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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 of somatic embryogenesis genes involved in induction.Average values of fragments per kilobase of exon model per million fragments mapped (FPKM) of genes involved in the induction of somatic embryogenesis 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 where (A), (B), and (C) are BBM-like maize genes with high sequence similarity to Brassica napus BABY BOOM (BnBBM1), (D) is maize LEAFY COTYLEDON1 (ZmLEC1), (E) is a maize gene with high sequence similarity to Arabidopsis thaliana LEAFY COTYLEDON2 (AtLEC2), and (F) is maize VIVIPARIOUS1 (VP1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).
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pone-0111407-g003: Gene expression of somatic embryogenesis genes involved in induction.Average values of fragments per kilobase of exon model per million fragments mapped (FPKM) of genes involved in the induction of somatic embryogenesis 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 where (A), (B), and (C) are BBM-like maize genes with high sequence similarity to Brassica napus BABY BOOM (BnBBM1), (D) is maize LEAFY COTYLEDON1 (ZmLEC1), (E) is a maize gene with high sequence similarity to Arabidopsis thaliana LEAFY COTYLEDON2 (AtLEC2), and (F) is maize VIVIPARIOUS1 (VP1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).

Mentions: Genes involved in embryogenic pathway initiations include BABY BOOM (BBM) and LEAFY COTYLEDON (LEC) genes [7]. In this study, we highlight three maize genes that showed high sequence similarity to the highly conserved AP2 binding domain of Brassica napus BBM (BnBBM1, accession number AF317904). GRMZM2G366434, GRMZM2G141638, and GRMZM2G139082 are 91.2%, 92.5%, and 93.2% similar to the translated amino acid sequence of BnBBM1, respectively (Figure S1). GRMZM2G366434 showed a 4-fold up-regulation relative to 0 h at 36, 48 and 72 h (Figure 3A), GRMZM2G141638 also increased during this time course (Figure 3B), and GRMZM2G139082 increased over 4-fold from 0 to 72 h (Figure 3C). These maize BBM-like genes were grouped into cluster 3.


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 of somatic embryogenesis genes involved in induction.Average values of fragments per kilobase of exon model per million fragments mapped (FPKM) of genes involved in the induction of somatic embryogenesis 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 where (A), (B), and (C) are BBM-like maize genes with high sequence similarity to Brassica napus BABY BOOM (BnBBM1), (D) is maize LEAFY COTYLEDON1 (ZmLEC1), (E) is a maize gene with high sequence similarity to Arabidopsis thaliana LEAFY COTYLEDON2 (AtLEC2), and (F) is maize VIVIPARIOUS1 (VP1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4214754&req=5

pone-0111407-g003: Gene expression of somatic embryogenesis genes involved in induction.Average values of fragments per kilobase of exon model per million fragments mapped (FPKM) of genes involved in the induction of somatic embryogenesis 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 where (A), (B), and (C) are BBM-like maize genes with high sequence similarity to Brassica napus BABY BOOM (BnBBM1), (D) is maize LEAFY COTYLEDON1 (ZmLEC1), (E) is a maize gene with high sequence similarity to Arabidopsis thaliana LEAFY COTYLEDON2 (AtLEC2), and (F) is maize VIVIPARIOUS1 (VP1). Bars indicate average mean ± SE (n = 4 for 0, 24, 36, and 48 h include technical and biological replicates; n = 2 for 72 h include only technical replicates).
Mentions: Genes involved in embryogenic pathway initiations include BABY BOOM (BBM) and LEAFY COTYLEDON (LEC) genes [7]. In this study, we highlight three maize genes that showed high sequence similarity to the highly conserved AP2 binding domain of Brassica napus BBM (BnBBM1, accession number AF317904). GRMZM2G366434, GRMZM2G141638, and GRMZM2G139082 are 91.2%, 92.5%, and 93.2% similar to the translated amino acid sequence of BnBBM1, respectively (Figure S1). GRMZM2G366434 showed a 4-fold up-regulation relative to 0 h at 36, 48 and 72 h (Figure 3A), GRMZM2G141638 also increased during this time course (Figure 3B), and GRMZM2G139082 increased over 4-fold from 0 to 72 h (Figure 3C). These maize BBM-like genes were grouped into cluster 3.

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