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Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (Triticum aestivum L.).

Zhang Y, Liu Z, Khan AA, Lin Q, Han Y, Mu P, Liu Y, Zhang H, Li L, Meng X, Ni Z, Xin M - Sci Rep (2016)

Bottom Line: Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in 'Chinese Spring' (CS) and 'Qing Mai 6' (QM).Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure.In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.

View Article: PubMed Central - PubMed

Affiliation: Qingdao Agricultural University, Qingdao, 266109, China.

ABSTRACT
Salt stress dramatically reduces crop yield and quality, but the molecular mechanisms underlying salt tolerance remain largely unknown. To explore the wheat transcriptional response to salt stress, we performed high-throughput transcriptome sequencing of 10-day old wheat roots under normal condition and 6, 12, 24 and 48 h after salt stress (HASS) in both a salt-tolerant cultivar and salt-sensitive cultivar. The results demonstrated global gene expression reprogramming with 36,804 genes that were up- or down-regulated in wheat roots under at least one stress condition compared with the controls and revealed the specificity and complexity of the functional pathways between the two cultivars. Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in 'Chinese Spring' (CS) and 'Qing Mai 6' (QM). Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure. In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.

No MeSH data available.


Related in: MedlinePlus

DAB staining, chlorophyll content measurement and comparative analysis of transcriptome profiles of wheat seedling root under salt stress.(A) DAB staining of root in QM and CS after salt stress at different stages. The staining color of root was darker in QM than in CS at 6, 12, 24, and 48HASS. (B) Chlorophyll content measurement of leaf in QM and CS before and after salt stress. The chlorophyll content is lower in CS than that in QM at 0, 6, 12, 24, and 48 HASS after salt stress, but no difference was examined before and after salt stress in neither CS nor QM. (C) Principal component analysis (PCA) of mRNA populations for QM and CS before and after salt stress. Principal components (PCs) 1 and 2 account for 48% and 40% of the variance, respectively. PCA plot shows two distinct groups of mRNA populations. Group I: CK for both QM (yellow) and CS (blue) at 6, 12, 24 and 48 HASS; Group II: Salt stressed QM (red) and CS (green) at 6, 12, 24 and 48 HASS. (D) Venn diagrams showing overlap of up- or down-regulated genes in response to salt stress at 6 (blue), 12 (yellow), 24 (green) and 48 HASS (red). QM: Qing Mai 6, CS: Chinese Spring.
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f1: DAB staining, chlorophyll content measurement and comparative analysis of transcriptome profiles of wheat seedling root under salt stress.(A) DAB staining of root in QM and CS after salt stress at different stages. The staining color of root was darker in QM than in CS at 6, 12, 24, and 48HASS. (B) Chlorophyll content measurement of leaf in QM and CS before and after salt stress. The chlorophyll content is lower in CS than that in QM at 0, 6, 12, 24, and 48 HASS after salt stress, but no difference was examined before and after salt stress in neither CS nor QM. (C) Principal component analysis (PCA) of mRNA populations for QM and CS before and after salt stress. Principal components (PCs) 1 and 2 account for 48% and 40% of the variance, respectively. PCA plot shows two distinct groups of mRNA populations. Group I: CK for both QM (yellow) and CS (blue) at 6, 12, 24 and 48 HASS; Group II: Salt stressed QM (red) and CS (green) at 6, 12, 24 and 48 HASS. (D) Venn diagrams showing overlap of up- or down-regulated genes in response to salt stress at 6 (blue), 12 (yellow), 24 (green) and 48 HASS (red). QM: Qing Mai 6, CS: Chinese Spring.

Mentions: QM is a common wheat cultivar in the Huang and Huai River Wheat Zone of China and has developed a widespread reputation for outstanding salt tolerance. Hydroponically grown QM exhibited a stronger root system and decreased H2O2 accumulation compared with the salt-sensitive cultivar CS at 6, 12, 24 and 48 hours after salt stress (HASS) with 150 mM NaCl, as shown by 3,3′-benzidine (DAB) staining (Fig. 1A). However, there was no difference in the leaf chlorophyll content after salt stress in either QM or CS, although a higher leaf chlorophyll content was found in QM compared with CS (Fig. 1B). Therefore, we next focused on the differences in the salt responses of the QM and CS roots by comparing their transcriptomes after a time-course of salt exposure.


Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (Triticum aestivum L.).

Zhang Y, Liu Z, Khan AA, Lin Q, Han Y, Mu P, Liu Y, Zhang H, Li L, Meng X, Ni Z, Xin M - Sci Rep (2016)

DAB staining, chlorophyll content measurement and comparative analysis of transcriptome profiles of wheat seedling root under salt stress.(A) DAB staining of root in QM and CS after salt stress at different stages. The staining color of root was darker in QM than in CS at 6, 12, 24, and 48HASS. (B) Chlorophyll content measurement of leaf in QM and CS before and after salt stress. The chlorophyll content is lower in CS than that in QM at 0, 6, 12, 24, and 48 HASS after salt stress, but no difference was examined before and after salt stress in neither CS nor QM. (C) Principal component analysis (PCA) of mRNA populations for QM and CS before and after salt stress. Principal components (PCs) 1 and 2 account for 48% and 40% of the variance, respectively. PCA plot shows two distinct groups of mRNA populations. Group I: CK for both QM (yellow) and CS (blue) at 6, 12, 24 and 48 HASS; Group II: Salt stressed QM (red) and CS (green) at 6, 12, 24 and 48 HASS. (D) Venn diagrams showing overlap of up- or down-regulated genes in response to salt stress at 6 (blue), 12 (yellow), 24 (green) and 48 HASS (red). QM: Qing Mai 6, CS: Chinese Spring.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4759826&req=5

f1: DAB staining, chlorophyll content measurement and comparative analysis of transcriptome profiles of wheat seedling root under salt stress.(A) DAB staining of root in QM and CS after salt stress at different stages. The staining color of root was darker in QM than in CS at 6, 12, 24, and 48HASS. (B) Chlorophyll content measurement of leaf in QM and CS before and after salt stress. The chlorophyll content is lower in CS than that in QM at 0, 6, 12, 24, and 48 HASS after salt stress, but no difference was examined before and after salt stress in neither CS nor QM. (C) Principal component analysis (PCA) of mRNA populations for QM and CS before and after salt stress. Principal components (PCs) 1 and 2 account for 48% and 40% of the variance, respectively. PCA plot shows two distinct groups of mRNA populations. Group I: CK for both QM (yellow) and CS (blue) at 6, 12, 24 and 48 HASS; Group II: Salt stressed QM (red) and CS (green) at 6, 12, 24 and 48 HASS. (D) Venn diagrams showing overlap of up- or down-regulated genes in response to salt stress at 6 (blue), 12 (yellow), 24 (green) and 48 HASS (red). QM: Qing Mai 6, CS: Chinese Spring.
Mentions: QM is a common wheat cultivar in the Huang and Huai River Wheat Zone of China and has developed a widespread reputation for outstanding salt tolerance. Hydroponically grown QM exhibited a stronger root system and decreased H2O2 accumulation compared with the salt-sensitive cultivar CS at 6, 12, 24 and 48 hours after salt stress (HASS) with 150 mM NaCl, as shown by 3,3′-benzidine (DAB) staining (Fig. 1A). However, there was no difference in the leaf chlorophyll content after salt stress in either QM or CS, although a higher leaf chlorophyll content was found in QM compared with CS (Fig. 1B). Therefore, we next focused on the differences in the salt responses of the QM and CS roots by comparing their transcriptomes after a time-course of salt exposure.

Bottom Line: Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in 'Chinese Spring' (CS) and 'Qing Mai 6' (QM).Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure.In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.

View Article: PubMed Central - PubMed

Affiliation: Qingdao Agricultural University, Qingdao, 266109, China.

ABSTRACT
Salt stress dramatically reduces crop yield and quality, but the molecular mechanisms underlying salt tolerance remain largely unknown. To explore the wheat transcriptional response to salt stress, we performed high-throughput transcriptome sequencing of 10-day old wheat roots under normal condition and 6, 12, 24 and 48 h after salt stress (HASS) in both a salt-tolerant cultivar and salt-sensitive cultivar. The results demonstrated global gene expression reprogramming with 36,804 genes that were up- or down-regulated in wheat roots under at least one stress condition compared with the controls and revealed the specificity and complexity of the functional pathways between the two cultivars. Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in 'Chinese Spring' (CS) and 'Qing Mai 6' (QM). Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure. In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.

No MeSH data available.


Related in: MedlinePlus