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Genome-wide identification and expression analysis of the CaNAC family members in chickpea during development, dehydration and ABA treatments.

Ha CV, Esfahani MN, Watanabe Y, Tran UT, Sulieman S, Mochida K, Nguyen DV, Tran LS - PLoS ONE (2014)

Bottom Line: Phylogenetic analysis of the chickpea and well-known stress-related Arabidopsis and rice NACs enabled us to predict several putative stress-related CaNACs.Nine-teen of the 23 CaNACs examined were found to be dehydration-responsive in chickpea roots and/or leaves in either ABA-dependent or -independent pathway.Our results have provided a solid foundation for selection of promising tissue-specific and/or dehydration-responsive CaNAC candidates for detailed in planta functional analyses, leading to development of transgenic chickpea varieties with improved productivity under drought.

View Article: PubMed Central - PubMed

Affiliation: Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan; National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, 100000, Vietnam.

ABSTRACT
The plant-specific NAC transcription factors (TFs) play important roles in regulation of diverse biological processes, including development, growth, cell division and responses to environmental stimuli. In this study, we identified the members of the NAC TF family of chickpea (Cicer arietinum) and assess their expression profiles during plant development and under dehydration and abscisic acid (ABA) treatments in a systematic manner. Seventy-one CaNAC genes were detected from the chickpea genome, including 8 membrane-bound members of which many might be involved in dehydration responses as judged from published literature. Phylogenetic analysis of the chickpea and well-known stress-related Arabidopsis and rice NACs enabled us to predict several putative stress-related CaNACs. By exploring available transcriptome data, we provided a comprehensive expression atlas of CaNACs in various tissues at different developmental stages. With the highest interest in dehydration responses, we examined the expression of the predicted stress-related and membrane-bound CaNACs in roots and leaves of chickpea seedlings, subjected to well-watered (control), dehydration and ABA treatments, using real-time quantitative PCR (RT-qPCR). Nine-teen of the 23 CaNACs examined were found to be dehydration-responsive in chickpea roots and/or leaves in either ABA-dependent or -independent pathway. Our results have provided a solid foundation for selection of promising tissue-specific and/or dehydration-responsive CaNAC candidates for detailed in planta functional analyses, leading to development of transgenic chickpea varieties with improved productivity under drought.

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Heatmap representation for expression of CaNAC genes in different tissues.(A) The expression data generated by 454 pyrosequencing of cDNA libraries prepared from shoots, roots, mature leaves, flower buds and young pods were obtained from CTDB. Elevated expression levels are indicated by increasing intensities of brown color expressed in RPM (reads per million) values. (B) The expression data generated by Illumina sequencing of RNA-seq libraries prepared from germinating seedling (GS), young leaf (YL), shoot apical meristem (SAM), flower bud stages (FB1-FB4) and flower stages (FL1-FL4) were obtained from CTDB. Blue and red color gradients indicate an increase or decrease, respectively, in transcript abundance represented in log2 values. NTLs, membrane-bound CaNACs; SNACs, stress-related CaNACs.
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pone-0114107-g004: Heatmap representation for expression of CaNAC genes in different tissues.(A) The expression data generated by 454 pyrosequencing of cDNA libraries prepared from shoots, roots, mature leaves, flower buds and young pods were obtained from CTDB. Elevated expression levels are indicated by increasing intensities of brown color expressed in RPM (reads per million) values. (B) The expression data generated by Illumina sequencing of RNA-seq libraries prepared from germinating seedling (GS), young leaf (YL), shoot apical meristem (SAM), flower bud stages (FB1-FB4) and flower stages (FL1-FL4) were obtained from CTDB. Blue and red color gradients indicate an increase or decrease, respectively, in transcript abundance represented in log2 values. NTLs, membrane-bound CaNACs; SNACs, stress-related CaNACs.

Mentions: Tissue-specific expression profiles are helpful as these data enable us to determine whether a gene of interest plays a role in defining the precise nature and function of given tissue(s). CTDB (www.nipgr.res.in/ctdb.html) provided a comprehensive transcriptome atlas that was generalized for young chickpea seedlings and various types of chickpea tissues collected at various stages of development, including roots, shoots, shoot apical meristem, young leaves, mature leaves, flower buds, flowers and young pods, using either 454 pyrosequencing (Figure 4A) [47] or Illumina sequencing (Figure 4B) [49]. Overall, the expression data for 44 CaNAC genes in these tissues could be retrieved from the CTDB, which were presented in a heatmap representation shown in Figure 4. According to the data, the CaNACs possess highly variable transcript abundance. For example, CaNAC01, CaNAC49 and CaNAC63 exhibited a very weak expression in all the tissues as compared with other CaNACs. The putatively predicted stress-related CaNACs (SNACs) (Figure 2) and the membrane-bound CaNTLs (Table 1) are among those with high transcript abundance measured in the tissues. A number of CaNAC genes exhibited differential expression patterns being specific in some particular tissues, such as CaNAC16, CaNAC20 and CaNAC50 (Figure 4A), while many of them appeared to be ubiquitously expressed in the tissues examined across the developmental stages. This phenomenon was also observed for the NAC genes in other plants, such as Arabidopsis, rice and soybean, suggesting that the functions of the NACs are diversified both in monocotic and dicotic plants [20], [40], [59], [63]. Additionally, increasing evidence has suggested that overexpression of tissue-specifically expressed genes can promote the development of that particular tissue. Transgenic Arabidopsis with overexpressed NAC1 and AtNAC2 genes, which are preferentially expressed in roots, displayed enhanced lateral root development [15], [64]. Overexpression of the rice SNAC1 gene, which was induced mainly in guard cells by drought, resulted in an enhanced stomatal function under drought, leading to an increase in drought tolerance [60]. Thus, taken together our results provide a first insight for the readers to link the CaNAC genes to their putative in planta functions through their temporal and spatial expression patterns.


Genome-wide identification and expression analysis of the CaNAC family members in chickpea during development, dehydration and ABA treatments.

Ha CV, Esfahani MN, Watanabe Y, Tran UT, Sulieman S, Mochida K, Nguyen DV, Tran LS - PLoS ONE (2014)

Heatmap representation for expression of CaNAC genes in different tissues.(A) The expression data generated by 454 pyrosequencing of cDNA libraries prepared from shoots, roots, mature leaves, flower buds and young pods were obtained from CTDB. Elevated expression levels are indicated by increasing intensities of brown color expressed in RPM (reads per million) values. (B) The expression data generated by Illumina sequencing of RNA-seq libraries prepared from germinating seedling (GS), young leaf (YL), shoot apical meristem (SAM), flower bud stages (FB1-FB4) and flower stages (FL1-FL4) were obtained from CTDB. Blue and red color gradients indicate an increase or decrease, respectively, in transcript abundance represented in log2 values. NTLs, membrane-bound CaNACs; SNACs, stress-related CaNACs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257607&req=5

pone-0114107-g004: Heatmap representation for expression of CaNAC genes in different tissues.(A) The expression data generated by 454 pyrosequencing of cDNA libraries prepared from shoots, roots, mature leaves, flower buds and young pods were obtained from CTDB. Elevated expression levels are indicated by increasing intensities of brown color expressed in RPM (reads per million) values. (B) The expression data generated by Illumina sequencing of RNA-seq libraries prepared from germinating seedling (GS), young leaf (YL), shoot apical meristem (SAM), flower bud stages (FB1-FB4) and flower stages (FL1-FL4) were obtained from CTDB. Blue and red color gradients indicate an increase or decrease, respectively, in transcript abundance represented in log2 values. NTLs, membrane-bound CaNACs; SNACs, stress-related CaNACs.
Mentions: Tissue-specific expression profiles are helpful as these data enable us to determine whether a gene of interest plays a role in defining the precise nature and function of given tissue(s). CTDB (www.nipgr.res.in/ctdb.html) provided a comprehensive transcriptome atlas that was generalized for young chickpea seedlings and various types of chickpea tissues collected at various stages of development, including roots, shoots, shoot apical meristem, young leaves, mature leaves, flower buds, flowers and young pods, using either 454 pyrosequencing (Figure 4A) [47] or Illumina sequencing (Figure 4B) [49]. Overall, the expression data for 44 CaNAC genes in these tissues could be retrieved from the CTDB, which were presented in a heatmap representation shown in Figure 4. According to the data, the CaNACs possess highly variable transcript abundance. For example, CaNAC01, CaNAC49 and CaNAC63 exhibited a very weak expression in all the tissues as compared with other CaNACs. The putatively predicted stress-related CaNACs (SNACs) (Figure 2) and the membrane-bound CaNTLs (Table 1) are among those with high transcript abundance measured in the tissues. A number of CaNAC genes exhibited differential expression patterns being specific in some particular tissues, such as CaNAC16, CaNAC20 and CaNAC50 (Figure 4A), while many of them appeared to be ubiquitously expressed in the tissues examined across the developmental stages. This phenomenon was also observed for the NAC genes in other plants, such as Arabidopsis, rice and soybean, suggesting that the functions of the NACs are diversified both in monocotic and dicotic plants [20], [40], [59], [63]. Additionally, increasing evidence has suggested that overexpression of tissue-specifically expressed genes can promote the development of that particular tissue. Transgenic Arabidopsis with overexpressed NAC1 and AtNAC2 genes, which are preferentially expressed in roots, displayed enhanced lateral root development [15], [64]. Overexpression of the rice SNAC1 gene, which was induced mainly in guard cells by drought, resulted in an enhanced stomatal function under drought, leading to an increase in drought tolerance [60]. Thus, taken together our results provide a first insight for the readers to link the CaNAC genes to their putative in planta functions through their temporal and spatial expression patterns.

Bottom Line: Phylogenetic analysis of the chickpea and well-known stress-related Arabidopsis and rice NACs enabled us to predict several putative stress-related CaNACs.Nine-teen of the 23 CaNACs examined were found to be dehydration-responsive in chickpea roots and/or leaves in either ABA-dependent or -independent pathway.Our results have provided a solid foundation for selection of promising tissue-specific and/or dehydration-responsive CaNAC candidates for detailed in planta functional analyses, leading to development of transgenic chickpea varieties with improved productivity under drought.

View Article: PubMed Central - PubMed

Affiliation: Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan; National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, 100000, Vietnam.

ABSTRACT
The plant-specific NAC transcription factors (TFs) play important roles in regulation of diverse biological processes, including development, growth, cell division and responses to environmental stimuli. In this study, we identified the members of the NAC TF family of chickpea (Cicer arietinum) and assess their expression profiles during plant development and under dehydration and abscisic acid (ABA) treatments in a systematic manner. Seventy-one CaNAC genes were detected from the chickpea genome, including 8 membrane-bound members of which many might be involved in dehydration responses as judged from published literature. Phylogenetic analysis of the chickpea and well-known stress-related Arabidopsis and rice NACs enabled us to predict several putative stress-related CaNACs. By exploring available transcriptome data, we provided a comprehensive expression atlas of CaNACs in various tissues at different developmental stages. With the highest interest in dehydration responses, we examined the expression of the predicted stress-related and membrane-bound CaNACs in roots and leaves of chickpea seedlings, subjected to well-watered (control), dehydration and ABA treatments, using real-time quantitative PCR (RT-qPCR). Nine-teen of the 23 CaNACs examined were found to be dehydration-responsive in chickpea roots and/or leaves in either ABA-dependent or -independent pathway. Our results have provided a solid foundation for selection of promising tissue-specific and/or dehydration-responsive CaNAC candidates for detailed in planta functional analyses, leading to development of transgenic chickpea varieties with improved productivity under drought.

Show MeSH
Related in: MedlinePlus