Molecular evolution of drought tolerance and wood strength related candidate genes in loblolly pine (Pinus taeda L.)

ADAMS, R. M., C. ROSENZWEIG, R. M. PEART, J. T. RITCHIE, B. A. MCCARL, J. D. GLYER, R. B. CURRY, J. W. JONES, K. J. BOOTE and L. H. ALLEN (1990): Global climate change and US agriculture. Nature 345(6272): 219-224.10.1038/345219a0Search in Google Scholar

AKASHI, H. (1999): Within- and between-species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238(1): 39-51.10.1016/S0378-1119(99)00294-2Search in Google Scholar

AL-RABAB’AH, M. A. and C. G. WILLIAMS (2002): Population dynamics of Pinus taeda L. based on nuclear microsatellites. Forest Ecol Manag 163(1-3): 263-271.10.1016/S0378-1127(01)00584-9Search in Google Scholar

AL-RABAB’AH, M. A. and C. G. WILLIAMS (2004): An ancient bottleneck in the Lost Pines of central Texas. Mol Ecol 13(5): 1075-1084.10.1111/j.1365-294X.2004.02142.x15078446Search in Google Scholar

BROWN, G. R., D. L. BASSONI, G. P. GILL, J. R. FONTANA, N. C. WHEELER, R. A. MEGRAW, M. F. DAVIS, M. M. SEWELL, G. A. TUSKAN and D. B. NEALE (2003): Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164(4): 1537-1546.Search in Google Scholar

BROWN, G. R., G. P. GILL, R. J. KUNTZ, C. H. LANGLEY and D. B. NEALE (2004): Nucleotide diversity and linkage disequilibrium in loblolly pine. P Natl Acad Sci USA 101(42): 15255-15260.10.1073/pnas.040423110152404715477602Search in Google Scholar

CARVALHO, A. B. and A. G. CLARK (1999): Intron size and natural selection. Nature 401(6751): 344-344.10.1038/4382710517631Search in Google Scholar

CASTILLO-DAVIS, C. I., S. L. MEKHEDOV, D. L. HARTL, E. V. KOONIN and F. A. KONDRASHOV (2002): Selection for short introns in highly expressed genes. Nat Genet 31(4): 415-418.10.1038/ng94012134150Search in Google Scholar

CHANG, S. J., J. D. PURYEAR, M. A. D. L. DIAS, E. A. FUNKHOUSER, R. J. NEWTON and J. CAIRNEY (1996): Gene expression under water deficit in loblolly pine (Pinus taeda): Isolation and characterization of cDNA clones. Physiol Plantarum 97(1): 139-148.10.1111/j.1399-3054.1996.tb00490.xSearch in Google Scholar

CHHATRE, V. E., T. D. BYRAM, D. B. NEALE, J. L. WEGRZYN and K. V. KRUTOVSKY (2013): Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations. Tree Genet Genomes 9(5): 1161-1178.10.1007/s11295-013-0624-xSearch in Google Scholar

COLLINS, R. A. (1988): Evidence of natural selection to maintain a functional domain outside of the ‘core’ in a large subclass of Group I introns. Nucleic Acids Res 16(6): 2705-2715.10.1093/nar/16.6.27053363992452404Search in Google Scholar

DESER, C., A. PHILLIPS, V. BOURDETTE and H. Y. TENG (2012): Uncertainty in climate change projections: the role of internal variability. Clim Dynam 38(3-4): 527-546.10.1007/s00382-010-0977-xSearch in Google Scholar

ECKERT, A. J., J. VAN HEERWAARDEN, J. L. WEGRZYN, C. D. NELSON, J. ROSS-IBARRA, S. C. GONZALEZ-MARTINEZ and D. B. NEALE (2010): Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185(3): 969-982.10.1534/genetics.110.115543290721220439779Search in Google Scholar

EDGAR, R. C. (2004): MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5): 1792-1797.10.1093/nar/gkh34039033715034147Search in Google Scholar

ERSOZ, E. S., M. H. WRIGHT, S. C. GONZALEZ-MARTINEZ, C. H. LANGLEY and D. B. NEALE (2010): Evolution of disease response genes in loblolly pine: Insights from candidate genes. PLoS One 5(12): e14234.10.1371/journal.pone.0014234299779221151911Search in Google Scholar

GALTIER, N., M. GOUY and C. GAUTIER (1996): SEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12(6): 543-548.10.1093/bioinformatics/12.6.5439021275Search in Google Scholar

GERNANDT, D. S., S. MAGALLON, G. G. LOPEZ, O. Z. FLORES, A. WILLYARD and A. LISTON (2008): Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci 169(8): 1086-1099.10.1086/590472Search in Google Scholar

GONZALEZ-MARTINEZ, S. C., E. ERSOZ, G. R. BROWN, N. C. WHEELER and D. B. NEALE (2006): DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172(3): 1915-1926.10.1534/genetics.105.047126145626116387885Search in Google Scholar

GONZALEZ-MARTINEZ, S. C., D. HUBER, E. ERSOZ, J. M. DAVIS and D. B. NEALE (2008): Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101(1): 19-26.Search in Google Scholar

GONZALEZ-MARTINEZ, S. C., N. C. WHEELER, E. ERSOZ, C. D. NELSON and D. B. NEALE (2007): Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175(1): 399-409.Search in Google Scholar

GRAHAM, S. W., R. G. OLMSTEAD and S. C. H. BARRETT (2002): Rooting phylogenetic trees with distant outgroups: A case study from the commelinoid monocots. Mol Biol Evol 19(10): 1769-1781.10.1093/oxfordjournals.molbev.a00399912270903Search in Google Scholar

HALL, T. A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.Search in Google Scholar

HOEGH-GULDBERG, O. and J. F. BRUNO (2010): The impact of climate change on the world’s marine ecosystems. Science 328(5985): 1523-1528.10.1126/science.118993020558709Search in Google Scholar

HUANG, J., B. ABT, G. KINDERMANN and S. GHOSH (2011): Empirical analysis of climate change impact on loblolly pine plantations in the southern United States. Nat Resour Model 24(4): 445-476.10.1111/j.1939-7445.2011.00098.xSearch in Google Scholar

HUDSON, R. R., M. KREITMAN and M. AGUADE (1987): A test of neutral molecular evolution based on nucleotide data. Genetics 116(1): 153-159.10.1093/genetics/116.1.153Search in Google Scholar

JACKSON, S. T., R. S. WEBB, K. H. ANDERSON, J. T. OVERPECK, T. WEBB, J. W. WILLIAMS and B. C. S. HANSEN (2000): Vegetation and environment in Eastern North America during the Last Glacial Maximum. Quaternary Sci Rev 19(6): 489-508.10.1016/S0277-3791(99)00093-1Search in Google Scholar

JUKES, T. H. and C. R. CANTOR (1969): Evolution of protein molecules, pp. 21-132. In: Mammalian protein metabolism, edited by M. N. MUNRO. Academic Press, New York.10.1016/B978-1-4832-3211-9.50009-7Search in Google Scholar

KIMURA, M. (1968): Evolutionary rate at molecular level. Nature 217(5129): 624-626.10.1038/217624a05637732Search in Google Scholar

KREITMAN, M. (2000): Methods to detect selection in populations with applications to the human. Annu Rev Genom Hum G 1: 539-559.10.1146/annurev.genom.1.1.53911701640Search in Google Scholar

KRUTOVSKY, K., T. BYRAM, R. WHETTEN, N. WHEELER, D. NEALE, M. LU, T. KORALEWSKI and C. LOOPSTRA (2013): PINEMAP + PineRefSeq = Future Forests.Search in Google Scholar

PINEMAP (Pine Integrated Network: Education, Mitigation, and Adaptation Project) Year 2 Annual Report | March 2012-February 2013 “Mapping the future of southern pine management in a changing world” (http://www.pinemap.org/reports/annual-reports/PINEMAP_Year_2_Annual_Report_FINAL.pdf) 6-27.Search in Google Scholar

KRUTOVSKY, K. V., J. BURCZYK, I. CHYBICKI, R. FINKELDEY, T. PYHÄJÄRVI and J. J. ROBLEDO-ARNUNCIO (2012): Gene low, spatial structure, local adaptation, and assisted migration in trees, pp. 71-116. In: Genomics of Tree Crops, edited by R. J. SCHNELL and P. M. PRIYADARSHAN. Springer.10.1007/978-1-4614-0920-5_4Search in Google Scholar

LI, W. H., C. I. WU and C. C. LUO (1985): A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2(2): 150-174.Search in Google Scholar

LIBRADO, P. and J. ROZAS (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.10.1093/bioinformatics/btp18719346325Search in Google Scholar

LYONS-WEILER, J., G. A. HOELZER and R. J. TAUSCH (1998): Optimal outgroup analysis. Biol J Linn Soc 64(4): 493-511.10.1111/j.1095-8312.1998.tb00346.xSearch in Google Scholar

MCDONALD, J. H. and M. KREITMAN (1991): Adaptive protein evolution at the Adh locus in Drosophila. Nature 351(6328): 652-654.10.1038/351652a01904993Search in Google Scholar

NEI, M. and T. GOJOBORI (1986): Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3(5): 418-426.Search in Google Scholar

PETER, G. and D. NEALE (2004): Molecular basis for the evolution of xylem lignification. Curr Opin Plant Biol 7(6): 737-742.10.1016/j.pbi.2004.09.00215491924Search in Google Scholar

SCHMIDTLING, R. C. (2001): Southern pine seed sources. USDA, Forest Service, Southern Research Station. GTR SRS-44.10.2737/SRS-GTR-44Search in Google Scholar

SCHMIDTLING, R. C., E. CARROLL and T. LAFARGE (1999): Allozyme diversity of selected and natural loblolly pine populations. Silvae Genet 48(1): 35-45.Search in Google Scholar

SCHMIDTLING, R. C. and V. HIPKINS (1998): Genetic diversity in longleaf pine (Pinus palustris): influence of historical and prehistorical events. Can J Forest Res 28(8): 1135-1145.10.1139/x98-102Search in Google Scholar

SEAGER, R., A. TZANOVA and J. NAKAMURA (2009): Drought in the southeastern United States: Causes, variability over the last millennium, and the potential for future hydroclimate change. J Climate 22(19): 5021-5045.10.1175/2009JCLI2683.1Search in Google Scholar

SMITH, A. B. (1994): Rooting molecular trees: problems and strategies. Biol J Linn Soc 51(3): 279-292.10.1111/j.1095-8312.1994.tb00962.xSearch in Google Scholar

SPERRY, J. S. (2003): Evolution of water transport and xylem structure. Int J Plant Sci 164(3): S115-S127.10.1086/368398Search in Google Scholar

TAJIMA, F. (1989): Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3): 585-595.10.1093/genetics/123.3.58512038312513255Search in Google Scholar

TAMURA, K., D. PETERSON, N. PETERSON, G. STECHER, M. NEI and S. KUMAR (2011): MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739.10.1093/molbev/msr121320362621546353Search in Google Scholar

THUILLER, W., S. LAVERGNE, C. ROQUET, I. BOULANGEAT, B. LAFOURCADE and M. B. ARAUJO (2011): Consequences of climate change on the tree of life in Europe. Nature 470(7335): 531-534.10.1038/nature0970521326204Search in Google Scholar

WELLS, O. O., G. L. SWITZER and R. C. SCHMIDTLING (1991): Geographic variation in Mississippi loblolly pine and sweetgum. Silvae Genet 40(3-4): 105-119.Search in Google Scholar

WILLIAMS, D. A., Y. Q. WANG, M. BORCHETTA and M. S. GAINES (2007): Genetic diversity and spatial structure of a keystone species in fragmented pine rockland habitat. Biol Conserv 138(1-2): 256-268.10.1016/j.biocon.2007.04.024Search in Google Scholar

WILLYARD, A., J. SYRING, D. S. GERNANDT, A. LISTON and R. CRONN (2007): Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Mol Biol Evol 24(1): 90-101.10.1093/molbev/msl13116997907Search in Google Scholar

WRAY, G. A., M. W. HAHN, E. ABOUHEIF, J. P. BALHOFF, M. PIZER, M. V. ROCKMAN and L. A. ROMANO (2003): The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20(9): 1377-1419.10.1093/molbev/msg14012777501Search in Google Scholar

WRIGHT, S. I. and B. CHARLESWORTH (2004): The HKA test revisited: A maximum-likelihood-ratio test of the standard neutral model. Genetics 168(2): 1071-1076.10.1534/genetics.104.026500144883315514076Search in Google Scholar

XU, S. Q., C. G. TAUER and C. D. NELSON (2008): Genetic diversity within and among populations of shortleaf pine (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.). Tree Genet Genomes 4(4): 859-868.10.1007/s11295-008-0158-9Search in Google Scholar