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. 2004 Aug;167(4):1883–1892. doi: 10.1534/genetics.103.025213

Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis.

Sonia Lall 1, Dan Nettleton 1, Rhonda DeCook 1, Ping Che 1, Stephen H Howell 1
PMCID: PMC1471002  PMID: 15342526

Abstract

Arabidopsis ecotypes, Columbia (Col) and Landsberg erecta (Ler), differ in their capacity to regenerate shoots in culture, as do many other cultivars and varieties of the same plant species. Recombinant inbred (RI) lines derived from a cross of Col x Ler were scored for shoot regeneration, and the Arabidopsis genome was scanned using composite interval mapping for loci associated with shoot regeneration. Three QTL were identified--a major one on chromosome 5 in which the Col parent contributed the superior allele and two minor QTL on chromosomes 1 and 4 in which the Ler parent contributed the superior alleles. The RI lines were binned into genotypic pools to isolate the effects of the major QTL on chromosome 5 while holding the minor QTL constant. To identify genes with expression levels that are associated with the allelic state of the major QTL on chromosome 5, oligonucleotide array expression patterns for genes in the LLC pool (Ler alleles at the minor QTL and a Col allele at the major QTL) were compared to those in the LLL pool (Ler alleles at all QTL). The genes that were significantly differentially expressed between the two pools included several encoding transcription factors and signaling or transposon-related proteins.

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Selected References

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  1. Banno H., Ikeda Y., Niu Q. W., Chua N. H. Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell. 2001 Dec;13(12):2609–2618. doi: 10.1105/tpc.010234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cary Andrew J., Che Ping, Howell Stephen H. Developmental events and shoot apical meristem gene expression patterns during shoot development in Arabidopsis thaliana. Plant J. 2002 Dec;32(6):867–877. doi: 10.1046/j.1365-313x.2002.01479.x. [DOI] [PubMed] [Google Scholar]
  3. Che Ping, Gingerich Derek J., Lall Sonia, Howell Stephen H. Global and hormone-induced gene expression changes during shoot development in Arabidopsis. Plant Cell. 2002 Nov;14(11):2771–2785. doi: 10.1105/tpc.006668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Churchill G. A., Doerge R. W. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. doi: 10.1093/genetics/138.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Daimon Yasufumi, Takabe Kazuo, Tasaka Masao. The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli. Plant Cell Physiol. 2003 Feb;44(2):113–121. doi: 10.1093/pcp/pcg038. [DOI] [PubMed] [Google Scholar]
  6. Fernando R. L., Nettleton D., Southey B. R., Dekkers J. C. M., Rothschild M. F., Soller M. Controlling the proportion of false positives in multiple dependent tests. Genetics. 2004 Jan;166(1):611–619. doi: 10.1534/genetics.166.1.611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gamborg O. L., Miller R. A., Ojima K. Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res. 1968 Apr;50(1):151–158. doi: 10.1016/0014-4827(68)90403-5. [DOI] [PubMed] [Google Scholar]
  8. Hwang I., Sheen J. Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature. 2001 Sep 27;413(6854):383–389. doi: 10.1038/35096500. [DOI] [PubMed] [Google Scholar]
  9. Imamura Aya, Kiba Takatoshi, Tajima Yoshinori, Yamashino Takafumi, Mizuno Takeshi. In vivo and in vitro characterization of the ARR11 response regulator implicated in the His-to-Asp phosphorelay signal transduction in Arabidopsis thaliana. Plant Cell Physiol. 2003 Feb;44(2):122–131. doi: 10.1093/pcp/pcg014. [DOI] [PubMed] [Google Scholar]
  10. Irizarry Rafael A., Hobbs Bridget, Collin Francois, Beazer-Barclay Yasmin D., Antonellis Kristen J., Scherf Uwe, Speed Terence P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249–264. doi: 10.1093/biostatistics/4.2.249. [DOI] [PubMed] [Google Scholar]
  11. Jansen R. C., Stam P. High resolution of quantitative traits into multiple loci via interval mapping. Genetics. 1994 Apr;136(4):1447–1455. doi: 10.1093/genetics/136.4.1447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kakimoto T. CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science. 1996 Nov 8;274(5289):982–985. doi: 10.1126/science.274.5289.982. [DOI] [PubMed] [Google Scholar]
  13. Li C., Wong W. H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):31–36. doi: 10.1073/pnas.011404098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lincoln C., Britton J. H., Estelle M. Growth and development of the axr1 mutants of Arabidopsis. Plant Cell. 1990 Nov;2(11):1071–1080. doi: 10.1105/tpc.2.11.1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lohrmann Jens, Harter Klaus. Plant two-component signaling systems and the role of response regulators. Plant Physiol. 2002 Feb;128(2):363–369. doi: 10.1104/pp.010907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Prakash A. Pavan, Kumar Prakash P. PkMADS1 is a novel MADS box gene regulating adventitious shoot induction and vegetative shoot development in Paulownia kawakamii. Plant J. 2002 Jan;29(2):141–151. doi: 10.1046/j.0960-7412.2001.01206.x. [DOI] [PubMed] [Google Scholar]
  17. Sakai H., Aoyama T., Oka A. Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J. 2000 Dec;24(6):703–711. doi: 10.1046/j.1365-313x.2000.00909.x. [DOI] [PubMed] [Google Scholar]
  18. Sakai H., Honma T., Aoyama T., Sato S., Kato T., Tabata S., Oka A. ARR1, a transcription factor for genes immediately responsive to cytokinins. Science. 2001 Nov 1;294(5546):1519–1521. doi: 10.1126/science.1065201. [DOI] [PubMed] [Google Scholar]
  19. Souer E., van Houwelingen A., Kloos D., Mol J., Koes R. The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell. 1996 Apr 19;85(2):159–170. doi: 10.1016/s0092-8674(00)81093-4. [DOI] [PubMed] [Google Scholar]
  20. Stock A. M., Robinson V. L., Goudreau P. N. Two-component signal transduction. Annu Rev Biochem. 2000;69:183–215. doi: 10.1146/annurev.biochem.69.1.183. [DOI] [PubMed] [Google Scholar]
  21. Tanaka H., Onouchi H., Kondo M., Hara-Nishimura I., Nishimura M., Machida C., Machida Y. A subtilisin-like serine protease is required for epidermal surface formation in Arabidopsis embryos and juvenile plants. Development. 2001 Dec;128(23):4681–4689. doi: 10.1242/dev.128.23.4681. [DOI] [PubMed] [Google Scholar]
  22. Valvekens D., Van Montagu M., Van Lijsebettens M. Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci U S A. 1988 Aug;85(15):5536–5540. doi: 10.1073/pnas.85.15.5536. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Von Groll Uritza, Berger Dieter, Altmann Thomas. The subtilisin-like serine protease SDD1 mediates cell-to-cell signaling during Arabidopsis stomatal development. Plant Cell. 2002 Jul;14(7):1527–1539. doi: 10.1105/tpc.001016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. West A. H., Stock A. M. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem Sci. 2001 Jun;26(6):369–376. doi: 10.1016/s0968-0004(01)01852-7. [DOI] [PubMed] [Google Scholar]
  25. Zeng Z. B. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. doi: 10.1093/genetics/136.4.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]

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