Transcript Profiling of Soybean Seed Development from Fertilization to Maturity

Transcript Profiling of Soybean Seed Development from Fertilization to Maturity

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The goal of this work is to gain a global overview of the genes whose expression levels change significantly during various stages of soybean seed development, from just a few days after fertilization to the stages of seed fill, maturation, and desiccation. Gene expression over five stages from four to twenty-four days after fertilization in whole seeds was measured using microarrays containing 38, 400 soybean cDNAs. Data were analyzed using two different methods---one based on standard error and two-fold differential expression, and the other based on p-value---with 821 and 8448 genes, respectively, found to be significant. These genes were grouped by the similarity of their expression profiles over the course of development using k-means clustering, and the genes were also divided by hand into ten functional categories based on their annotations. Additionally, data obtained previously (Jones 2004) over five stages of soybean cotyledon development from mid-maturation through desiccation using microarrays containing more than 27, 000 soybean cDNAs was reevaluated using a p-value filter. The expression level changes of selected genes were also retested in these older stages using a second, highly repetitive oligo microarray. The information gained from these studies can reveal trends in gene expression patterns during many key stages in the process of soybean seed development. Changes in the expression of genes related to cell wall enzymes, for example, were observed throughout the early stages of development, as well as apparent differences between the expression of genes related to the photosystems. A variety of expression patterns were found in genes related to flavonoid synthesis enzymes also. Additionally, a number of genes with embryo-specific annotations were found to be significant during these early, post-fertilization stages of seed development. In the older cotyledon stages, genes related to cell growth and maintenance, as well as to energy processes, were found to be more highly expressed at the earlier stages of development, while genes involved in transcription were often over-expressed at the later, desiccating stages of development. This may indicate the transcripts or products of these genes are stored in the quiescent seeds for use in early stages of imbibition and germination.... design and unincorporated nucleotides were removed using a QIAquick PCR purification kit (Qiagen, Valencia, CA) according to the manufacturera#39;s instructions. ... The slides were then spun dry in an Eppendorf 5810R centrifuge at 800 rpm.

Title:Transcript Profiling of Soybean Seed Development from Fertilization to Maturity
Author: Sarah I. Jones
Publisher:ProQuest - 2009

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