Association genetics reveal candidate gene SNPs affecting wood properties in Pinus radiata

Australian Forestry

Volumn 73, Issue 3, 2010, Pages 185-190

  Dillon, S K ^a   Nolan, M F ^a   Wu, H ^a   Southerton, S G ^a  

^a CSIRO   (Australia)

Author keywords

Genetic variation; Marker aided selection; Molecular markers; Phenotypic variation; Pinus radiata; Wood properties

Indexed keywords

GENES; MAPPING; WOOD;

GENETIC VARIATION; MARKER-AIDED SELECTION; MOLECULAR MARKER; PHENOTYPIC VARIATIONS; PINUS RADIATA; WOOD PROPERTIES;

FORESTRY;

FORESTRY; GENES; MAPPING; PINUS RADIATA; WOOD; WOOD PROPERTIES;

PINUS RADIATA;

EID: 77957841197     PISSN: 00049158     EISSN: None     Source Type: Journal    
DOI: 10.1080/00049158.2010.10676326     Document Type: Article

References (42)

1. Aliona, I., Quinn, M., Shoop, E., Swope, K., St Cyr, S., Carlis, J., Riedl, J., Retzel, E., Campbell, M. M., Sederoff, R., and Whetten, R. W., 1998. Analysis of xylem formation in pine by cDNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 95:9693–9698.
2. Aranzana, M. J., Kim, S., Zhao, K. Y., Bakker, E., Horton, M., Jakob, K., Lister, C., Molitor, J., Shindo, C., Tang, C. L., Toomajian, C., Traw, B., Zheng, H. G, Bergelson, J., Dean, C., Marjoram, R., and Nordborg, M., 2005. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genetics, 1:531–539.
3. Baltunis, B. S., Wu, H. X., and Powell, M. B., 2007. Inheritance of density, microfibril angle, and modulus of elasticity in juvenile wood of Pinus radiata at two locations in Australia. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere, 37:2164–2174.
4. Belo, A., Zheng, P. Z, Luck, S., Shen, B., Meyer, D. J., Li, B. L., Tingey, S., and Rafalski, A., 2008. Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Molecular Genetics and Genomics, 279:1–10.
5. Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., and Buckler, E. S., 2007. Tassel:software for association mapping of complex traits in diverse samples. Bioinformatics, 23:2633–2635.
6. Cato, S., McMillan, L., Donaldson, L., Richardson, T., Echt, C., and Gardner, R., 2006. Wood formation from the base to the crown in Pinus radiata gradients of tracheid wall thickness, wood density, radial growth rate and gene expression. Plant Molecular Biology, 60:565–581.
7. Devey, M. E., Carson, S. D., Nolan, M. F., Matheson, A. C., Riini, C. T., and Hohepa, J., 2004a. QTL associations for density and diameter in Pinus radiata and the potential for marker-aided selection. Theoretical and Applied Genetics, 108:516–524.
8. Devey, M. E., Groom, K. A., Nolan, M. F., Bell, J. C., Dudzinski, M. J., Old, K. M., Matheson, A. C., and Moran, G. F., 2004b. Detection and verification of quantitative trait loci for resistance to Dothistroma needle blight in. Pinus radiata. Theoretical and Applied Genetics, 108:1056–1063.
9. Doyle, J. J., and Doyle, J. L., 1990. Isolation of plant DNA from fresh tissue. Focus, 12:13–15.
10. Dungey, H. S., Matheson, A. C., Kain, D., and Evans, R., 2006. Genetics of wood stiffness and its component traits in. Pinus radiata. Canadian Journal of Forest Research, 36:1165–1178.
11. Eldridge, K. G., 1978. Refreshing the Genetic Resources of Radiata Pine Plantations. CSIRO Division of Forest Research:Genetics Section Report Number, 7:120
12. Evans, D. M., and Cardon, L. R., 2005. A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations. American Journal of Human Genetics, 76:681–687.
13. Gapare, W. J., Wu, H. X., and Abarquez, A., 2006. Genetic control of the time of transition from juvenile to mature wood in Pinus radiata D. Don. Annals of Forest Science, 63:871–878.
14. Gonzalez-Martinez, S. C., Wheeler, N. C., Ersoz, E., Nelson, C. D., and Neale, D. B., 2007. Association genetics in Pinus taeda L. I. Wood property traits. Genetics, 175:399–409.
15. Gonzalez-Martinez, S. C., Huber, D., Ersoz, E., Davis, J. M., and Neale, D. B., 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity, 101:19–26.
16. Henderson, C. R., 1975. Best linear unbiased estimation and prediction under a selection model. Biometrics, 31:423–447.
17. Ingvarsson, P. K., Garcia, M. V., Hall, D., Luquez, V., and Jansson, S., 2006. Clinal variation in phyb2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen (. Populus tremula). Genetics, 172:1845–1853.
18. Kibblewhite, R. P., 1999. Designer fibres for improved papers through exploiting genetic variation in wood microstructure. Appita Journal, 52:429
19. Kreitman, M., 1983. Nucleotide polymorphism at the alcohol—dehydrogenase locus of. Drosophila melanogaster. Nature, 304:412–417.
20. Krutovsky, K. V., and Neale, D. B., 2005. Nucleotide diversity and linkage disequilibrium in cold-hardiness—and wood quality-related candidate genes in Douglas-fir. Genetics, 171:2029–2041.
21. Kumar, S., Echt, C., Wilcox, P. L., and Richardson, T. E., 2004. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theoretical and Applied Genetics, 108:292–298.
22. Li, X., Wu, H., Dillon, S., and Southerton, S. G., 2009. Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. BMC Genomics, 10 (41):1–18.
23. Matheson, A. C., Devey, M. E., Gordon, T. L., Werner, W., Vogler, D. R., Balocchi, C., and Carson, M. J., 2006. Heritability of response to inoculation by pine pitch canker of seedlings of radiata pine. Australian Forestry, 69:101–106.
24. Nairn, C. J., Lennon, D. M., Wood-Jones, A., Nairn, A. V., and Dean, J. F.D., 2008. Carbohydrate-related genes and cell wall biosynthesis in vascular tissues of loblolly pine (. Pinus taeda). Tree Physiology, 28:1099–1110.
25. Neale, D. B., and Savolainen, O., 2004. Association genetics of complex traits in conifers. Trends in Plant Science, 9:325–330.
26. Oh, S., Park, S., and Han, K. H., 2003. Transcriptional regulation of secondary growth in. Arabidopsis thaliana. Journal of Experimental Botany, 54:2709–2722.
27. Olsen, K. M., Halldorsdottir, S. S., Stinchcombe, J. R., Weinig, C., Schmitt, J., and Purugganan, M. D., 2004. Linkage disequilibrium mapping of Arabidopsis cry2 flowering time alleles. Genetics, 167:1361–1369.
28. Oraguzie, N. C., and Wilcox, P. L., 2007. An Overview of Association Mapping. New York:Springer Science+Business Media.
29. Palaisa, K. A., Morgante, M., Williams, M., and Rafalski, A., 2003. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell, 15:1795–1806.
30. Paux, E., Tamasloukht, M., Ladouce, N., Sivadon, P., and Grima-Pettenati, J., 2004. Identification of genes preferentially expressed during wood formation in. Eucalyptus. Plant Molecular Biology, 55:263–280.
31. Paux, E., Carocha, V., Marques, C., de Sousa, A. M., Borralho, N., Sivadon, P., and Grima-Pettenati, J., 2005. Transcript profiling of Eucalyptus xylem genes during tension wood formation. New Phytologist, 167:89–100.
32. Pavy, N., Paule, C., Parsons, L., Crow, J. A., Morency, M. J., Cooke, J., Johnson, J. E., Noumen, E., Guillet-Claude, C., Butterfield, Y., Barber, S., Yang, G., Liu, J., Stott, J., Kirkpatrick, R., Siddiqui, A., Holt, R., Marra, M., Seguin, A., Retzel, E., Bousquet, J., and MacKay, J., 2005. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics, 6 (144):1–19.
33. Pritchard, J. K., Stephens, M., and Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics, 155:945–959.
34. Sanger, F., Nicklen, S., and Coulson, A. R., 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74:5463–5467.
35. Shen, R., Fan, J. B., Campbell, D., Chang, W. H., Chen, J., Doucet, D., Yeakley, J., Bibikova, M., Garcia, E. W., McBride, C., Steemers, F., Garcia, F., Kermani, B. G., Gunderson, K., and Oliphant, A., 2005. High-throughput snp genotyping on universal bead arrays. Mutation Research—Fundamental and Molecular Mechanisms of Mutagenesis, 573:70–82.
36. Storey, J. D., and Tibshirani, R., 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences USA, 100:9440–9445.
37. Thornsberry, J. M., Goodman, M. M., Doebley, J., Kresovich, S., Nielsen, D., and Buckler, E. S., 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics, 28:286–289.
38. Thumma, B. R., Nolan, M. R., Evans, R., and Moran, G. F., 2005. Polymorphisms in cinnamoyl coa reductase (ccr) are associated with variation in microfibril angle in Eucalyptus spp. Genetics, 171:1257–1265.
39. Wu, H. X., Matheson, A. C., and Abarquez, A., 2002. Inbreeding in Pinus radiata. IV:The effect of inbreeding on wood density. Annals of Forest Science, 59:557–562.
40. Yuan, Z., Yao, X., Zhang, D. B., Sun, Y., and Huang, H., 2007. Genome-wide expression profiling in seedlings of the Arabidopsis mutant uro that is defective in the secondary cell wall formation. Journal of Integrative Plant Biology, 49:1754–1762.
41. Zhao, K., Aranzana, M., Kim, S., Lister, C., Shindo, C., Tang, C., Toomajian, C., Zheng, C., Dean, C., Marjoram, P., and Nordborg, M., 2007. An Arabidopsis example of association mapping in structured samples. PLoS Genetics, 3:71–82.
42. Zhong, R. Q., Lee, C. H., Zhou, J. L., McCarthy, R. L., and Ye, Z. H., 2008. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in. Arabidopsis. Plant Cell, 20:2763–2782.