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Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

Brown AV, Hudson KA - BMC Plant Biol. (2015)

Bottom Line: Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development.The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets.These results help validate functional annotation for soybean genes and promoters.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. brown637@purdue.edu.

ABSTRACT

Background: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon.

Results: To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence.

Conclusions: The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.

No MeSH data available.


Related in: MedlinePlus

Regulation of N and S transporter genes. Differentially expressed genes annotated as N transporters in (a) cotyledons and (b) leaves. Blue and green lines represent nitrate transporters, pink and red lines represent ammonium transporters. Solid lines represent genes that were differentially expressed in both tissues, while dashed lines show genes that were differentially expressed in either cotyledons or leaves. Genes annotated as sulfate transporters from the cotyledons are shown in (c) and from the leaves in (d) Y-axis is log2 scale
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Fig4: Regulation of N and S transporter genes. Differentially expressed genes annotated as N transporters in (a) cotyledons and (b) leaves. Blue and green lines represent nitrate transporters, pink and red lines represent ammonium transporters. Solid lines represent genes that were differentially expressed in both tissues, while dashed lines show genes that were differentially expressed in either cotyledons or leaves. Genes annotated as sulfate transporters from the cotyledons are shown in (c) and from the leaves in (d) Y-axis is log2 scale

Mentions: A significant number of genes included in cotyledon profile 6 (upregulated early) are annotated as sulfate transporters. Nitrogen (N), Potassium (K), Phosphorus (P), and Sulfur (S) are major nutrients mobilized from yellowing leaves to new growth or developing seeds. It was shown that N, P, K, and S levels drop dramatically during Arabidopsis leaf senescence, with a loss of over 60 % of the initial nutrient content [25]. To understand the role of transcriptional regulation in the process of nutrient mobilization, we examined the response of the all of genes annotated as transporters of nitrogen, sulfur, potassium, or phosphorus. Approximately half of the annotated or BLASTP-identified N transport genes were expressed at levels below the threshold of detection of this experiment, but many of the transporter genes expressed at high levels were identified as differentially regulated. These genes are listed in Additional file 8. Fig. 4 shows the differentially expressed N (ammonium and nitrate) and S transporters in the cotyledon and leaves. The upregulated nitrate transporters predominantly belong to the NPF2, NPF4, and NPF7 families, with an affinity for nitrate or dipeptide transport, and related to the Arabidopsis NRT1.7 with a role in source-sink remobilization of N [26, 27]. Consistent with results from Arabidopsis, nitrogen and sulfate transporter genes are expressed at higher levels in the later stages of both the leaves and cotyledon. Of 39 transcript models annotated as sulfate transporters, 22 were upregulated between stages C-I and C-II in cotyledons, and 14 were significantly upregulated in leaf tissues, and eleven of these were common to both sets. N transporters were also upregulated in both leaves and cotyledons. Potassium and phosphate transporters were differentially expressed during leaf and cotyledon development and senescence, but demonstrated less coordinated regulation (Additional file 8).Fig. 4


Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

Brown AV, Hudson KA - BMC Plant Biol. (2015)

Regulation of N and S transporter genes. Differentially expressed genes annotated as N transporters in (a) cotyledons and (b) leaves. Blue and green lines represent nitrate transporters, pink and red lines represent ammonium transporters. Solid lines represent genes that were differentially expressed in both tissues, while dashed lines show genes that were differentially expressed in either cotyledons or leaves. Genes annotated as sulfate transporters from the cotyledons are shown in (c) and from the leaves in (d) Y-axis is log2 scale
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492100&req=5

Fig4: Regulation of N and S transporter genes. Differentially expressed genes annotated as N transporters in (a) cotyledons and (b) leaves. Blue and green lines represent nitrate transporters, pink and red lines represent ammonium transporters. Solid lines represent genes that were differentially expressed in both tissues, while dashed lines show genes that were differentially expressed in either cotyledons or leaves. Genes annotated as sulfate transporters from the cotyledons are shown in (c) and from the leaves in (d) Y-axis is log2 scale
Mentions: A significant number of genes included in cotyledon profile 6 (upregulated early) are annotated as sulfate transporters. Nitrogen (N), Potassium (K), Phosphorus (P), and Sulfur (S) are major nutrients mobilized from yellowing leaves to new growth or developing seeds. It was shown that N, P, K, and S levels drop dramatically during Arabidopsis leaf senescence, with a loss of over 60 % of the initial nutrient content [25]. To understand the role of transcriptional regulation in the process of nutrient mobilization, we examined the response of the all of genes annotated as transporters of nitrogen, sulfur, potassium, or phosphorus. Approximately half of the annotated or BLASTP-identified N transport genes were expressed at levels below the threshold of detection of this experiment, but many of the transporter genes expressed at high levels were identified as differentially regulated. These genes are listed in Additional file 8. Fig. 4 shows the differentially expressed N (ammonium and nitrate) and S transporters in the cotyledon and leaves. The upregulated nitrate transporters predominantly belong to the NPF2, NPF4, and NPF7 families, with an affinity for nitrate or dipeptide transport, and related to the Arabidopsis NRT1.7 with a role in source-sink remobilization of N [26, 27]. Consistent with results from Arabidopsis, nitrogen and sulfate transporter genes are expressed at higher levels in the later stages of both the leaves and cotyledon. Of 39 transcript models annotated as sulfate transporters, 22 were upregulated between stages C-I and C-II in cotyledons, and 14 were significantly upregulated in leaf tissues, and eleven of these were common to both sets. N transporters were also upregulated in both leaves and cotyledons. Potassium and phosphate transporters were differentially expressed during leaf and cotyledon development and senescence, but demonstrated less coordinated regulation (Additional file 8).Fig. 4

Bottom Line: Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development.The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets.These results help validate functional annotation for soybean genes and promoters.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. brown637@purdue.edu.

ABSTRACT

Background: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon.

Results: To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence.

Conclusions: The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.

No MeSH data available.


Related in: MedlinePlus