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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.


Matrix correlation based on physiological trait and expression data. Water use efficiencies (W) ratio and FPKM (F) ratio matrices are performed by mantel test via Spearman’s rank correlation method. The mantel test is conducted on 15 495 transcripts of M. lutarioriparius (i=1, 2, …, 15 495). Each correlation is conducted by 10 000 permutations.
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Figure 1: Matrix correlation based on physiological trait and expression data. Water use efficiencies (W) ratio and FPKM (F) ratio matrices are performed by mantel test via Spearman’s rank correlation method. The mantel test is conducted on 15 495 transcripts of M. lutarioriparius (i=1, 2, …, 15 495). Each correlation is conducted by 10 000 permutations.

Mentions: As described above, the levels of gene expression for 18 503 transcripts were estimated based on transcript abundance calculated using FPKM. In order to identify the candidate genes responsible for the change of WUE in the new environment, a new method was explored for non-model species without reference genomes. First, genes were weeded out with the median FPKM value of zero and 15 495 genes were left for further analysis. For each gene, the FPKM value of each individual in QG was divided by the value in JH, with all combinations,which resulted in a 39×39 matrix, as it did for the WUE value. The 39×39 WUE matrix was then correlated with each 39×39 FPKM matrix by mantel test using Spearman’s rank correlation method (Fig. 1). The analyses were conducted using vegan package (version 2.0–10) in the R statistical environment release 3.0.2. Thus, a Spearman’s rank correlation coefficient was generated for each gene while using a 10 000 permutation test to assess its statistical significance.


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)

Matrix correlation based on physiological trait and expression data. Water use efficiencies (W) ratio and FPKM (F) ratio matrices are performed by mantel test via Spearman’s rank correlation method. The mantel test is conducted on 15 495 transcripts of M. lutarioriparius (i=1, 2, …, 15 495). Each correlation is conducted by 10 000 permutations.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Matrix correlation based on physiological trait and expression data. Water use efficiencies (W) ratio and FPKM (F) ratio matrices are performed by mantel test via Spearman’s rank correlation method. The mantel test is conducted on 15 495 transcripts of M. lutarioriparius (i=1, 2, …, 15 495). Each correlation is conducted by 10 000 permutations.
Mentions: As described above, the levels of gene expression for 18 503 transcripts were estimated based on transcript abundance calculated using FPKM. In order to identify the candidate genes responsible for the change of WUE in the new environment, a new method was explored for non-model species without reference genomes. First, genes were weeded out with the median FPKM value of zero and 15 495 genes were left for further analysis. For each gene, the FPKM value of each individual in QG was divided by the value in JH, with all combinations,which resulted in a 39×39 matrix, as it did for the WUE value. The 39×39 WUE matrix was then correlated with each 39×39 FPKM matrix by mantel test using Spearman’s rank correlation method (Fig. 1). The analyses were conducted using vegan package (version 2.0–10) in the R statistical environment release 3.0.2. Thus, a Spearman’s rank correlation coefficient was generated for each gene while using a 10 000 permutation test to assess its statistical significance.

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.