Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

The genetic control of gene expression during shoot development in Arabidopsis thaliana was analyzed by combining quantitative trait loci (QTL) and microarray analysis. Using oligonucleotide array data from 30 recombinant inbred lines derived from a cross of Columbia and Landsberg erecta ecotypes, the Arabidopsis genome was scanned for marker-by-gene linkages or so-called expression QTL (eQTL). Single-feature polymorphisms (SFPs) associated with sequence disparities between ecotypes were purged from the data. SFPs may alter the hybridization efficiency between cDNAs from one ecotype with probes of another ecotype. In genome scans, five eQTL hot spots were found with significant marker-by-gene linkages. Two of the hot spots coincided with classical QTL conditioning shoot regeneration, suggesting that some of the heritable gene expression changes observed in this study are related to differences in shoot regeneration efficiency between ecotypes. Some of the most significant eQTL, particularly those at the shoot regeneration QTL sites, tended to show cis-chromosomal linkages in that the target genes were located at or near markers to which their expression was linked. However, many linkages of lesser significance showed expected “trans-effects,” whereby a marker affects the expression of a target gene located elsewhere on the genome. Some of these eQTL were significantly linked to numerous genes throughout the genome, suggesting the occurrence of large groups of coregulated genes controlled by single markers.

[1]  E. Petretto,et al.  Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease , 2005, Nature Genetics.

[2]  Andrew I Su,et al.  Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics' , 2005, Nature Genetics.

[3]  Robert W. Williams,et al.  Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function , 2005, Nature Genetics.

[4]  R. Bošković,et al.  Genetical polymorphism of acc synthase and ACC oxidase in Apple selections bred in Čačak , 2005 .

[5]  Steen Knudsen,et al.  Alternative mapping of probes to genes for Affymetrix chips , 2004, BMC Bioinformatics.

[6]  D. Nettleton,et al.  Quantitative Trait Loci Associated With Adventitious Shoot Formation in Tissue Culture and the Program of Shoot Development in Arabidopsis , 2004, Genetics.

[7]  Michael Black,et al.  Role of transposable elements in heterochromatin and epigenetic control , 2004, Nature.

[8]  T. Komatsuda,et al.  Genetic mapping of a quantitative trait locus (QTL) that enhances the shoot differentiation rate in Hordeum vulgare L. , 1993, Theoretical and Applied Genetics.

[9]  I. Holme,et al.  Quantitative trait loci affecting plant regeneration from protoplasts of Brassica oleracea , 2004, Theoretical and Applied Genetics.

[10]  T. Laux,et al.  Apical meristems: the plant's fountain of youth. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[12]  R. Stoughton,et al.  Genetics of gene expression surveyed in maize, mouse and man , 2003, Nature.

[13]  Detlef Weigel,et al.  Large-scale identification of single-feature polymorphisms in complex genomes. , 2003, Genome research.

[14]  Ritsert C. Jansen,et al.  Studying complex biological systems using multifactorial perturbation , 2003, Nature Reviews Genetics.

[15]  S. Howell,et al.  Developmental events and shoot apical meristem gene expression patterns during shoot development in Arabidopsis thaliana. , 2002, The Plant journal : for cell and molecular biology.

[16]  S. Takada,et al.  Embryonic shoot apical meristem formation in higher plants , 2002, Journal of Plant Research.

[17]  D. Gingerich,et al.  Global and Hormone-Induced Gene Expression Changes during Shoot Development in Arabidopsis , 2002, The Plant Cell Online.

[18]  Ingo Schubert,et al.  Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[20]  R. Doerge Multifactorial genetics: Mapping and analysis of quantitative trait loci in experimental populations , 2002, Nature Reviews Genetics.

[21]  J. Nap,et al.  Genetical genomics : the added value from segregation , 2001 .

[22]  M. Candela,et al.  Use of recombinant inbred lines (RILs) to identify, locate and map major genes and quantitative trait loci involved with in vitro regeneration ability in Arabidopsis thaliana , 2001, Theoretical and Applied Genetics.

[23]  R. Wilson,et al.  The Complete Sequence of a Heterochromatic Island from a Higher Eukaryote , 2000, Cell.

[24]  F. Taguchi-Shiobara,et al.  Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L. , 1997, Theoretical and Applied Genetics.

[25]  B. Wakimoto,et al.  Heterochromatin and gene expression in Drosophila. , 1995, Annual review of genetics.

[26]  C. Lister,et al.  Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana , 1993 .

[27]  R. Pierik Micropropagation of ornamental plants. , 1991 .

[28]  M. Van Montagu,et al.  Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[29]  F. J. Anscombe,et al.  THE TRANSFORMATION OF POISSON, BINOMIAL AND NEGATIVE-BINOMIAL DATA , 1948 .