@article{morris_scott_chang_sederoff_d o'malley_kadla_2004, title={Metabolic profiling: A new tool in the study of wood formation}, volume={52}, ISSN={["1520-5118"]}, DOI={10.1021/jf034688l}, abstractNote={In the realm of plant genomics, metabolic profiling has become a valuable tool with which to assess the effect of genetic and/or environmental factors on plant development. This paper reports the first application of metabolic profiling on differentiating xylem tissue of loblolly pine. A protocol is presented for the analysis of loblolly pine xylem tissue. The effects of sample preparation, extraction, and derivatization on the corresponding metabolite profiles and yields have been investigated and are reported. Gas chromatography-mass spectroscopy has been used to quantify >60 polar and lipophilic metabolites from wood-forming tissue. It was possible to assign chemical structures to approximately half of these compounds. Comparison of six loblolly pine genotypes, three high cellulose (50-52%) and three medium (45-48%) cellulose, showed distinct metabolic profiles. Principal component analysis enabled the assignment of metabolic phenotypes using these large data sets. Metabolic phenotype clustering occurred in which the three high-cellulose genotypes were segregated from the medium-cellulose genotypes. These results demonstrate the use of metabolic profiling for the study of wood-forming tissue and as a tool in functional genomics.}, number={6}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={Morris, CR and Scott, JT and Chang, HM and Sederoff, RR and D O'Malley and Kadla, JF}, year={2004}, month={Mar}, pages={1427–1434} }
 @article{wu_grissom_mckeand_o'malley_2004, title={Phenotypic plasticity of fine roots increases plant productivity in pine seedlings}, volume={4}, journal={BMC Ecology}, author={Wu, R. and Grissom, J. E. and McKeand, S. E. and O'Malley, D. M.}, year={2004}, pages={14} }
 @article{stasolla_scott_egertsdotter_kadla_d o'malley_sederoff_zyl_2003, title={Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient Pinus taeda cultured cells}, volume={41}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(03)00051-2}, abstractNote={Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.}, number={5}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Stasolla, C and Scott, J and Egertsdotter, U and Kadla, J and D O'Malley and Sederoff, R and Zyl, L}, year={2003}, month={May}, pages={439–445} }
 @article{komulainen_brown_mikkonen_karhu_garcia-gil_d o'malley_lee_neale_savolainen_2003, title={Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda}, volume={107}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-003-1312-2}, abstractNote={A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F(1) progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Komulainen, P and Brown, GR and Mikkonen, M and Karhu, A and Garcia-Gil, MR and D O'Malley and Lee, B and Neale, DB and Savolainen, O}, year={2003}, month={Aug}, pages={667–678} }
 @article{dimmel_mackay_courchene_kadla_scott_dm o'malley_mckeand_2002, title={Pulping and bleaching of partially CAD-deficient wood}, volume={22}, ISSN={["0277-3813"]}, DOI={10.1081/WCT-120016260}, abstractNote={ABSTRACT Mutant loblolly pine trees that are partially deficient in cinnamyl alcohol dehydrogenase (CAD) have been studied as a possible new source of pulpwood. Young (4- and 6-year-old) partially CAD-deficient pine trees are ˜20% more easily delignified (pulping and bleaching) and provide similar pulp yields to that of similarly aged normal pines grown on the same plots. Bleached pulp from a 6-year-old partially CAD-deficient pine tree displayed better strength properties than the same age normal pine tree; this probably reflects the milder pulping conditions needed in the case of the partially CAD-deficient tree. Studies also were conducted on a limited number of 14-year-old trees from a different genetic background. In contrast to the results with young trees, no real differences in ease of delignification, pulp yields, bleached pulp strength properties, and wood specific gravities were observed with the 14-year-old trees. There would likely be no penalty if partially CAD-deficient trees were used for lumber products. The rapid growth of partially CAD-deficient trees could make them a valuable pulpwood.}, number={4}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Dimmel, DR and MacKay, JJ and Courchene, CE and Kadla, JF and Scott, JT and DM O'Malley and McKeand, SE}, year={2002}, pages={235–248} }
 @inproceedings{o'malley_scott_harkins_kadia_mckeand_chang_2001, title={Cinnamyl alcohol dehydrogenase (cad) and genomic approaches to manipulating wood properties in loblolly pine}, booktitle={7th Brazilian Symposium on the Chemistry of Lignins and Other Wood Components}, author={O'Malley, D. and Scott, J. and Harkins, D. and Kadia, J. and McKeand, S. and Chang, H-M}, year={2001}, pages={19–24} }
 @article{ralph_lapierre_marita_kim_lu_hatfield_ralph_chapple_franke_hemm_et al._2001, title={Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR}, volume={57}, ISSN={["0031-9422"]}, DOI={10.1016/S0031-9422(01)00109-1}, abstractNote={Studying lignin-biosynthetic-pathway mutants and transgenics provides insights into plant responses to perturbations of the lignification system, and enhances our understanding of normal lignification. When enzymes late in the pathway are downregulated, significant changes in the composition and structure of lignin may result. NMR spectroscopy provides powerful diagnostic tools for elucidating structures in the difficult lignin polymer, hinting at the chemical and biochemical changes that have occurred. COMT (caffeic acid O-methyl transferase) downregulation in poplar results in the incorporation of 5-hydroxyconiferyl alcohol into lignins via typical radical coupling reactions, but post-coupling quinone methide internal trapping reactions produce novel benzodioxane units in the lignin. CAD (cinnamyl alcohol dehydrogenase) downregulation results in the incorporation of the hydroxycinnamyl aldehyde monolignol precursors intimately into the polymer. Sinapyl aldehyde cross-couples 8-O-4 with both guaiacyl and syringyl units in the growing polymer, whereas coniferyl aldehyde cross-couples 8-O-4 only with syringyl units, reflecting simple chemical cross-coupling propensities. The incorporation of hydroxycinnamyl aldehyde and 5-hydroxyconiferyl alcohol monomers indicates that these monolignol intermediates are secreted to the cell wall for lignification. The recognition that novel units can incorporate into lignins portends significantly expanded opportunities for engineering the composition and consequent properties of lignin for improved utilization of valuable plant resources.}, number={6}, journal={PHYTOCHEMISTRY}, author={Ralph, J and Lapierre, C and Marita, JM and Kim, H and Lu, FC and Hatfield, RD and Ralph, S and Chapple, C and Franke, R and Hemm, MR and et al.}, year={2001}, month={Jul}, pages={993–1003} }
 @article{myburg_remington_dm o'malley_sederoff_whetten_2001, title={High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer}, volume={30}, ISSN={["0736-6205"]}, DOI={10.2144/01302tt04}, abstractNote={ Amplified fragment length polymorphism (AFLP) analysis is currently the most powerful and efficient technique for the generation of large numbers of anonymous DNA markers in plant and animal genomes. We have developed a protocol for high-throughput AFLP analysis that allows up to 70 000 polymorphic marker genotype determinations per week on a single automated DNA sequencer. This throughput is based on multiplexed PCR amplification of AFLP fragments using two different infrared dyelabeled primer combinations. The multiplexed AFLPs are resolved on a two-dye, model 4200 LI-COR® automated DNA sequencer, and the digital images are scored using semi-automated scoring software specifically designed for complex AFLP banding patterns (AFLP-Quantar™). Throughput is enhanced by using high-quality genomic DNA templates obtained by a 96-well DNA isolation procedure. }, number={2}, journal={BIOTECHNIQUES}, author={Myburg, AA and Remington, DL and DM O'Malley and Sederoff, RR and Whetten, RW}, year={2001}, month={Feb}, pages={348-+} }
 @article{lambeth_lee_d o'malley_wheeler_2001, title={Polymix breeding with parental analysis of progeny: an alternative to full-sib breeding and testing}, volume={103}, ISSN={["0040-5752"]}, DOI={10.1007/s001220100627}, number={6-7}, journal={THEORETICAL AND APPLIED GENETICS}, author={Lambeth, C and Lee, BC and D O'Malley and Wheeler, N}, year={2001}, month={Nov}, pages={930–943} }
 @article{highsmith_frampton_d o'malley_richmond_webb_2001, title={Susceptibility of parent and interspecific F1 hybrid pine trees to tip moth damage in a coastal North Carolina planting}, volume={31}, ISSN={["0045-5067"]}, DOI={10.1139/cjfr-31-5-919}, number={5}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={Highsmith, MT and Frampton, J and D O'Malley and Richmond, J and Webb, M}, year={2001}, month={May}, pages={919–923} }
 @article{retzlaff_handest_dm o'malley_mckeand_topa_2001, title={Whole-tree biomass and carbon allocation of juvenile trees of loblolly pine (Pinus taeda): influence of genetics and fertilization}, volume={31}, ISSN={["1208-6037"]}, DOI={10.1139/x01-017}, abstractNote={To assess the contribution of belowground biomass allocation towards total carbon (C) allocation of two provenances of loblolly pine (Pinus taeda L.), we examined the total biomass allocation of a fast- and slow-growing family from each provenance. Since planting on a xeric, infertile site in Scotland County, N.C., U.S.A., trees in this study have been subjected to one of two nutrient treatments: optimal nutrition or control (no fertilization). Total biomass of 24 (1 tree/family plot × 2 families × 2 provenances × 2 treatments × 3 blocks) 5-year-old (juvenile) trees was harvested in January 1998. Fertilization increased total root, total shoot, and total tree biomass in all families as compared with harvested trees in control plots. Fertilization also increased biomass of coarse-root, woody-root, taproot, stem, branch, and foliar components of families as compared with trees in control plots. Although there were treatment and family differences in standing-crop biomass of the total root, total shoot, total tree, and various individual root and shoot components, the percent biomass (whole-tree) allocation to these tissues remained similar across treatments. Total nonstructural carbohydrate (TNC) analysis indicated some treatment, family, and provenance differences in TNC concentrations and partitioning to starch and soluble sugars. At the time of harvest, TNC concentrations of belowground tissues were much higher than those of aboveground tissues, and enhanced partitioning towards starch in root tissues indicates an important C storage role for belowground tissues at this time. Indeed, more than 90% of the trees starch content was present in root tissue in January. Although constrained by a sample size of three harvested trees per family, this study suggests that biomass allocation on a whole-tree level was similar between fast- and slow-growing families of different provenances of juvenile loblolly pine and was not affected by fertilizer treatment.}, number={6}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Retzlaff, WA and Handest, JA and DM O'Malley and McKeand, SE and Topa, MA}, year={2001}, month={Jun}, pages={960–970} }
 @article{remington_o'malley_2000, title={Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda}, volume={54}, number={5}, journal={Evolution}, author={Remington, D. L. and O'Malley, D. M.}, year={2000}, pages={1580–1589} }
 @article{clark_wentworth_dm o'malley_2000, title={Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae)}, volume={87}, ISSN={["1537-2197"]}, DOI={10.2307/2656885}, abstractNote={Development of conservation strategies for Fraser fir (Abies fraseri) in the southern Appalachian Mountains depends in part on recognition of the extent to which Fraser fir is genetically distinct from the closely related balsam (A. balsamea) and intermediate (A. balsamea var. phanerolepis) fir. These sibling species have exhibited intergrading, clinal variation in morphological, chemical, and genetic characteristics in prior research. Chloroplast microsatellite markers were polymerase chain reaction amplified from genomic DNA samples of 78 individuals representing the geographic ranges of Fraser, balsam, and intermediate fir. Gene diversity levels at two loci ranged among taxa from 0.65 to 0.84. Allele frequencies demonstrated significant differentiation among taxa, with RST values of 0.36 and 0.10. Haplotype diversity and D2SH were highest for balsam fir and lowest for intermediate fir. A haplotype network analysis based on allele size distribution for the two loci revealed two distinct clusters of haplotypes and population‐specific haplotypes. Ninety‐two percent of the haplotypes in one cluster were from balsam fir and intermediate fir, and 84% of the haplotypes in the other cluster were from Fraser fir and intermediate fir. The genetic differentiation of chloroplast DNA markers provides justification for the recognition of Fraser fir as a distinct Management Unit (MU) for conservation purposes, regardless of its taxonomic classification.}, number={6}, journal={AMERICAN JOURNAL OF BOTANY}, author={Clark, CM and Wentworth, TR and DM O'Malley}, year={2000}, month={Jun}, pages={774–782} }
 @misc{o'malley_sederoff_grattapaglia_2000, title={Methods for within family selection in woody perennials using genetic markers}, volume={6,054,634}, number={2000 Apr. 25}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={O'Malley, D. M. and Sederoff, R. R. and Grattapaglia, D.}, year={2000} }
 @article{mckeand_grissom_handest_o'malley_allen_2000, title={Responsiveness of diverse provenances of loblolly pine to fertilization - age 4 results}, volume={10}, DOI={10.1300/j091v10n01_10}, journal={Journal of Sustainable Forestry}, author={McKeand, Steven and Grissom, J. E. and Handest, J. A. and O'Malley, D. M. and Allen, H. L.}, year={2000}, pages={87–94} }
 @article{wu_grissom_o'malley_mckeand_2000, title={Root architectural plasticity to nutrient stress in two contrasting ecotypes of loblolly pine}, volume={10}, ISBN={1054-9811}, DOI={10.1300/j091v10n03_13}, number={3}, journal={Journal of Sustainable Forestry}, author={Wu, R. L. and Grissom, J. E. and O'Malley, D. M. and McKeand, Steven}, year={2000}, pages={307} }
 @article{rongling_zeng_mckeand_o'malley_2000, title={The case for molecular mapping in forest tree breeding}, volume={19}, number={2000}, journal={Plant Breeding Reviews}, author={Rongling, W. and Zeng, Z.-B. and McKeand and O'Malley, D. M.}, year={2000}, pages={41–68} }
 @article{remington_o'malley_2000, title={Whole-genome characterization of embryonic stage inbreeding depression in a selfed loblolly pine family}, volume={155}, number={1}, journal={Genetics}, author={Remington, D.L. and O'Malley, D.M.}, year={2000}, pages={337–348} }
 @article{wu_remington_mackay_mckeand_dm o'malley_1999, title={Average effect of a mutation in lignin biosynthesis in loblolly pine}, volume={99}, ISSN={["0040-5752"]}, DOI={10.1007/s001220051287}, abstractNote={Cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) is a monolignol biosynthetic enzyme that catalyzes the final step of lignin subunit biosynthesis in higher plants. Recently, a mutant allele of the cad gene, cad-n1, encoding for the CAD enzyme, was discovered in loblolly pine. By reducing the expression of the cad gene, this mutant has a decreased lignin content and major changes in the lignin composition in wood. In this study, we found that the substitution of a wild-type allele by cad-n1 was associated with a significant effect on 2nd-year shoot elongation in a half-sib family of loblolly pine (designated family 7-1037). The average effect of cad-n1 appeared to increase with tree growth and was greater for stem radial growth than height growth. An increase of 14.1% in de-barked volume in year 4 was associated with cad-n1. Co-segregation analysis indicated that the cad locus itself might represent a gene that governs stem growth in pine. The significance of the mutation cad-n1 for tree growth and wood processing is discussed.}, number={3-4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Wu, RL and Remington, DL and MacKay, JJ and McKeand, SE and DM O'Malley}, year={1999}, month={Aug}, pages={705–710} }
 @article{remington_whetten_liu_dm o'malley_1999, title={Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda}, volume={98}, ISSN={["0040-5752"]}, DOI={10.1007/s001220051194}, abstractNote={De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Remington, DL and Whetten, RW and Liu, BH and DM O'Malley}, year={1999}, month={Jun}, pages={1279–1292} }
 @article{marques_vasquez-kool_carocha_ferreira_dm o'malley_liu_sederoff_1999, title={Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E-globulus}, volume={99}, ISSN={["1432-2242"]}, DOI={10.1007/s001220051400}, number={6}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Vasquez-Kool, J and Carocha, VJ and Ferreira, JG and DM O'Malley and Liu, BH and Sederoff, R}, year={1999}, month={Oct}, pages={936–946} }
 @misc{amerson_wilcox_sederoff_kuhlman_o'malley_grattapaglia_1999, title={Methods for within family selection of disease resistance in woody perennials using genetic markers}, volume={5,908,978}, number={1999 June 1}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Amerson, H. V. and Wilcox, P. and Sederoff, R. R. and Kuhlman, E. G. and O'Malley, D. M. and Grattapaglia, D.}, year={1999} }
 @article{mackay_presnell_jameel_taneda_d o'malley_sederoff_1999, title={Modified lignin and delignification with a CAD-deficient loblolly pine}, volume={53}, ISSN={["0018-3830"]}, DOI={10.1515/HF.1999.067}, abstractNote={Summary}, number={4}, journal={HOLZFORSCHUNG}, author={MacKay, J and Presnell, T and Jameel, H and Taneda, H and D O'Malley and Sederoff, R}, year={1999}, pages={403–410} }
 @article{wu_dm o'malley_mckeand_1999, title={Understanding the genetic architecture of a quantitative trait in gymnosperms by genotyping haploid megagametophytes}, volume={99}, ISSN={["0040-5752"]}, DOI={10.1007/s001220051411}, number={6}, journal={THEORETICAL AND APPLIED GENETICS}, author={Wu, RL and DM O'Malley and McKeand, SE}, year={1999}, month={Oct}, pages={1031–1038} }
 @article{marques_araujo_ferreira_whetten_dm o'malley_liu_sederoff_1998, title={AFLP genetic maps of Eucalyptus globulus and E-tereticornis}, volume={96}, ISSN={["1432-2242"]}, DOI={10.1007/s001220050795}, number={6-7}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Araujo, JA and Ferreira, JG and Whetten, R and DM O'Malley and Liu, BH and Sederoff, R}, year={1998}, month={May}, pages={727–737} }
 @misc{mackay_o'malley_whetten_sederoff_1998, title={Method of altering lignin in trees}, volume={5,824,842}, number={1998 Oct. 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={MacKay, J. and O'Malley, D. and Whetten, R. and Sederoff, R.}, year={1998} }
 @article{wu_dm o'malley_1998, title={Nonlinear genotypic response to macro- and microenvironments}, volume={96}, ISSN={["1432-2242"]}, DOI={10.1007/s001220050787}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Wu, RL and DM O'Malley}, year={1998}, month={Apr}, pages={669–675} }
 @article{ralph_mackay_hatfield_omalley_whetten_sederoff_1997, title={Abnormal lignin in a loblolly pine mutant}, volume={277}, ISSN={["1095-9203"]}, DOI={10.1126/science.277.5323.235}, abstractNote={
            Novel lignin is formed in a mutant loblolly pine (
            Pinus taeda
            L.) severely depleted in cinnamyl alcohol dehydrogenase (E.C. 1.1.1.195), which converts coniferaldehyde to coniferyl alcohol, the primary lignin precursor in pines. Dihydroconiferyl alcohol, a monomer not normally associated with the lignin biosynthetic pathway, is the major component of the mutant's lignin, accounting for ∼30 percent (versus ∼3 percent in normal pine) of the units. The level of aldehydes, including new 2-methoxybenzaldehydes, is also increased. The mutant pines grew normally indicating that, even within a species, extensive variations in lignin composition need not disrupt the essential functions of lignin.
          }, number={5323}, journal={SCIENCE}, author={Ralph, J and MacKay, JJ and Hatfield, RD and OMalley, DM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={235–239} }
 @inproceedings{mckeand_grissom_o'malley_allen_1997, title={Early growth response of diverse families of loblolly pine to nutrient amendments on a poor site}, booktitle={Proceedings of the 24th Southern Forest Tree Improvement Conference}, author={McKeand, S. E. and Grissom, J. E. and O'Malley, D. M. and Allen, H. L.}, year={1997}, pages={267–274} }
 @article{mackay_omalley_presnell_booker_campbell_whetten_sederoff_1997, title={Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={94}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.94.15.8255}, abstractNote={
            We have discovered a mutant loblolly pine (
            Pinus taeda
            L.) in which expression of the gene encoding cinnamyl alcohol dehydrogenase (CAD; EC
            1.1.1.195
            ) is severely reduced. The products of CAD, cinnamyl alcohols, are the precursors of lignin, a major cell wall polymer of plant vascular tissues. Lignin composition in this mutant shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lignin composition in pine. The recessive
            cad-n1
            allele, which causes this phenotype, was discovered in a tree heterozygous for this mutant allele. It is inherited as a simple Mendelian locus that maps to the same genomic region as the
            cad
            locus. In mutant plants, CAD activity and abundance of
            cad
            RNA transcript are low, and free CAD substrate accumulates to a high level. The wood of the mutant is brown, whereas the wood in wild types is nearly white. The wood phenotype resembles that of brown midrib (
            bm
            ) mutants and some transgenic plants in which xylem is red-brown due to a reduction in CAD activity. However, unlike transgenics with reduced CAD, the pine mutant has decreased lignin content. Wood in which the composition of lignin varies beyond previous expectations still provides vascular function and mechanical support.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={MacKay, JJ and OMalley, DM and Presnell, T and Booker, FL and Campbell, MM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={8255–8260} }
 @inbook{o'malley_whetten_1997, title={Molecular markers and forest trees}, booktitle={DNA markers: Protocols, applications, and overviews}, publisher={New York: Wiley-VCH}, author={O'Malley, D. M. and Whetten, R.}, editor={G. Caetano-Anolles, P. M. GresshoffEditor}, year={1997}, pages={237–257} }
 @inproceedings{o'malley_grattapaglia_chaparro_wilcox_amerson_liu_whetten_mckeand_kuhlman_mccord_et al._1996, title={Molecular markers,  forest genetics, and tree breeding}, DOI={10.1007/978-1-4899-0280-1_7}, abstractNote={Several years ago, Strauss et al. (1992) thoughtfully evaluated the application of molecular markers in forest tree breeding for marker aided selection. The purpose of their paper was to emphasize the limitations and shortcomings of marker-aided selection particularly in conifers. They argued that studies of quantitative trait loci identified in agronomic crops, which have significant utility (e.g. Stuber, 1992; Stuber et al., 1992), are of little relevance to assessing the potential for marker aided selection in populations of forest trees, and that the near term usefulness of molecular markers for forest tree breeding will be limited. The major barriers to application included cost, the lack of association of markers with traits across breeding populations due to linkage equilibrium, variation in expression of loci affecting quantitative traits due to differences in genetic background, genotype environment interactions, and stability of marker-trait associations over multiple generations. In addition, Strauss et al. (1992) noted that marker-aided selection would be most useful for within family selection, where the economic values of the traits are high, the trait heritabilities are low, and where markers are able to explain much of the genetic variance. However, they argued that important traits in forest trees such as wood volume, are likely to be controlled by large numbers of genes with small effects, and therefore, are unlikely to have useful marker trait associations.}, booktitle={Genomes of Plants and Animals: 21 Stadler Genetics Symposium}, publisher={Plenum Press,  NY}, author={O'Malley, D. M. and Grattapaglia, D. and Chaparro, J. X. and Wilcox, P. L. and Amerson, H. V. and Liu, B-H and Whetten, R. and McKeand, Steven and Kuhlman, E. G. and McCord, S. and et al.}, editor={Gustafson, J. P. and Flavell, R. B.Editors}, year={1996}, pages={87–102} }
 @inproceedings{crane_o'malley_mckeand_sederoff_1995, title={Detection of QTLs for economically important traits in loblolly pine}, booktitle={Proceedings of the 23rd Southern Forest Tree Improvement Conference}, author={Crane, B. S. and O'Malley, D. M. and McKeand, S. E. and Sederoff, R. R.}, year={1995}, pages={119} }
 @article{o'malley_mckeand_1994, title={Marker assisted selection for breeding value in forest trees}, volume={1}, journal={Forest Genetics}, author={O'Malley, D. M. and McKeand, S. E.}, year={1994}, pages={231–242} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_crane_amerson_werner_liu_o'malley_whetten_et al._1993, title={Application of genetic markers to tree breeding}, booktitle={Proceedings of the 22nd Southern Forest Tree Improvement Conference}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Crane, B. and Amerson, H. and Werner, D. and Liu, B. H. and O'Malley, D. and Whetten, R. and et al.}, year={1993}, pages={452–463} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_werner_amerson_mckeand_bridgwater_whetten_o'malley_et al._1992, title={Mapping in woody plants with RAPD markers: application to breeding in forestry and horticulture}, booktitle={Proceedings of the Symposium on the Applications of RAPD Technology to Plant Breeding}, publisher={Joint Plant Breeding Symposium Series,  Crop Science Society of America, American Society for Horticultural Science, and American Genetics Association}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Werner, D. and Amerson, H. and McKeand, S. and Bridgwater, F. and Whetten, R. and O'Malley, D. and et al.}, year={1992}, pages={37–40} }
 @article{omalley_porter_sederoff_1992, title={PURIFICATION, CHARACTERIZATION, AND CLONING OF CINNAMYL ALCOHOL-DEHYDROGENASE IN LOBLOLLY-PINE (PINUS-TAEDA L)}, volume={98}, ISSN={["0032-0889"]}, DOI={10.1104/pp.98.4.1364}, abstractNote={Cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1. 195) has been purified to homogeneity from differentiating xylem tissue and developing seeds of loblolly pine (Pinus taeda L.). The enzyme is a dimer with a native molecular weight of 82,000 and a subunit molecular weight of 44,000, and is the only form of CAD involved in lignification in differentiating xylem. High levels of loblolly pine CAD enzyme were found in nonlignifying seed tissue. Characterization of the enzyme from both seeds and xylem demonstrated that the enzyme is the same in both tissues. The enzyme has a high affinity for coniferaldehyde (K(m) = 1.7 micromolar) compared with sinapaldehyde (K(m) in excess of 100 micromolar). Kinetic data strongly suggest that coniferin is a noncompetitive inhibitor of CAD enzyme activity. Protein sequences were obtained for the N-terminus (28 amino acids) and for two other peptides. Degenerate oligonucleotide primers based on the protein sequences were used to amplify by polymerase chain reaction a 1050 base pair DNA fragment from xylem cDNA. Nucleotide sequence from the cloned DNA fragment coded for the N-terminal protein sequence and an internal peptide of CAD. The N-terminal protein sequence has little similarity with the lambdaCAD4 clone isolated from bean (MH Walter, J Grima-Pettenati, C Grand, AM Boudet, CJ Lamb [1988] Proc Natl Acad Sci USA 86:5546-5550), which has homology with malic enzyme.}, number={4}, journal={PLANT PHYSIOLOGY}, author={OMALLEY, DM and PORTER, S and SEDEROFF, RR}, year={1992}, month={Apr}, pages={1364–1371} }