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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.


Gene Ontology (GO)slim categorization of differentially expressed probe sets. Panel (a) describes the percentage of probe sets annotated to different GOslim functional categories. Panel (b) describes the percentage of probe sets annotated to different GOslim biological process categories The percentage of probe sets annotated to a GOslim category is equal to the number of probe sets annotated to terms in that GOslim category/total number of probe sets annotated to any term in this ontology times 100. The light-gray bars illustrate data from the 97 probe sets differentially expressed between Minsoy and Archer and the dark-gray bars represent all the other probe sets on the array whose expression was detected in 2007 and 2008. * indicates that the results of the 97 differentially expressed probe sets differed from those of all other detected probe sets on the array with a p-value < 0.1 and ** indicates the results differed with a p-value < 0.05 using Fisher's exact test.
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f0010: Gene Ontology (GO)slim categorization of differentially expressed probe sets. Panel (a) describes the percentage of probe sets annotated to different GOslim functional categories. Panel (b) describes the percentage of probe sets annotated to different GOslim biological process categories The percentage of probe sets annotated to a GOslim category is equal to the number of probe sets annotated to terms in that GOslim category/total number of probe sets annotated to any term in this ontology times 100. The light-gray bars illustrate data from the 97 probe sets differentially expressed between Minsoy and Archer and the dark-gray bars represent all the other probe sets on the array whose expression was detected in 2007 and 2008. * indicates that the results of the 97 differentially expressed probe sets differed from those of all other detected probe sets on the array with a p-value < 0.1 and ** indicates the results differed with a p-value < 0.05 using Fisher's exact test.

Mentions: As the 97 transcripts found to be differentially expressed in both years analyzed may be more likely to play important roles in controlling differences in seed development and metabolism, including potentially differences in some agronomic traits, than genes that were found to be differentially expressed in only one of the years analyzed, further analyses and discussion are focused on these 97 transcripts. Annotation information for all probe sets that were differentially expressed in either year between either the parental cultivars or the two RILs analyzed is also provided in Supplementary Files 4 and 5. Approximately 78% of the 97 probe sets differentially expressed in Minsoy and Archer in both years analyzed were annotated based on their homology to Arabidopsis thaliana gene models or to protein sequences from other organisms (Supplementary File 6). Probe sets were classified based on their GOslim descriptions and the percentages of probe sets assigned to each GOslim category were calculated (Fig. 2). As shown in Fig. 2, many probe sets fall into the “unknown” or “other” categories for molecular functions or biological processes. Probe sets involved in receptor binding/activity and protein binding were overrepresented compared with the remaining expressed transcripts. The finding that probe sets involved in receptor binding/activity or protein binding are overrepresented among the differentially expressed probe sets is interesting as genes with these activities may be more likely than most genes to play important roles in signal transduction pathways. For biological process, probe sets in the protein metabolism category were underrepresented among the differentially expressed probe sets.


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)

Gene Ontology (GO)slim categorization of differentially expressed probe sets. Panel (a) describes the percentage of probe sets annotated to different GOslim functional categories. Panel (b) describes the percentage of probe sets annotated to different GOslim biological process categories The percentage of probe sets annotated to a GOslim category is equal to the number of probe sets annotated to terms in that GOslim category/total number of probe sets annotated to any term in this ontology times 100. The light-gray bars illustrate data from the 97 probe sets differentially expressed between Minsoy and Archer and the dark-gray bars represent all the other probe sets on the array whose expression was detected in 2007 and 2008. * indicates that the results of the 97 differentially expressed probe sets differed from those of all other detected probe sets on the array with a p-value < 0.1 and ** indicates the results differed with a p-value < 0.05 using Fisher's exact test.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Gene Ontology (GO)slim categorization of differentially expressed probe sets. Panel (a) describes the percentage of probe sets annotated to different GOslim functional categories. Panel (b) describes the percentage of probe sets annotated to different GOslim biological process categories The percentage of probe sets annotated to a GOslim category is equal to the number of probe sets annotated to terms in that GOslim category/total number of probe sets annotated to any term in this ontology times 100. The light-gray bars illustrate data from the 97 probe sets differentially expressed between Minsoy and Archer and the dark-gray bars represent all the other probe sets on the array whose expression was detected in 2007 and 2008. * indicates that the results of the 97 differentially expressed probe sets differed from those of all other detected probe sets on the array with a p-value < 0.1 and ** indicates the results differed with a p-value < 0.05 using Fisher's exact test.
Mentions: As the 97 transcripts found to be differentially expressed in both years analyzed may be more likely to play important roles in controlling differences in seed development and metabolism, including potentially differences in some agronomic traits, than genes that were found to be differentially expressed in only one of the years analyzed, further analyses and discussion are focused on these 97 transcripts. Annotation information for all probe sets that were differentially expressed in either year between either the parental cultivars or the two RILs analyzed is also provided in Supplementary Files 4 and 5. Approximately 78% of the 97 probe sets differentially expressed in Minsoy and Archer in both years analyzed were annotated based on their homology to Arabidopsis thaliana gene models or to protein sequences from other organisms (Supplementary File 6). Probe sets were classified based on their GOslim descriptions and the percentages of probe sets assigned to each GOslim category were calculated (Fig. 2). As shown in Fig. 2, many probe sets fall into the “unknown” or “other” categories for molecular functions or biological processes. Probe sets involved in receptor binding/activity and protein binding were overrepresented compared with the remaining expressed transcripts. The finding that probe sets involved in receptor binding/activity or protein binding are overrepresented among the differentially expressed probe sets is interesting as genes with these activities may be more likely than most genes to play important roles in signal transduction pathways. For biological process, probe sets in the protein metabolism category were underrepresented among the differentially expressed probe sets.

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.