S.04-06, Somatic Cell Genetics and Molecular Genetics of Trees, (8/12/97) in Qubec City, Canada.
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Workshop presentation at the Forest Tree Genome Workshop, Institute of Forest Genetics, Placerville, California (7/27/97 - 7/30/97). Invited by D.B. Neale to give 8 hr of lectures and lab demonstrations covering basic aspects of molecular markers and their uses in forest genetics. The audience consisted of National Forest geneticists, university professors and international post-docs. Moderator of session on Mapping Genes for Disease Resistance at the Forest Tree Genome Workshop of the Plant Genome II International Conference (1/28/94) in San Diego, California Meeting presentations Echt C (2008) Guidelines for ex Situ Conservation of National Forests Genetic Resources. Invited talk presented at the Regional Geneticists Meeting, RMRS lab, Fort Collins, CO. May 13-14 2008. Echt C, Saha S, Nelson CD (2008) An integrated, annotated microsatellite map for loblolly pine. IUFRO-CTIA Joint Meeting. Adaptation, Breeding and Conservation in the Era of Forest Tree Genomics and Environmental Change. Quebec City, Canada. 25-28 August. Echt C, R Whetten, CD Nelson, Peterson DG, Krutovsky K, Yuceer C, Dean JFD. (2008) A Proposal for New Pine Resources for Mapping and Sequence Assembly. Poster presented at International Plant and Animal Genome XVI. San Diego, California. January 12-16, 2008. P503 Nelson CD, Peterson DG, C Echt, Whetten R, Krutovsky K, Yuceer C, Dean JFD. (2008) Pine Physical Mapping and Genome Sequencing. C Echt, R Whetten, CD Nelson, DG Peterson, K Krutovsky, C Yuceer, JFD Dean. (2008) Poster presented at International Plant and Animal Genome XVI. San Diego, California. January 12-16, 2008. P505 Echt C, Deemer D, Josserand S, Saha S, Nelson CD. (2007) New loblolly pine microsatellite markers for mapping and population genetics. Southern Forest Tree Improvement Conference/Western Forest Genetic Association Joint Meeting: Tree Improvement in North America: Past, Present and Future. June 19-22, 2007, Galveston, Texas. Lstibrek M, Echt C, Nelson CD, El-Kassaby YA, Mullin TJ. (2007) Computer simulation of Marker-Directed Population Improvement. Southern Forest Tree Improvement Conference/Western Forest Genetic Association Joint Meeting: Tree Improvement in North America: Past, Present and Future. June 19-22, 2007, Galveston, Texas. Nelson, CD, Josserand S, Echt C, Koppelman J (2006) Loblolly pine SSR markers for shortleaf pine genetics. Shortleaf Pine Symposium: Restoration and Ecology in the Ozarks. November 7-9 2006, Springfield, Missouri. Koppelman J, Parsons E, Scott B, Collantes J, Eggert LS, Josserand J, Echt C, Nelson CD (2006) Phylogeographic analyses and evaluation of shortleaf pine populations structure in
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Missouri. Shortleaf Pine Symposium: Restoration and Ecology the in Ozarks. November 7-9 2006, Springfield, Missouri. Echt CS, Saha S, Deemer D, Nelson CD (2006) Evaluation of Pine EST-SSR Markers. Forest Tree Workshop, Plant and Animal Genome International Conference XIV, San Diego, 14-18 Jan 2006. (Workshop Abstract W117). Oral presentation by Echt based on work analyzed by Echt. Nelson initiated project, Saha was a student that contributed bioinformatic data and assisted with laboratory evaluations, Deemer was lead technician for generating data. Tefler E, Nelson CD, Echt CS, Wilcox P. (2006) Comparative Mapping in Pinus radiata and P. taeda Reveals Co-Location of Wood Density-Related QTL. Plant and Animal Genome International Conference XIV, San Diego, 14-18 Jan 2006. (Workshop Abstract W118). Oral presentation by Wilcox who also did the analysis. Echt and Nelson contributed markers and data, Teffler was lead technician in New Zealand. Nelson CD, Echt CS, S Surya, Josserand S, Deemer D (2006) Towards a Complete Loblolly Pine Genetic Map for Application in Marker-Directed Population Improvement (MDPI). Invited presentation, IUFRO (Division 2, Unit 2.04.06) Tree Biotechnology 2005 Meeting, November 6-11, 2006, University of Pretoria, Pretoria, South Africa. Nelson CD, Echt CS, Bridgewater FE (2005) Microsatellite DNA Variation within the University/Industry Tree Improvement Cooperatives Loblolly Pine Founder Population. 28th Southern Forest Tree Improvement Conference 20-23 June 2005, Raleigh, North Carolina. (Abstract published in meeting program book.) Nelson gave the oral presentation on the spatial genetic structure of natural stands of loblolly pine. Echt contributed to population genetic data analysis. Bridgewater initiated the Founder Project study. Nelson CD, Echt CS (2006) Role of Genetic Markers in Loblolly Pine Selection and Breeding. Agenda2020 National Meeting, November 7-9 2006, Washington, DC. Saha S, Echt CS, Cordonnier-Pratt MM, Pratt L, Liang C, Chagn D, Plomion C, Peterson DG, Nelson CD. (2004) Development of EST-SSR Markers for Southern Pines. IUFRO Joint Conference of Population Genetics and Genomics Working Groups: Population, Evolutionary And Ecological Genomics of Forest Trees. Asilomar Conference Grounds, Pacific Grove, California. 13-17 Sept. 2004. Poster presented by Echt. McMillan LK, Cato SA, Wilcox PL, Echt CS (2004) Candidate Gene Selection in Pinus radiata - Finding the Needles in the Haystack. Forest Genetics Workshop, Plant and Animal Genome International Conference XII, San Diego, 10-14 Jan 2004. Oral presentation by McMillan; Abstract W84. Wilcox PL, Cato SA, McMillan L, Powers M, Burdon RD, Echt CS. (2004) Patterns of Linkage Disequilibrium in Pinus radiata. Forest Genetics Workshop, Plant and Animal Genome International Conference XII, San Diego, 10-14 Jan 2004. Oral presentation by Wilcox; Abstract W89.
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Echt CS (2002) Wood, a material in evolution. An invited talk at the 8th International Pacific Rim Biotechnology Conference, November 1, 2002 in Auckland, New Zealand. Echt CS (2001) Xylem gene expression, SSR and EST mapping in Pinus radiata. An invited talk at the International Conference on Wood, Breeding, and Biotechnology, June 11-14, 2001 in Bordeaux, France. Echt CS (1999) Forestry Genomics. An invited talk at the 14th Symposium of the Federation of Asian and Oceanian Biochemists and Molecular Biologists, November 28 December 3, 1999 in Dunedin, New Zealand. Echt CS (1998) Use of microsatellite markers in management of conifer forest species. An invited talk at the Symposium of Forest Genetics, March 9, 1998, Trinity College, Dublin, Ireland. Echt CS (1997) Types, uses and interpretation of molecular markers in forest genetics. An invited talk given at the Western Forest Genetics Association Biotechnology Symposium, 4 August 1997, Berkeley, California. Echt CS (1997) Red pine population structuring is evident with chloroplast SSR haplotypes. Joint meeting of the IUFRO Working Parties; Somatic Cell Genetics and Molecular Genetics of Trees. Quebec City, Canada, August 12-16. Oral presentation #58. Echt CS (1997) Use of molecular genetic markers in forest management. In: Communicating the role of silviculture in managing the national forests: Proceedings of the National Silviculture Workshop, 1997 May 19-22; Warren, PA. General Technical Report NE238. Radnor, PA: U.S. Department of Agriculture, Forest Service, Northeast Forest Experiment Station. pp. 134-139. Was also given as an oral presentation. Echt C, Nelson CD, Harry D (1996) PCR-based codominant markers for forest genetics. An invited talk given by Echt at the Scientific Regional Information and Exchange Group (SRIEG) Meeting, Novel Applications of Molecular Markers in Forest Trees: The Next Five Years June 23-26, Houston Texas. Echt C, P May-Marquardt (1996) Use of white pine microsatellite primers in other conifer species. Scientific Regional Information and Exchange Group (SRIEG) Meeting, Novel Applications of Molecular Markers in Forest Trees: The Next Five Years June 23-26, Houston Texas. Poster presentation by Marquardt. Echt C, P May-Marquardt, L DeVerno, CD Nelson (1996) DNA fingerprinting in conifers using inter-SSR PCR. Scientific Regional Information and Exchange Group Meeting, Novel Applications of Molecular Markers in Forest Trees: The Next Five Years June 2326, Houston Texas. Poster presentation by Marquardt.
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Nelson CD, B Crane, P May-Marquardt, CS Echt (1996) Homologous SSR markers and iSSR-PCR fingerprinting in two pine genomes. Plant Genome IV, International Conference on the Status of Plant Genome Research. January 13-19, San Diego, California. Poster abstract #50, pp. 39. Poster presentations by Echt. Marquardt P, C Echt (1995) Simple sequence repeats as genetic markers in gymnosperms. Poster presentation by Echt at the Joint meeting of IUFRO Working Parties in Somatic Cell Genetics and Molecular Genetics, S.04-07, S.04-06, Gent, Belgium. History of recent research activities: Current research: I have derived microsatellite (SSR) markers from enriched genomic libraries and from public EST data. Mapping data for these markers and for previously reported SSR, RFLP and ESTP markers were combined to generate a new loblolly pine consensus map of 462 markers. Of the 234 mapped SSR markers 171 were newly developed, 81 of which were EST-SSRs. I also obtained marker data for an additional 50 new EST-SSR loci that did not segregate in either mapping population and obtained estimates of population gene diversity for 160 SSR loci. I assigned new and previously reported pine EST marker sequences to pine unigenes found in NCBI UniGenes and in DFCI Plant Gene Indices. Gene Ontology (GO) assignments were then made for each EST marker based on the translated protein sequence similarity between the pine unigene and an NCBI curated reference sequence (RefSeq database). Unigene and GO assignments, along with linkage data, aided in identifying duplicated and paralogous marker loci on the map. Sufficient numbers of microsatellite markers are now available for use in loblolly pine population genetic studies and for seed orchard and tree improvement applications. I am a member of a team of a US Forest Service multi-disciplinary team of pondberry (Lindera melissifolia) investigators. As the geneticist on the team I conduct conservation genetic studies of the endangered pondberry. I have found appreciable levels of genetic heterozygosity and genetic spatial structure within and between pondberry stands across the species range. I discovered that colonies of pondberry may be genetically heterogeneous, although the majority of plants growing in colonies are vegetative clones. The presence of unique genotypes within a clonal colony of stems suggests seedling establishment, although other mechanisms have not yet been ruled out. This is significant because there has been no reports of natural regeneration by sexual reproduction for pondberry. I also characterized SSR markers for genetic analysis of pondberry and used them to determined genetic fingerprints of tissue culture propagated pondberry clones. Prior activities, New Zealand: In my last position I managed three major research programs investigating gene-assisted selection, corewood mitigation, and marker development and genome mapping. All research was with radiata pine.
The gene assisted selection (GAS) program was born out of my Projects findings that some
differentially expressed xylem genes appear to be associated with quantitative trait variation for wood density. In its first year my team has designed a powerful association test of 2000 random trees from which we have collected needle tissue for DNA extraction and increment cores for densitometry measurements. The samples were genotyped with microsatellite markers and
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candidate gene SNPs and the data analyzed for linkage disequilibrium, statistically valid associations between sequence variation and trait variation, and quantitative trait nucleotide mapping. I helped formulate a multidisciplinary corewood mitigation program comprised of clonal selection, quantitative trait locus (QTL) mapping and gene discovery. Now in its third year, the team I manage has established a clonally replicated field trial of 280 families (about 5000 trees total), discovered a dozen QTLs for juvenile wood density, and found two genes exhibiting allele-specific expression differences between developing mature and juvenile wood. Upon starting at Forest Research I directed a two year effort that placed 250 microsatellite loci and 30 EST loci on the a comprehensive radiata genome map. Those markers have since been used by the Project to detect about fifteeen new QTLs for juvenile wood density. A subset are being used by collaborators in the Conifer Comparative Genome Project for genome map alignment among Pinus taeda, P. pinaster, and P. radiata, and by several other laboratories in the US and Europe for mapping and population genetics studies. Prior activities, US Forest Service: Population genetic diversity in red pine, Pinus resinosa was first demonstrated by Echt et al. (1997). Variation in paternally inherited chloroplast microsatellites, cpSSRs, was used to study population genetic structure in red pine (Pinus resinosa), a species that is characterized by morphological uniformity, no reported allozyme variation, and limited RAPD variation. From nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were found among 159 individuals surveyed in seven populations dispersed throughout red pines natural range. All populations could be distinguished from each other by their haplotype compositions. Frequency distributions of pairwise SSR length differences among individuals within subpopulations, as well as among all individuals sampled, provided molecular evidence for a metapopulation structure, and for rapid recovery from a major population bottleneck. More extensive sampling of red pine populations is planned (see collaborative research with B Epperson, below.) Because SSR markers are expensive and time consuming to develop, it would be beneficial if common primer pairs could be used among related species, thus reducing marker development costs for individual species. Echt et al. (1999) evaulated SSR primers from P. strobus, P. taeda and P. radiata for marker amplification in other conifer species. In general, P. strobus dinucleotide SSR primers work well in related soft pines, e.g. P. lambertiana and P. cembra, but generally do not amplify informative loci in hard pine species, or in other conifers. Similarly P. radiata dinucleotide SSR primers work well in related hard pine species, but not in soft pines or other conifers. Echt and Nelson (1997) constructed the first genome map of a soft pine species, P. strobus. The 12 pine chromosomes of pine were represented on a haploid genome map having 95 RAPD markers and 5 SSR markers placed in 12 major and several minor linkage groups. Perhaps the most interesting aspect of the study was that previous linkage data for two hard pine species, P. pinaster and P. taeda, were reanalyzed and comparisons made of estimated genome lengths among the three pine species. Virtually identical genome lengths for each species were found, suggesting a conserved rate of recombination among pines. The intended applications of a white pine genome map are genetic analysis of disease resistance traits,
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comparative studies of genome organization among pines, and optimized selection of markers for population genetic studies. Echt and May-Marquardt (1997) did the first comprehensive survey of simple sequence repeat (SSR) frequencies in a gymnosperm species. Of the 47 possible SSR sequence motifs having repeats of 2, 3 and 4 nucleotides, frequency estimates were made for 23 SSR motifs in loblolly pine and 34 SSR motifs in white pine. The two species shared similar frequencies for most SSRs, and also shared similar frequencies with the human genome for a number of trinucleotide motifs. The only large difference observed between the pine species was for the most abundant SSR; (AC)n repeats were twice as abundant in white pine as in loblolly pine. Knowledge of SSR frequencies has been used to decide which SSRs are the most and least worthy of marker development efforts. The development and characterization of the first simple sequence repeat (SSR, or microsatellite DNA) markers for a soft pine species, Pinus strobus, were reported by Echt et al. (1996). The study demonstrated that in white pine SSR markers are highly informative and harbor at least three times as much allelic diversity than isozymes. Other researchers in pine genetics now use the seventeen (AC)n white pine markers.
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References for Craig S. Echt Dr. C. Dana Nelson, Project Leader US Forest Service, Southern Research Station Southern Institute of Forest Genetics 23332 MS Hwy 67 Saucier, Mississppi [phone] x210 [e-mail] Dr. Phil Wilcox Scion Sala Street Rotorua, New Zealand [e-mail] Dr. Tom Richardson, CEO Scion Sala Street Rotorua, New Zealand [e-mail] Dr. David Neale USDA Forest Service Department of Environmental Horticulture University of California - Davis Davis, CA 95616 USA [phone] [e-mail] Dr. Ron Sederoff Forest Biotechnology North Carolina State University Raleigh, North Carolina 27695 USA [phone] [e-mail] Dr. Giovanni Vendramin Forest Tree Breeding Institute/CNR Via Atto Vannucci 13 Florence, Italy 50134 ++39 55 461071 [e-mail]
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