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Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Salvo SA, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF - PLoS ONE (2014)

Bottom Line: We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium.Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study.Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America.

ABSTRACT
Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.

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Gene expression changes in early somatic embryogenesis.Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.
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pone-0111407-g001: Gene expression changes in early somatic embryogenesis.Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.

Mentions: In order to gain an understanding of genes expressed in this time course study, we selected genes differentially expressed by at least 8-fold compared to the control time point (0 h). Comparison of gene expression patterns across the surveyed time points indicated that the largest number of genes with a change in expression profile was from 0 to 24 h (Figure 1). This is supported by the observation that 1,856 genes were expressed at (or greater than) an 8-fold change when comparing 0 vs 24 h, 1,559 genes at an 8-fold change when comparing 0 vs 36 h, 1,496 genes at an 8-fold change when comparing 0 vs 48 h, and 1,488 genes at an 8-fold change when comparing 0 vs 72 h. Similarly, comparisons at other time points revealed 177, 45, and 41 genes differentially expressed 8-fold in comparisons of 24 vs 36, 36 vs 48, and 48 vs 72 h, respectively. Most genes differentially expressed at 8-fold were up-regulated. For example, 72%, 67%, 66%, and 72% of the genes differentially expressed when compared to 0 h were up-regulated at 24, 36, 48, and 72 h time points, respectively (Table S4). When considering a 2-fold change in expression, 8,174 genes were differentially expressed when comparing 0 vs 24 h, 6,737 genes when comparing 0 vs 36 h, 6,444 genes when comparing 0 vs 48 h, and 6,580 when comparing 0 vs 72 h.


Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Salvo SA, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF - PLoS ONE (2014)

Gene expression changes in early somatic embryogenesis.Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214754&req=5

pone-0111407-g001: Gene expression changes in early somatic embryogenesis.Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.
Mentions: In order to gain an understanding of genes expressed in this time course study, we selected genes differentially expressed by at least 8-fold compared to the control time point (0 h). Comparison of gene expression patterns across the surveyed time points indicated that the largest number of genes with a change in expression profile was from 0 to 24 h (Figure 1). This is supported by the observation that 1,856 genes were expressed at (or greater than) an 8-fold change when comparing 0 vs 24 h, 1,559 genes at an 8-fold change when comparing 0 vs 36 h, 1,496 genes at an 8-fold change when comparing 0 vs 48 h, and 1,488 genes at an 8-fold change when comparing 0 vs 72 h. Similarly, comparisons at other time points revealed 177, 45, and 41 genes differentially expressed 8-fold in comparisons of 24 vs 36, 36 vs 48, and 48 vs 72 h, respectively. Most genes differentially expressed at 8-fold were up-regulated. For example, 72%, 67%, 66%, and 72% of the genes differentially expressed when compared to 0 h were up-regulated at 24, 36, 48, and 72 h time points, respectively (Table S4). When considering a 2-fold change in expression, 8,174 genes were differentially expressed when comparing 0 vs 24 h, 6,737 genes when comparing 0 vs 36 h, 6,444 genes when comparing 0 vs 48 h, and 6,580 when comparing 0 vs 72 h.

Bottom Line: We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium.Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study.Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America.

ABSTRACT
Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.

Show MeSH
Related in: MedlinePlus