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E-GEOD-21598 - Identification of genes differentially expressed between developing seeds of different soybean varieties

Status
Released on 29 April 2015, last updated on 2 May 2015
Organism
Glycine max
Samples (54)
Array (1)
Protocols (7)
Description
Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits. The soybean plants of two soybean varieties Minsoy and Archer and two recombinant inbred lines from the cross that are similar in maturity but differ in yield were grown in St Paul, Minnesota during the summers of 2007 and 2008. In 2007, each line was planted as a single row. In 2008, a randomized complete block (RCB) design was used and each line had 3 replicates planted 1-2 weeks apart. Within each replicate, two rows per line were planted. Seeds were harvested at three developmental stages, namely, seed length = 2 mm, 3.5 mm, and 5-6 mm, which correspond approximately to soybean reproductive stages R4, R5 and early R6, respectively. In 2007 three independent samples were collected for each line and developmental stage. In 2008, two seed samples (one from each row) were collected for each line at each stage within each replicate. The pairs of seed samples were then pooled. Thus, three sets of independent tissue samples were collected for RNA extraction and hybridization on Affymetrix microarrys.
Experiment type
transcription profiling by array 
Contacts
Fumiaki Katagiri, James H Orf, Jane Glazebrook, Rongshuang Lin, Susan I Gibson
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-21598.idf.txt
Sample and data relationshipE-GEOD-21598.sdrf.txt
Raw data (2)E-GEOD-21598.raw.1.zip, E-GEOD-21598.raw.2.zip
Processed data (1)E-GEOD-21598.processed.1.zip
Array designA-AFFY-59.adf.txt
Links