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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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K-means clustering of genes expressed during early somatic embryogenesis.Log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in genes with greater than zero FPKM expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium grouped by expression trends as uncentered Pearson’s correlation coefficient in six k-means clusters.
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pone-0111407-g002: K-means clustering of genes expressed during early somatic embryogenesis.Log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in genes with greater than zero FPKM expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium grouped by expression trends as uncentered Pearson’s correlation coefficient in six k-means clusters.

Mentions: The induction of somatic embryogenesis involves a complex coordination of multiple pathways [20], [21]. Genes involved in hormone response, signal transduction, stress response, transcriptional regulation and cellular reorganization have been described previously [7], [9], [20]. We sought to determine if our maize transcriptome data supported concepts and models regarding these major biological functions during the very early stages of embryogenic tissue culture initiation. Using k-means clustering with six clusters, we identified groups of genes with similar expression patterns including: (1) up-regulated and then down-regulated during the developmental window highlighted in this study, (2) both up- and down-regulated during the time course, (3) genes with an expression trend towards increased up-regulation from 0 to 24 h, (4) genes with a higher up-regulation later in the time course at 36, 48 and 72 h compared to all other genes expressed in the developmental window, (5) genes with an expression trend towards large-scale down-regulation from 0 to 24 h, and (6) genes with constitutive expression throughout the study (Figure 2 and Table S6).


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)

K-means clustering of genes expressed during early somatic embryogenesis.Log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in genes with greater than zero FPKM expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium grouped by expression trends as uncentered Pearson’s correlation coefficient in six k-means clusters.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111407-g002: K-means clustering of genes expressed during early somatic embryogenesis.Log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in genes with greater than zero FPKM expressed in immature zygotic embryo explants of maize inbred line A188 at 0, 24, 36, 48, and 72 h after placement on culture initiation medium grouped by expression trends as uncentered Pearson’s correlation coefficient in six k-means clusters.
Mentions: The induction of somatic embryogenesis involves a complex coordination of multiple pathways [20], [21]. Genes involved in hormone response, signal transduction, stress response, transcriptional regulation and cellular reorganization have been described previously [7], [9], [20]. We sought to determine if our maize transcriptome data supported concepts and models regarding these major biological functions during the very early stages of embryogenic tissue culture initiation. Using k-means clustering with six clusters, we identified groups of genes with similar expression patterns including: (1) up-regulated and then down-regulated during the developmental window highlighted in this study, (2) both up- and down-regulated during the time course, (3) genes with an expression trend towards increased up-regulation from 0 to 24 h, (4) genes with a higher up-regulation later in the time course at 36, 48 and 72 h compared to all other genes expressed in the developmental window, (5) genes with an expression trend towards large-scale down-regulation from 0 to 24 h, and (6) genes with constitutive expression throughout the study (Figure 2 and Table S6).

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