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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.


The distribution of gene expression change patterns of the candidate genes. Fold changes of gene expression levels are expressed in log2 (FPKM ratio), where the FPKM ratio was calculated as the ratio of FPKM (QG) to FPKM (JH). FPKM (JH) and FPKM (QG) values represent the average expression levels of each transcript in the experimental fields in Jiangxia of Hubei Province (JH) and Qingyang of Gansu Province (QG), respectively. The log-ratios beyond zero represent up-regulated genes, while the ratio of 1 and –1 mean 2-fold up-regulation and down-regulation, respectively.
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Figure 3: The distribution of gene expression change patterns of the candidate genes. Fold changes of gene expression levels are expressed in log2 (FPKM ratio), where the FPKM ratio was calculated as the ratio of FPKM (QG) to FPKM (JH). FPKM (JH) and FPKM (QG) values represent the average expression levels of each transcript in the experimental fields in Jiangxia of Hubei Province (JH) and Qingyang of Gansu Province (QG), respectively. The log-ratios beyond zero represent up-regulated genes, while the ratio of 1 and –1 mean 2-fold up-regulation and down-regulation, respectively.

Mentions: The fold changes of average expression levels of the candidate genes between the two sites ranged from 0.26 to 15.60 (see Supplementary Table S2 at JXB online). Compared with those in JH, 72.92% and 27.08% of the genes were up-regulated and down-regulated in QG, and 29.2% and 6.25% of the candidates were up-regulated and down-regulated more than 2-fold, respectively (Fig. 3). Fourteen genes were up-regulated more than 2-fold including three photosynthesis-related genes, three stomatal regulation-related, and four abiotic stress-related. Three genes down-regulated more than 2-fold belonged to the ‘Other’ functional category.


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)

The distribution of gene expression change patterns of the candidate genes. Fold changes of gene expression levels are expressed in log2 (FPKM ratio), where the FPKM ratio was calculated as the ratio of FPKM (QG) to FPKM (JH). FPKM (JH) and FPKM (QG) values represent the average expression levels of each transcript in the experimental fields in Jiangxia of Hubei Province (JH) and Qingyang of Gansu Province (QG), respectively. The log-ratios beyond zero represent up-regulated genes, while the ratio of 1 and –1 mean 2-fold up-regulation and down-regulation, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: The distribution of gene expression change patterns of the candidate genes. Fold changes of gene expression levels are expressed in log2 (FPKM ratio), where the FPKM ratio was calculated as the ratio of FPKM (QG) to FPKM (JH). FPKM (JH) and FPKM (QG) values represent the average expression levels of each transcript in the experimental fields in Jiangxia of Hubei Province (JH) and Qingyang of Gansu Province (QG), respectively. The log-ratios beyond zero represent up-regulated genes, while the ratio of 1 and –1 mean 2-fold up-regulation and down-regulation, respectively.
Mentions: The fold changes of average expression levels of the candidate genes between the two sites ranged from 0.26 to 15.60 (see Supplementary Table S2 at JXB online). Compared with those in JH, 72.92% and 27.08% of the genes were up-regulated and down-regulated in QG, and 29.2% and 6.25% of the candidates were up-regulated and down-regulated more than 2-fold, respectively (Fig. 3). Fourteen genes were up-regulated more than 2-fold including three photosynthesis-related genes, three stomatal regulation-related, and four abiotic stress-related. Three genes down-regulated more than 2-fold belonged to the ‘Other’ functional category.

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.