@article{remington_purugganan_2002, title={GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): Molecular evolution of growth regulators in a rapidly diversifying plant lineage}, volume={19}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a004218}, abstractNote={Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin approximately 6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, approximately 900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions.}, number={9}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Remington, DL and Purugganan, MD}, year={2002}, month={Sep}, pages={1563–1574} }
 @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{remington_ungerer_purugganan_2001, title={Map-based cloning of quantitative trait loci: progress and prospects}, volume={78}, number={3}, journal={Genetical Research}, author={Remington, D. L. and Ungerer, M. C. and Purugganan, M. D.}, year={2001}, pages={213–218} }
 @article{remington_thornsberry_matsuoka_wilson_whitt_doeblay_kresovich_goodman_buckler_2001, title={Structure of linkage disequilibrium and phenotypic associations in the maize genome}, volume={98}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.201394398}, abstractNote={
            Association studies based on linkage disequilibrium (LD) can
 provide high resolution for identifying genes that may contribute to
 phenotypic variation. We report patterns of local and genome-wide LD in
 102 maize inbred lines representing much of the worldwide genetic
 diversity used in maize breeding, and address its implications for
 association studies in maize. In a survey of six genes, we found that
 intragenic LD generally declined rapidly with distance
 (
            r
            2
            < 0.1 within 1500 bp), but rates
 of decline were highly variable among genes. This rapid decline
 probably reflects large effective population sizes in maize during its
 evolution and high levels of recombination within genes. A set of 47
 simple sequence repeat (SSR) loci showed stronger evidence of
 genome-wide LD than did single-nucleotide polymorphisms (SNPs) in
 candidate genes. LD was greatly reduced but not eliminated by grouping
 lines into three empirically determined subpopulations. SSR data also
 supplied evidence that divergent artificial selection on flowering time
 may have played a role in generating population structure. Provided the
 effects of population structure are effectively controlled, this
 research suggests that association studies show great promise for
 identifying the genetic basis of important traits in maize with very
 high resolution.
          }, number={20}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Remington, DL and Thornsberry, JM and Matsuoka, Y and Wilson, LM and Whitt, SR and Doeblay, J and Kresovich, S and Goodman, MM and Buckler, ES}, year={2001}, month={Sep}, pages={11479–11484} }
 @article{costa_pot_dubos_frigerio_pionneau_bodenes_bertocchi_cervera_remington_plomion_2000, title={A genetic map of Maritime pine based on AFLP, RAPD and protein markers}, volume={100}, ISSN={["0040-5752"]}, DOI={10.1007/s001220050006}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, author={Costa, P and Pot, D and Dubos, C and Frigerio, JM and Pionneau, C and Bodenes, C and Bertocchi, E and Cervera, MT and Remington, DL and Plomion, C}, year={2000}, month={Jan}, pages={39–48} }
 @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{cervera_remington_frigerio_storme_ivens_boerjan_plomion_2000, title={Improved AFLP analysis of tree species}, volume={30}, ISSN={["0045-5067"]}, DOI={10.1139/cjfr-30-10-1608}, abstractNote={Amplified fragment length polymorphism (AFLP) is a high-throughput, molecular-marker technique that is used increasingly in a variety of genetic analyses. Here, the conditions for carrying out AFLP analysis have been established for different tree species, including both angiosperm and gymnosperm trees, with genome sizes ranging from 0.54 to 38 pg DNA/2C. Specific parameters have been determined to provide informative and reproducible AFLP fingerprints of peach (Prunus persica L.), eucalypt, oak, poplar, and loblolly pine (Pinus taeda L.). Typically, 80-130 amplified DNA fragments (i.e., loci analyzed per primer combination) were obtained. Subsequently, these AFLP conditions were evaluated for intra- and inter-specific genetic variability studies as well as for genome mapping purposes of woody species. This work demonstrates that AFLP is a powerful tool in forest tree genetics.}, number={10}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={Cervera, MT and Remington, D and Frigerio, JM and Storme, V and Ivens, B and Boerjan, W and Plomion, C}, year={2000}, month={Oct}, pages={1608–1616} }
 @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} }