Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development

Becerra, Cristian; Puigdomenech, Pere; Vicient, Carlos M
January 2006
BMC Genomics;2006, Vol. 7, p38
Academic Journal
Background: Plant seeds are complex organs in which maternal tissues, embryo and endosperm, follow distinct but coordinated developmental programs. Some morphogenetic and metabolic processes are exclusively associated with seed development. The goal of this study was to explore the feasibility of incorporating the available online bioinformatics databases to discover Arabidopsis genes specifically expressed in certain organs, in our case immature seeds. Results: A total of 11,032 EST sequences obtained from isolated immature seeds were used as the initial dataset (178 of them newly described here). A pilot study was performed using EST virtual subtraction followed by microarray data analysis, using the Genevestigator tool. These techniques led to the identification of 49 immature seed-specific genes. The findings were validated by RT-PCR analysis and in situ hybridization. Conclusion: We conclude that the combined in silico data analysis is an effective data mining strategy for the identification of tissue-specific gene expression.


Related Articles

  • A comparative map viewer integrating genetic maps for Brassica and Arabidopsis. Lim, Geraldine A. C.; Jewell, Erica G.; Xi Li; Erwin, Timothy A.; Love, Christopher; Batley, Jacqueline; Spangenberg, German; Edwards, David // BMC Plant Biology;2007, Vol. 7, p1 

    Background: Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for Brassica species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the...

  • Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species. Wu, Gideon C.-T.; Feng-Chi Chen // Evolutionary Bioinformatics;2012, Issue 8, p389 

    What causes the variations in evolutionary rates is fundamental to molecular evolution. However, in plants, the causes of within-gene evolutionary rate variations remain underexplored. Here we use the principal component regression to examine the contributions of eleven exon features to the...

  • Involvement of hormones and KNOXI genes in early Arabidopsis seedling development. Souček, Přemysl; Klíma, Petr; Reková, Alena; Brzobohatý, Břetislav // Journal of Experimental Botany;Oct2007, Vol. 58 Issue 13, p3797 

    Plant hormones control plant development by modulating the expression of regulatory genes, including homeobox-containing KNOXI genes. However, much remains to be elucidated about the interactions involved. Therefore, hormonal regulation of KNOXI gene expression was investigated using hormone...

  • Perspectives in Experimental Botany. Changes in gene expression in the () and () mutants of L. Vincent, Carlos M.; Bies-Etheve, Natacha; Delseny, Michel // Journal of Experimental Botany;Jun2000, Vol. 51 Issue 347 

    Examines the effects of Arabidopsis thaliana L. leafy cotyledon (lec1) and fusca3 (fus3) mutations on gene expression during seed development. Gene promoter activity in leafy cotyledon seeds; Transgenic analysis using 5'-promoter deletions; Effects of lec1 and fus3 mutations on proteins...

  • Mapping by VESGEN of Leaf Venation Patterning in Arabidopsis thaliana with Bioinformatic Dimensions of Gene Expression. Parsons-Wingerter, Patricia; Vickerman, Mary B.; Paul, Anna-Lisa; Ferl, Robert J. // Gravitational & Space Biology;Aug2014, Vol. 25 Issue 1, p68 

    The leaf venation of angiosperms is key to their terrestirial dominance. These higher land plants include maple, corn, and ISS model organism Arabidopsis thaliana. The venation-dependent photosynthetic capacity of angiosperm leaves is largely responsible for terrestrial production of glucose and...

  • Genome-wide survey and expression analysis of the OSCA gene family in rice. Yunshuang Li; Fang Yuan; Zhaohong Wen; Yihao Li; Fang Wang; Tao Zhu; Wenqing Zhuo; Xi Jin; Yingdian Wang; Heping Zhao; Zhen-Ming Pei; Shengcheng Han // BMC Plant Biology;10/26/2015, Vol. 15, p1 

    Background: Reception of and response to exogenous and endogenous osmotic changes is important to sustain plant growth and development, as well as reproductive formation. Hyperosmolality-gated calcium-permeable channels (OSCA) were first characterised as an osmosensor in Arabidopsis and are...

  • Seed size mystery.  // Garden;Feb2010, Vol. 135 Issue 2, p78 

    The article reports on the discovery of the gene acting the base of developing seeds of Arabidopsis, a tiny annual weed.

  • Wheat vacuolar H-ATPase subunit B cloning and its involvement in salt tolerance. Li Wang; Xiaoliang He; Yanjun Zhao; Yinzhu Shen; Zhanjing Huang // Planta;Jun2011, Vol. 234 Issue 1, p1 

    Wheat vacuolar H-ATPases (V-ATPase) subunit B, named TaVB, was isolated from the salt-tolerant wheat RH8706-49 and used to transform Arabidopsis plants. TaVB-expressed Arabidopsis has a higher germination rate, root length, V-H-ATPase activity, and overall salt tolerance than the wild type,...

  • Mapping a diploid wheat abscisic acid 8′-hydroxylase homologue in the seed dormancy QTL region on chromosome 5Am. Nakamura, Shingo; Chono, Makiko; Abe, Fumitaka; Miura, Hideho // Euphytica;Jan2010, Vol. 171 Issue 1, p111 

    In Arabidopsis, two genes of abscisic acid (ABA) 8′-hydroxylase ( cytochrome P450 ( CYP) 707A1 and A2) have been found to play important roles in seed dormancy through the regulation of ABA content in seeds. In order to examine the role of wheat ABA 8′-hydroxylase gene in seed...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics