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Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land.

Fan Y, Wang Q, Kang L, Liu W, Xu Q, Xing S, Tao C, Song Z, Zhu C, Lin C, Yan J, Li J, Sang T - J. Exp. Bot. (2015)

Bottom Line: The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location.It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation.The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.

No MeSH data available.


Related in: MedlinePlus

(A) Hierarchical clustering of 48 candidate genes differentially expressed between individuals in JH (left) and QG (right). The normalized gene expression values (FPKM) of candidate genes of each individual are used for the cluster display. The colour scale (representing the normalized gene expression) is shown at the bottom. The genes which share similar expression patterns are divided into four groups, (B) Cluster 1, (C) Cluster 2, (D) Cluster 3, and (E) Cluster 4. For the full names of abbreviations in annotation see Table 2. Up-regulated (+), down-regulated (–), up-regulated more than 2-fold (2+), down-regulated more than 2-fold (2–).
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Figure 4: (A) Hierarchical clustering of 48 candidate genes differentially expressed between individuals in JH (left) and QG (right). The normalized gene expression values (FPKM) of candidate genes of each individual are used for the cluster display. The colour scale (representing the normalized gene expression) is shown at the bottom. The genes which share similar expression patterns are divided into four groups, (B) Cluster 1, (C) Cluster 2, (D) Cluster 3, and (E) Cluster 4. For the full names of abbreviations in annotation see Table 2. Up-regulated (+), down-regulated (–), up-regulated more than 2-fold (2+), down-regulated more than 2-fold (2–).

Mentions: Cluster analysis of the 48 candidate genes with normalized expression levels revealed four major groups (Fig. 4A). Cluster 1 comprised nine genes that were expressed largely at higher levels in JH than in QG (Fig. 4B). It contained four genes related to abiotic stress responses and one gene ‘MluLR3628’ encoding the ORMDL family protein involved in protein folding in the endoplasmic reticulum. The functions of MluLR4945, MluLR16034, MluLR12611, and MluLR13061 were related to abiotic stress and encoded lecithin-cholesterol acyltransferase-like 1 (LCAT1-like), cyclophilin type peptidyl-prolyl cis-trans isomerase (cyclophilin type PPIase), methyl-CpG binding domain 106 protein, and lysine-specific histone demethylase 1 (LSD1), respectively.


Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land.

Fan Y, Wang Q, Kang L, Liu W, Xu Q, Xing S, Tao C, Song Z, Zhu C, Lin C, Yan J, Li J, Sang T - J. Exp. Bot. (2015)

(A) Hierarchical clustering of 48 candidate genes differentially expressed between individuals in JH (left) and QG (right). The normalized gene expression values (FPKM) of candidate genes of each individual are used for the cluster display. The colour scale (representing the normalized gene expression) is shown at the bottom. The genes which share similar expression patterns are divided into four groups, (B) Cluster 1, (C) Cluster 2, (D) Cluster 3, and (E) Cluster 4. For the full names of abbreviations in annotation see Table 2. Up-regulated (+), down-regulated (–), up-regulated more than 2-fold (2+), down-regulated more than 2-fold (2–).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4588889&req=5

Figure 4: (A) Hierarchical clustering of 48 candidate genes differentially expressed between individuals in JH (left) and QG (right). The normalized gene expression values (FPKM) of candidate genes of each individual are used for the cluster display. The colour scale (representing the normalized gene expression) is shown at the bottom. The genes which share similar expression patterns are divided into four groups, (B) Cluster 1, (C) Cluster 2, (D) Cluster 3, and (E) Cluster 4. For the full names of abbreviations in annotation see Table 2. Up-regulated (+), down-regulated (–), up-regulated more than 2-fold (2+), down-regulated more than 2-fold (2–).
Mentions: Cluster analysis of the 48 candidate genes with normalized expression levels revealed four major groups (Fig. 4A). Cluster 1 comprised nine genes that were expressed largely at higher levels in JH than in QG (Fig. 4B). It contained four genes related to abiotic stress responses and one gene ‘MluLR3628’ encoding the ORMDL family protein involved in protein folding in the endoplasmic reticulum. The functions of MluLR4945, MluLR16034, MluLR12611, and MluLR13061 were related to abiotic stress and encoded lecithin-cholesterol acyltransferase-like 1 (LCAT1-like), cyclophilin type peptidyl-prolyl cis-trans isomerase (cyclophilin type PPIase), methyl-CpG binding domain 106 protein, and lysine-specific histone demethylase 1 (LSD1), respectively.

Bottom Line: The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location.It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation.The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.

No MeSH data available.


Related in: MedlinePlus