Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana

Genetics

Volumn 167, Issue 2, 2004, Pages 907-917

  Wolyn, David J ^a   Borevitz, Justin O ^b   Loudet, Olivier ^b   Schwartz, Chris ^b   Maloof, Julin ^d   Ecker, Joseph R ^b   Berry, Charles C ^c   Chory, Joanne ^b,e  

^a UNIVERSITY OF GUELPH   (Canada)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; BLUE LIGHT; DARKNESS; DNA HYBRIDIZATION; DNA MICROARRAY; ECOTYPE; FAR RED LIGHT; GENE FREQUENCY; GENE LOCATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC MODEL; GENETIC POLYMORPHISM; INBRED STRAIN; LIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHOTORECEPTOR; PLANT GROWTH; POPULATION SIZE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RED LIGHT; SEEDLING; WHITE LIGHT;

ARABIDOPSIS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; HYPOCOTYL; LIGHT; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUANTITATIVE TRAIT LOCI; VARIATION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 3142721878     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.024810     Document Type: Article

References (41)

1. AHMAD, M., and A. R. CASHMORE, 1993 Hy4 of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366: 162-166.
2. AHMAD, M., and A. R. CASHMORE, 1997 The blue-light receptor cryptochrome 1 shows functional dependence on phytochrome A or phytochrome B in Arabidopsis thaliana. Plant J. 11: 421-427.
3. ALONSO-BLANCO, C., S. EL-DIN EL-ASSAL, G. COUPLAND and M. KOORNNEEF, 1998 Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana. Genetics 149: 749-764.
4. BOREVITZ, J. O., J. N. MALOOF, J. LUTES, T. DABI, J. L. REDFERN et al., 2002 Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics 160: 683-696.
5. BOREVITZ, J. O., D. LIANG, D. PLOUFFE, H.-R. CHANG, T. ZHU et al., 2003 Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13: 513-523.
6. BOTTO, J. F., and H. SMITH, 2002 Differential genetic variation in adaptive strategies to a common environmental signal in Arabidopsis accessions: phytochrome-mediated shade avoidance. Plant Cell Environ. 25: 53-63.
7. BOTTO, J. F., C. ALONSO-BLANCO, I. GARARÓN, R. A. SÁNCHEZ and J. J. CASAL, 2003 The Cape Verde Island allele of cryptochrome 2 enhances cotyledon unfolding in the absence of blue light in Arabidopsis. Plant Physiol. 133: 1547-1556.
8. CHURCHILL, G. A., and R. W. DOERGE, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
9. CHURCHILL, G. A., J. J. GIOVANNONI and S. D. TANKSLEY, 1993 Pooled-sampling makes high resolution mapping practical with DNA markers. Proc. Natl. Acad. Sci. USA 90: 16-20.
10. CLEVELAND, W. S., E. GROSSE and W. M. SHYU, 1992 Local regression models, pp. 309-376 in Statistical Models in S, edited by J. M. CHAMBERS and T. J. HASTIE. Wadsworth, Pacific Grove, CA.
11. DEHESH, K., C. FRANCI, B. M. PARKS, K. A. SEELEY, T. W. SHORT et al., 1993 Arabidopsis HY8 locus encodes phytochrome A. Plant Cell 5: 1081-1088.
12. EL-ASSAL, S. E.-D., G. ALONSO-BLANCO, A. J. M. PEETERS, V. RAZ and M. KOORNNEEF, 2001 A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat. Genet. 29: 435-440.
13. GUO, H., H. DUONG, N. MA and C. LIN, 1999 The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue light-dependent post-transcriptional mechanism. Plant J. 19: 279-287.
14. IRIZARRY, R. A., B. M. BOLSTAD, F. COLLIN, L. M. COPE, B. HOBBS et al., 2003 Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31: e15.
15. JANSEN, R. C., and P. STAM, 1994 High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
16. JIANG, C., and Z-B. ZENG, 1995 Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.
17. KEVEI, E., and F. NAGY, 2003 Phytochrome controlled signalling cascades in higher plants. Physiol. Plant 117: 305-313.
18. KOBAYASHI, Y., and H. KOYAMA, 2002 QTL analysis of Al tolerance in recombinant inbred lines of Arabidopsis thaliana. Plant Cell Physiol. 43: 1526-1533.
19. KOORNNEEF, M., E. ROLFF and C.J.P. SPRUIT, 1980 Genetic control of light inhibited hypocotyl elongation in Arabidopsis thaliana (L.) Heynh. Z. Pflanzenphysiol. 100: 147-160.
20. LANDER, E. S., P. GREEN, J. ABRAHAMSON, A. BARLOW, M. J. DALY et al., 1987 MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
21. LOUDET, O., S. CHAILLOU, P. MERIGOUT J. TALBOTEC and F. DANIEL-VEDELE, 2003a Quantitative trait-loci analysis of nitrogen use efficiency in Arabidopsis. Plant Physiol. 131: 345-358.
22. LOUDET, O., S. CHAILLOU, A. KRAPP and F. DANIEL-VEDELE, 2003b Quantitative trait loci analysis of water and anion contents in interaction with nitrogen availability in Arabidopsis thaliana. Genetics 163: 711-722.
23. MACKAY, T. F. C., 2001 Quantitative trait loci in Drosophila. Nat. Rev. Genet. 2: 11-20.
24. MALOOF, J. N., J. O. BOREVITZ, T. DABI, J. LUTES, R. B. NEHRING et al., 2001 Natural variation in light sensitivity of Arabidopsis. Nat. Genet. 29: 441-446.
25. MAS, P., P. F. DEVLIN, S. PANDA and S. A. KAY, 2000 Functional interaction of phytochrome B and cryptochrome 2. Nature 408: 207-211.
26. MICHELMORE, R. W., I. PARAN and R. V. KESSILI, 1991 Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88: 9828-9832.
27. MONTE, E., J. M. ALONSO, J. R. ECKER, Y. ZHANG, X. LI et al., 2003 Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell 15: 1962-1980.
28. NEFF, M. M., and J. CHORY, 1998 Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development. Plant Physiol. 118: 27-35.
29. PARKS, B. M., and P. H. QUAIL, 1993 hy8, a new class of Arabidopsis long hypocotyl mutants deficient in functional phytochrome A. Plant Cell 5: 39-48.
30. QUAIL, P. H., 2002 Phytochrome photosensory signalling networks. Nat. Rev. Mol. Cell Biol. 3: 85-93.
31. REED, J. W., P. NAGPAL, D. S. POOLE, M. FURUYA and J. CHORY, 1993 Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell 5: 147-157.
32. REED J. W., A. NAGATANI, T. D. ELICH, M. FAGAN and J. CHORY, 1994 Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol. 104: 1139-1149.
33. SOMERS, D. E., R. A. SHARROCK, J. M. TEPPERMAN and P. H. QUAIL, 1991 The hy3 long hypocotyl mutant of Arabidopsis is deficient in phytochrome B. Plant Cell 3: 1263-1274.
34. TANKSLEY, S. D., 1993 Mapping polygenes. Annu. Rev. Genet. 27: 205-233.
35. WANG, H., and X. W. DENG, 2003 Dissecting the phytochrome A-dependent signaling network in higher plants. Trends Plant Sci. 8: 172-178.
36. WEINIG, C., M. C. UNGERER, L. A. DORN, N. C. KANE, Y. TOYONAGA et al., 2002 Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments. Genetics 162: 1875-1884.
37. WESTER, L., D. E. SOMERS, T. CLACK and R. A. SHARROCK, 1994 Transgenic complementation of the hy3 phytochrome B mutation and response to PHYB gene copy number in Arabidopsis. Plant J. 5: 261-272.
38. WHITELAM, G. C., E. JOHNSON, J. PENG, P. CAROL, M. L. ANDERSON et al., 1993 Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell 5: 757-768.
39. WILSON, I. W., C. L. SCHIFF, D. E. HUGHES and S. C. SOMERVILLE, 2001 Quantitative trait loci analysis of powdery mildew disease resistance in the Arabidopsis thaliana accession Kashmir-1. Genetics 158: 1301-1309.
40. YANOVSKY, M. J., J. J. CASAL and J. P. LUPPI, 1997 The VFL loci, polymorphic between ecotypes Landsberg erecta and Columbia, dissect two branches of phytochrome A signal transduction that correspond to very-low-fluence and high-irradiance responses. Plant J. 12: 659-667.
41. ZENG, Z-B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.