Systems genetics of environmental response in the mature wheat embryo

Genetics

Volumn 194, Issue 1, 2013, Pages 265-270

  Munkvold, Jesse D ^a,c   Laudencia Chingcuanco, Debbie ^b   Sorrells, Mark E ^a  

^a Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^b WESTERN REGIONAL RESEARCH CENTER   (United States)

^c Keygene Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYSACCHARIDE;

ARTICLE; CATABOLISM; CELL FUNCTION; CELL VACUOLE; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENE MAPPING; GENETIC ANALYSIS; GENETIC REGULATION; GOLGI COMPLEX; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN LOCALIZATION; QUANTITATIVE TRAIT LOCUS; TRITICUM AESTIVUM;

CHROMOSOME MAPPING; CROSSES, GENETIC; ENVIRONMENT; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENES, PLANT; GENETIC LINKAGE; QUANTITATIVE TRAIT LOCI; SEEDS; TRITICUM;

TRITICUM AESTIVUM;

EID: 84877094635     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.150052     Document Type: Article

References (54)

1. Bassel, G. W., H. Lan, E. Glaab, D. J. Gibbs, T. Gerjets et al., 2011 Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc. Natl. Acad. Sci. USA 108: 9709-9714.
2. Basten, C., B. Weir, and Z. Zeng, 1994 Zmap: a QTL cartographer, pp. 65-66 in Proceedings of the 5th World Congress on Genetics Applied to Livestock Production: Computing Strategies and Software, edited by C. Smith, J. Gavora, B. Benkel, J. Chesnais, W. Fairfull et al. Organizing Committee, 5th World Congress on Genetics Applied to Livestock Production, Guelph, Ontario, Canada.
3. Basten, C., B. Weir, and Z.-B. Zeng, 2002 QTL Cartographer. Department of Statistics, North Carolina State University, Raleigh, NC.
4. Baumberger, N., and D. C. Baulcombe, 2005 Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102: 11928-11933.
5. Bowtell, D., and J. Sambrook, 2003 DNA Microarrays: A Molecular Cloning Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
6. Brem, R. B., and L. Kruglyak, 2005 The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102: 1572-1577.
7. Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
8. Carlson, M. R., B. Zhang, Z. Fang, P. S. Mischel, S. Horvath et al., 2006 Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics 7: 40.
9. Consonni, C., P. Bednarek, M. Humphry, F. Francocci, S. Ferrari et al., 2010 Tryptophan- derived metabolites are required for antifungal defense in the Arabidopsis mlo2 mutant. Plant Physiol. 152: 1544-1561.
10. Decook, R., S. Lall, D. Nettleton, and S. H. Howell, 2006 Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics 172: 1155-1164.
11. Dixon, D. P., B. G. Davis, and R. Edwards, 2002 Functional divergence in the glutathione transferase superfamily in plants. Identification of two classes with putative functions in redox homeostasis in Arabidopsis thaliana. J. Biol. Chem. 277: 30859-30869.
12. Drost, D. R., C. I. Benedict, A. Berg, E. Novaes, C. R. Novaes et al., 2010 Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc. Natl. Acad. Sci. USA 107: 8492-8497.
13. Druka, A., E. Potokina, Z. Luo, N. Jiang, X. Chen et al., 2010 Expression quantitative trait loci analysis in plants. Plant Biotechnol. J. 8: 10-27.
14. Fuller, T. F., A. Ghazalpour, J. E. Aten, T. A. Drake, A. J. Lusis et al., 2007 Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm. Genome 18: 463-472.
15. Gibson, G., and B. Weir, 2005 The quantitative genetics of transcription. Trends Genet. 21: 616-623.
16. Holloway, B., S. Luck, M. Beatty, J. A. Rafalski, and B. Li, 2011 Genome-wide expression quantitative trait loci (eQTL) analysis in maize. BMC Genomics 12: 336.
17. Huang Da, W., B. T. Sherman, and R. A. Lempicki, 2009a Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37: 1-13.
18. Huang Da, W., B. T. Sherman, and R. A. Lempicki, 2009b Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4: 44-57.
19. Jansen, R. C., and J. P. Nap, 2001 Genetical genomics: the added value from segregation. Trends Genet. 17: 388-391.
20. Jordan, M. C., D. J. Somers, and T. W. Banks, 2007 Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci. Plant Biotechnol. J. 5: 442-453.
21. Kang, M., M. Fokar, H. Abdelmageed, and R. D. Allen, 2011 Arabidopsis SAP5 functions as a positive regulator of stress responses and exhibits E3 ubiquitin ligase activity. Plant Mol. Biol. 75: 451-466.
22. Keurentjes, J. J., J. Fu, I. R. Terpstra, J. M. Garcia, G. Van Den Ackerveken et al., 2007 Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc. Natl. Acad. Sci. USA 104: 1708-1713.
23. Kojima, S., A. Bohner, B. Gassert, L. Yuan, and N. Von Wiren, 2007 AtDUR3 represents the major transporter for highaffinity urea transport across the plasma membrane of nitrogendeficient Arabidopsis roots. Plant J. 52: 30-40.
24. Landry, C. R., J. Oh, D. L. Hartl, and D. Cavalieri, 2006 Genomewide scan reveals that genetic variation for transcriptional plas-ticity in yeast is biased towards multi-copy and dispensable genes. Gene 366: 343-351.
25. Langfelder, P., and S. Horvath, 2007 Eigengene networks for studying the relationships between co-expression modules. BMC Syst. Biol. 1: 54.
26. Langfelder, P., and S. Horvath, 2008 WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559.
27. Langfelder, P., R. Luo, M. C. Oldham, and S. Horvath, 2011 Is my network module preserved and reproducible? PLOS Comput. Biol. 7: e1001057.
28. Lee, I., B. Ambaru, P. Thakkar, E. M. Marcotte, and S. Y. Rhee, 2010 Rational association of genes with traits using a genome- scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28: 149-156.
29. Li, Y., O. A. Alvarez, E. W. Gutteling, M. Tijsterman, J. Fu et al., 2006 Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet 2: e222.
30. Liu, L. H., U. Ludewig, W. B. Frommer, and N. Von Wiren, 2003 AtDUR3 encodes a new type of high-affinity urea/H+ symporter in Arabidopsis. Plant Cell 15: 790-800.
31. Lorenzo, O., J. M. Chico, J. J. Sanchez-Serrano, and R. Solano, 2004 JASMONATE- INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonateregulated defense responses in Arabidopsis. Plant Cell 16: 1938-1950.
32. McGrath, K. C., B. Dombrecht, J. M. Manners, P. M. Schenk, C. I. Edgar et al., 2005 Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol. 139: 949-959.
33. Mishina, T. E., and J. Zeier, 2007 Bacterial non-host resistance: interactions of Arabidopsis with non-adapted Pseudomonas syringae strains. Physiol. Plant. 131: 448-461.
34. Moscou, M. J., N. Lauter, B. Steffenson, and R. P. Wise, 2011 Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genet. 7: e1002208.
35. Mounet, F., A. Moing, V. Garcia, J. Petit, M. Maucourt et al., 2009 Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol. 149: 1505-1528.
36. Munkvold, J. D., J. Tanaka, D. Benscher, and M. E. Sorrells, 2009 Mapping quantitative trait loci for preharvest sprouting in white wheat. Theor. Appl. Genet. 119: 1223-1235.
37. Oldham, M. C., S. Horvath, and D. H. Geschwind, 2006 Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc. Natl. Acad. Sci. USA 103: 17973-17978.
38. Potokina, E., A. Druka, Z. Luo, R. Wise, R. Waugh et al., 2008 Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant J. 53: 90-101.
39. Pumphrey, M., J. Bai, D. Laudencia-Chingcuanco, O. Anderson, and B. S. Gill, 2009 Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 181: 1147-1157.
40. Qi, L. L., B. Echalier, S. Chao, G. R. Lazo, G. E. Butler et al., 2004 A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168: 701-712.
41. Quackenbush, J., 2002 Microarray data normalization and transformation. Nat. Genet. 32(Suppl.): 496-501.
42. Saeed, A. I., V. Sharov, J. White, J. Li, W. Liang et al., 2003 TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378.
43. Schadt, E. E., S. A. Monks, T. A. Drake, A. J. Lusis, N. Che et al., 2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
44. Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang et al., 2003 Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504.
45. Smith, E. N., and L. Kruglyak, 2008 Gene-environment interaction in yeast gene expression. PLoS Biol. 6: e83.
46. Thines, B., L. Katsir, M. Melotto, Y. Niu, A. Mandaokar et al., 2007 JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling. Nature 448: 661-665.
47. Wang, X., B. M. Basnayake, H. Zhang, G. Li, W. Li et al., 2009 The Arabidopsis ATAF1, a NAC transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens. Mol. Plant Microbe Interact. 22: 1227-1238.
48. West, M. A., K. Kim, D. J. Kliebenstein, H. Van Leeuwen, R. W. Michelmore et al., 2007 Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175: 1441-1450.
49. Xu, X., C. Chen, B. Fan, and Z. Chen, 2006 Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell 18: 1310-1326.
50. Yang, Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng et al., 2002 Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15.
51. Zhang, X., A. J. Cal, and J. O. Borevitz, 2011 Genetic architecture of regulatory variation in Arabidopsis thaliana. Genome Res. 21: 725-733.
52. Zhang, B., and S. Horvath, 2005 A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Molec. Biol. 4: 1128.
53. Zheng, M. S., H. Takahashi, A. Miyazaki, H. Hamamoto, J. Shah et al., 2004 Up-regulation of Arabidopsis thaliana NHL10 in the hypersensitive response to cucumber mosaic virus infection and in senescing leaves is controlled by signalling pathways that differ in salicylate involvement. Planta 218: 740-750.
54. Zheng, Z., S. A. Qamar, Z. Chen, and T. Mengiste, 2006 Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. Plant J. 48: 592-605.