Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://link.springer.com/doi/10.1007/s00122-005-1977-9 below:

Designing a microarray experiment to estimate dominance in maize (Zea mays L.)

Experiments using cDNA microarrays for the identification of genes with certain expression patterns require a thoughtfully planned design. This study was conducted to determine an optimal design for a microarray experiment to estimate differential gene expression between hybrids and their parental inbred lines in maize (i.e. dominance). It has two features: the contrasts of interest contain more than two genotypes and the procedure may be customised to other microarray experiments where different effects may influence hybridisation signals. A mixed model was used to include all important effects. Impacts during growth of the plant material were taken into consideration as well as those occurring during hybridisation. The results of a preliminary experiment were used to determine which effects were to be included in the model, and data from another microarray experiment were used to estimate variance components. In order to select good designs, an optimality criterion adapted to the problem of differential gene expression between hybrids and their parental inbred lines was defined. Two approaches were used to determine an optimal design: the first one simplifies the problem by dividing it into several subproblems, whereas the second is more sophisticated and uses a simulated annealing (SA) algorithm. We found that the first approach constitutes a useful means for designing microarray experiments to study this problem. Using the more sophisticated SA approach the design can be further improved.

This is a preview of subscription content, log in via an institution to check access.

Springer+ Basic

€34.99 /Month

• Get 10 units per month
• Download Article/Chapter or eBook
• 1 Unit = 1 Article or 1 Chapter
• Cancel anytime

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

• Angelis L, Bora-Senta E, Moyssiadis C (2001) Optimal exact experimental designs with correlated errors through a simulated annealing algorithm. Comput Stat Data Anal 37:275–296

  MathSciNet  Google Scholar 

• Auger DL, Gray AD, Ream TS, Kato A, Coe EH, Birchler JA (2004) Non-additive gene expression in diploid and triploid hybrids of maize. Genetics 169:389–397

  PubMed  Google Scholar 

• Birchler JA, Auger DL, Riddle NC (2003) In search of the molecular basis of heterosis. Plant Cell 15:2236–2239

  CAS  PubMed  Google Scholar 

• Darwin C (1876) The effects of cross and self-fertilization in the vegetal kingdom. John Murray, London

  Google Scholar 

• East EM (1908) Inbreeding in corn. Rep Conn Agric Exp Stn 1907:419–428

  Google Scholar 

• Freeman GH (1976) On the selection of designs for comparative experiments. Biometrics 32:195–199

  Google Scholar 

• Gibson G, Riley-Berger R, Harshman L, Kopp A, Vacha S, Nuzhdin S, Wayne M (2004) Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167:1791–1799

  CAS  PubMed  Google Scholar 

• Guo M, Rupe MA, Danilevskaya ON, Yang X, Hu Z (2003) Genome-wide mRNA profiling reveals heterochromic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J 36:30–44

  CAS  PubMed  Google Scholar 

• Hetz W, Hochholdinger F, Schwall M, Feix G (1996) Isolation and characterisation of rtcs, a mutant deficient in the formation of nodal roots. Plant J 10:845–857

  CAS  Google Scholar 

• John JA, Williams ER (1995) Cyclic and computer generated designs. Chapman & Hall, London

  Google Scholar 

• Kerr MK (2003) Design considerations for efficient and effective microarray studies. Biometrics 59:822–828

  PubMed  MathSciNet  Google Scholar 

• Kerr MK, Churchill GA (2001) Experimental design for gene expression microarrays. Biostatistics 2:183–201

  PubMed  Google Scholar 

• Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671–680

  Google Scholar 

• Kollipara KP, Saab IN, Wych RD, Lauer MJ and Singletary GW (2002) Expression profiling of reciprocal maize hybrids divergent for cold germination and desiccation tolerance. Plant Physiol 129:974–992

  CAS  PubMed  Google Scholar 

• Lamkey KR, Edwards JW (1998) Heterosis: Theory and estimation. In: Proc 34th Illinois Corn Breeders’ School. Urbana, pp 62–77

• Nakazono M, Qiu F, Borsuk LA, Schnable PS (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize (Erratum in: Plant Cell 15:1049). Plant Cell 15:583–596

  CAS  PubMed  Google Scholar 

• Ni NZ, Sun Q, Liu Z, Wu L, Wang X (2000) Identification of a hybrid-specific expressed gene encoding novel RNA-binding protein in wheat seedling leaves using differential display of mRNA. Mol Gen Genet 263:934–938

  CAS  PubMed  Google Scholar 

• Pearce SC (1974) Optimality of design in plot experiments. In: Proc 8th Int Biometric Conf. Constanta, Romania

• Schnable PS, Hochholdinger F, Nakazono M (2004) Global expression profiling applied to plant development. Curr Opin Plant Biol 7:50–56

  CAS  PubMed  Google Scholar 

• Shull GH (1908) The composition of a field of maize. Rep Am Breed Assoc 4:296–301

  Google Scholar 

• Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839

  CAS  PubMed  Google Scholar 

• Yang X, Ye K, Hoeschele I (2002) Some E-optimal designs for cDNA microarray experiments. In: ASA Proc Joint Stat Meet. Madison, ASA, Wis., pp 3853–3954

Download references

This project was supported by the DFG (German Research Foundation) in the framework program “Heterosis in Plants” (research grants HO 2249/6-1 and PI 377/7-1). Work on the mutant rtcs in F.H.S laboratory is supported by DFG Grant HO2249/4-1.

1. Institute for Crop Production and Grassland Research, University of Hohenheim, Fruwirthstr 23, 70599, Stuttgart, Germany

   B. Keller, K. Emrich & H.-P. Piepho

2. Department of General Genetics, Center for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany

   N. Hoecker, M. Sauer & F. Hochholdinger

1. B. Keller
2. K. Emrich
3. N. Hoecker
4. M. Sauer
5. F. Hochholdinger
6. H.-P. Piepho

Correspondence to H.-P. Piepho.

Communicated by R. Bernardo

Keller, B., Emrich, K., Hoecker, N. et al. Designing a microarray experiment to estimate dominance in maize (Zea mays L.). Theor Appl Genet 111, 57–64 (2005). https://doi.org/10.1007/s00122-005-1977-9

Download citation

• Received: 06 August 2004

• Accepted: 19 February 2005

• Published: 11 May 2005

• Issue Date: June 2005

• DOI: https://doi.org/10.1007/s00122-005-1977-9

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4