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Identification of differentially expressed genes between developing seeds of different soybean cultivars.

Lin R, Glazebrook J, Katagiri F, Orf JH, Gibson SI - Genom Data (2015)

Bottom Line: Soybean is a major source of protein and oil and a primary feedstock for biodiesel production.Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits.To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, 1500 Gortner Ave., Saint Paul, MN 55108, USA.

ABSTRACT
Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits. Others of these probe sets may be involved in regulation of general seed development or metabolism. All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.

No MeSH data available.


Comparison of differentially expressed probe sets between Minsoy and Archer. A comparison was made for each developmental stage to identify probe sets differentially expressed in both 2007 and 2008 (panels a, b, c); then the numbers from the three stages were combined in panel (d). In panels (a), (b) and (c), the number in the left circle represents probe sets unique to 2007, the number in the right circle represents probe sets unique to 2008, and the number in the center area represents probe sets common to 2007 and 2008. Panel (d) illustrates the distribution of probe sets common to 2007 and 2008 among the three stages.
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f0005: Comparison of differentially expressed probe sets between Minsoy and Archer. A comparison was made for each developmental stage to identify probe sets differentially expressed in both 2007 and 2008 (panels a, b, c); then the numbers from the three stages were combined in panel (d). In panels (a), (b) and (c), the number in the left circle represents probe sets unique to 2007, the number in the right circle represents probe sets unique to 2008, and the number in the center area represents probe sets common to 2007 and 2008. Panel (d) illustrates the distribution of probe sets common to 2007 and 2008 among the three stages.

Mentions: Using the cutoffs described above, a total of 574 probe sets were found to be differentially expressed between the two parental cultivars in 2007 and 232 probe sets were found to be differentially expressed between the two parental cultivars in 2008. These differentially expressed probe sets are distributed approximately equally among the three developmental stages tested and a substantial number of these probe sets were found to be differentially expressed at more than one developmental stage (Fig. 1). The higher number of differentially expressed probe sets in 2007 compared with 2008 may be related to the fact that replicate samples were collected from a single row in 2007 and thus may have had lower variability than the replicate samples collected from multiple rows in 2008. About 48% and 45% of the differentially expressed probe sets were expressed at higher levels in Minsoy than in Archer in 2007 and 2008, respectively. Thus, the number of probe sets that are expressed at higher levels in Minsoy is approximately equal to the number of probe sets that are expressed at higher levels in Archer. The union of the differentially expressed probe sets identified in 2007 and 2008 is 700; data for expression values, fold changes and q-values for these genes are available in Supplementary file 4.


Identification of differentially expressed genes between developing seeds of different soybean cultivars.

Lin R, Glazebrook J, Katagiri F, Orf JH, Gibson SI - Genom Data (2015)

Comparison of differentially expressed probe sets between Minsoy and Archer. A comparison was made for each developmental stage to identify probe sets differentially expressed in both 2007 and 2008 (panels a, b, c); then the numbers from the three stages were combined in panel (d). In panels (a), (b) and (c), the number in the left circle represents probe sets unique to 2007, the number in the right circle represents probe sets unique to 2008, and the number in the center area represents probe sets common to 2007 and 2008. Panel (d) illustrates the distribution of probe sets common to 2007 and 2008 among the three stages.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664686&req=5

f0005: Comparison of differentially expressed probe sets between Minsoy and Archer. A comparison was made for each developmental stage to identify probe sets differentially expressed in both 2007 and 2008 (panels a, b, c); then the numbers from the three stages were combined in panel (d). In panels (a), (b) and (c), the number in the left circle represents probe sets unique to 2007, the number in the right circle represents probe sets unique to 2008, and the number in the center area represents probe sets common to 2007 and 2008. Panel (d) illustrates the distribution of probe sets common to 2007 and 2008 among the three stages.
Mentions: Using the cutoffs described above, a total of 574 probe sets were found to be differentially expressed between the two parental cultivars in 2007 and 232 probe sets were found to be differentially expressed between the two parental cultivars in 2008. These differentially expressed probe sets are distributed approximately equally among the three developmental stages tested and a substantial number of these probe sets were found to be differentially expressed at more than one developmental stage (Fig. 1). The higher number of differentially expressed probe sets in 2007 compared with 2008 may be related to the fact that replicate samples were collected from a single row in 2007 and thus may have had lower variability than the replicate samples collected from multiple rows in 2008. About 48% and 45% of the differentially expressed probe sets were expressed at higher levels in Minsoy than in Archer in 2007 and 2008, respectively. Thus, the number of probe sets that are expressed at higher levels in Minsoy is approximately equal to the number of probe sets that are expressed at higher levels in Archer. The union of the differentially expressed probe sets identified in 2007 and 2008 is 700; data for expression values, fold changes and q-values for these genes are available in Supplementary file 4.

Bottom Line: Soybean is a major source of protein and oil and a primary feedstock for biodiesel production.Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits.To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, 1500 Gortner Ave., Saint Paul, MN 55108, USA.

ABSTRACT
Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits. Others of these probe sets may be involved in regulation of general seed development or metabolism. All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.

No MeSH data available.