Flux of transcript patterns during soybean seed development

Abstract

Background: To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. A subset of these genes on a highly-repetitive 70-mer oligonucleotide microarray was also used to support the results.

Results: It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of highest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages.

Conclusions: Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using two different types of microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination.

Figure 1

Timeline of development in soybean seeds from mid-maturation to desiccation. Fresh weight range in mg shown on Y axis. Dotted bar indicates the reference tissue. Reproductive (R) developmental stages according to [1] shown below each stage are approximate.

Figure 2

The expression profiles of 2227 soybean cDNAs in cotyledons, divided into eleven k-means clusters (PVSets). All of these genes have p-values ≤ 0.05 in at least three of the five stages. Normalized ratio intensities are shown on the Y axis. The five stages of development are marked on the X axis, from youngest to oldest (left to right): 1 = 25-50 mg, 2 = 75-100 mg, 3 = 400-500 mg, 4 = yellow, 5 = dry seed. Sets are numbered randomly by GeneSpring. Set numbers and the total number of genes per set are shown at the top of each set.

Figure 3

Fold change for selected transcription factors in two array formats. The stages dry seed vs. 100-200 mg cotyledon are compared. Y-axis shows fold change, X-axis shows nineteen transcription factors found to increase in expression at the dry seed stage using Array Format 1. Numbers along X-axis correlate to Table 2. Yellow bars represent fold change in Array Format 1; blue bars represent fold change in Array Format 2. Fold changes are based on normalized ratios. Stars indicate standard error of measurement is >0.5. Error bars show standard error of each measurement. The actual p-values and standard errors are shown in Table 2.

Figure 4

Expression data from four transcription factors across five stages and two array formats. X-axes show the five stages of development, each compared to the reference tissue. Y-axes show the ratio of the expression in the developmental stage compared to the reference. Diamonds (connected by lines) indicate the ratio according to Array Format 1. Squares indicate the ratio according to Array Format 2. Solid markers indicate measurement has p-value ≤ 0.05. All measurements shown have standard error ≤ 0.5. The name of the gene is shown below each graph. Note that scales differ slightly across graphs.

Figure 5

Expression profiles of genes annotated as two storage proteins. Data according to Array Format 1. Glycinin is shown at top, in grey; conglycinin is shown at bottom, in black. X-axes show the five stages of development, each compared to the reference tissue. Y-axes show the ratio of the expression in the developmental stage compared to the reference. All measurements shown have standard error ≤ 0.5. All fourteen genes annotated as glycinin, and fifteen genes annotated as conglycinin, from Array Format 1 are shown.

Figure 6

Expression data from four storage protein genes across five stages and two array formats. Genes annotated as glycinin (upper left) or conglycinin (other three). X-axes show the five stages of development, each compared to the reference tissue. Y-axes show the ratio of the expression in the developmental stage compared to the ratio. Diamonds (connected by lines) indicate the ratio according to Array Format 1. Squares indicate the ratio according to Array Format 2. Solid markers indicate measurement has p-value ≤ 0.05. All measurements shown have standard error ≤ 0.5.