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Transcription profiles of boron-deficiency-responsive genes in citrus rootstock root by suppression subtractive hybridization and cDNA microarray.

Zhou GF, Liu YZ, Sheng O, Wei QJ, Yang CQ, Peng SA - Front Plant Sci (2015)

Bottom Line: Boron (B) deficiency has seriously negative effect on citrus production.All these results indicated that CC was more tolerant than TO to B-deficiency stress.The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University Wuhan, China ; National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University Ganzhou, China.

ABSTRACT
Boron (B) deficiency has seriously negative effect on citrus production. Carrizo citrange (CC) has been reported as a B-deficiency tolerant rootstock. However, the molecular mechanism of its B-deficiency tolerance remained not well-explored. To understand the molecular basis of citrus rootstock to B-deficiency, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potential important or novel genes responsive to B-deficiency. Firstly four SSH libraries were constructed for the root tissue of two citrus rootstocks CC and Trifoliate orange (TO) to compare B-deficiency treated and non-treated plants. Then 7680 clones from these SSH libraries were used to construct a cDNA array and microarray analysis was carried out to verify the expression changes of these clones upon B-deficiency treatment at various time points compared to the corresponding controls. A total of 139 unigenes that were differentially expressed upon B-deficiency stress either in CC or TO were identified from microarray analysis, some of these genes have not previously been reported to be associated with B-deficiency stress. In this work, several genes involved in cell wall metabolism and transmembrane transport were identified to be highly regulated under B-deficiency stress, and a total of 23 metabolic pathways were affected by B-deficiency, especially the lignin biosynthesis pathway, nitrogen metabolism, and glycolytic pathway. All these results indicated that CC was more tolerant than TO to B-deficiency stress. The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus.

No MeSH data available.


Related in: MedlinePlus

Number of differentially expressed clones/genes. (A) Number of SSH cDNA clones significantly up- or down-regulated in Trifoliate orange and Carrizo citrange in response to boron deficient stress at various time points. (B,C) Venn diagram illustrates the number of unique genes up- (B) or down-regulated (C) by boron deficient stress in either or both rootstocks.
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Figure 3: Number of differentially expressed clones/genes. (A) Number of SSH cDNA clones significantly up- or down-regulated in Trifoliate orange and Carrizo citrange in response to boron deficient stress at various time points. (B,C) Venn diagram illustrates the number of unique genes up- (B) or down-regulated (C) by boron deficient stress in either or both rootstocks.

Mentions: Forward and reverse subtractions were conducted between root tissues from B-deficiency stress and non-stress CC and TO plants, respectively. One thousand nine hundred and twenty clones were randomly picked from each SSH library. In total, 7680 clones from the four SSH libraries were amplified and used for microarray analysis. The insert size of the SSH clones was from 0.45 to 0.75 kb, and most of them were around 0.55 kb. RNA samples from the root tissues at the stages of 6, 12, and 24 h after B-deficiency stress and the same time points of non-treated control plants were used for microarray hybridization. In total, 2266 and 1184 differentially expressed cDNA clones (FDR <0.01 and fold change ≥ 2) from either CC or TO were identified under B-deficiency conditions, respectively. As shown in Figure 3A, the expression patterns of CC and TO were similar at 6 and 12 h, but distinct at 24 h. At 6 and 12 h time point, there was no significant difference between CC and TO; However, after 24 h treatment the number of differentially expressed cDNA clones of CC was 5.2 and 8.2 fold higher in up- and down-regulated genes, respectively, compared to TO.


Transcription profiles of boron-deficiency-responsive genes in citrus rootstock root by suppression subtractive hybridization and cDNA microarray.

Zhou GF, Liu YZ, Sheng O, Wei QJ, Yang CQ, Peng SA - Front Plant Sci (2015)

Number of differentially expressed clones/genes. (A) Number of SSH cDNA clones significantly up- or down-regulated in Trifoliate orange and Carrizo citrange in response to boron deficient stress at various time points. (B,C) Venn diagram illustrates the number of unique genes up- (B) or down-regulated (C) by boron deficient stress in either or both rootstocks.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4309116&req=5

Figure 3: Number of differentially expressed clones/genes. (A) Number of SSH cDNA clones significantly up- or down-regulated in Trifoliate orange and Carrizo citrange in response to boron deficient stress at various time points. (B,C) Venn diagram illustrates the number of unique genes up- (B) or down-regulated (C) by boron deficient stress in either or both rootstocks.
Mentions: Forward and reverse subtractions were conducted between root tissues from B-deficiency stress and non-stress CC and TO plants, respectively. One thousand nine hundred and twenty clones were randomly picked from each SSH library. In total, 7680 clones from the four SSH libraries were amplified and used for microarray analysis. The insert size of the SSH clones was from 0.45 to 0.75 kb, and most of them were around 0.55 kb. RNA samples from the root tissues at the stages of 6, 12, and 24 h after B-deficiency stress and the same time points of non-treated control plants were used for microarray hybridization. In total, 2266 and 1184 differentially expressed cDNA clones (FDR <0.01 and fold change ≥ 2) from either CC or TO were identified under B-deficiency conditions, respectively. As shown in Figure 3A, the expression patterns of CC and TO were similar at 6 and 12 h, but distinct at 24 h. At 6 and 12 h time point, there was no significant difference between CC and TO; However, after 24 h treatment the number of differentially expressed cDNA clones of CC was 5.2 and 8.2 fold higher in up- and down-regulated genes, respectively, compared to TO.

Bottom Line: Boron (B) deficiency has seriously negative effect on citrus production.All these results indicated that CC was more tolerant than TO to B-deficiency stress.The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University Wuhan, China ; National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University Ganzhou, China.

ABSTRACT
Boron (B) deficiency has seriously negative effect on citrus production. Carrizo citrange (CC) has been reported as a B-deficiency tolerant rootstock. However, the molecular mechanism of its B-deficiency tolerance remained not well-explored. To understand the molecular basis of citrus rootstock to B-deficiency, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potential important or novel genes responsive to B-deficiency. Firstly four SSH libraries were constructed for the root tissue of two citrus rootstocks CC and Trifoliate orange (TO) to compare B-deficiency treated and non-treated plants. Then 7680 clones from these SSH libraries were used to construct a cDNA array and microarray analysis was carried out to verify the expression changes of these clones upon B-deficiency treatment at various time points compared to the corresponding controls. A total of 139 unigenes that were differentially expressed upon B-deficiency stress either in CC or TO were identified from microarray analysis, some of these genes have not previously been reported to be associated with B-deficiency stress. In this work, several genes involved in cell wall metabolism and transmembrane transport were identified to be highly regulated under B-deficiency stress, and a total of 23 metabolic pathways were affected by B-deficiency, especially the lignin biosynthesis pathway, nitrogen metabolism, and glycolytic pathway. All these results indicated that CC was more tolerant than TO to B-deficiency stress. The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus.

No MeSH data available.


Related in: MedlinePlus