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Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall

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ABSTRACT

Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13–171 folds) compared to shoots. Comparative expression analysis of those genes between tuberous root developmental stages showed 11–97 folds increase in transcripts in fully developed roots compared to young rootlets, thereby implying their association in biosynthesis, accumulation and storage of primary metabolites towards root biomass. Cluster analysis revealed a positive correlation with the gene expression data for different stages of tuberous root formation in A. heterophyllum. The outcome of this study can be useful in genetic improvement of A. heterophyllum for root biomass yield.

Electronic supplementary material: The online version of this article (doi:10.1007/s13205-016-0466-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Expression status of tuberous root development genes in tuberous root developmental stages (R1–R5) of A. heterophyllum. Error bars represent mean ± SD for data recorded in triplicates (repeated thrice)
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Fig2: Expression status of tuberous root development genes in tuberous root developmental stages (R1–R5) of A. heterophyllum. Error bars represent mean ± SD for data recorded in triplicates (repeated thrice)

Mentions: The relative role of 15 genes showing higher expression in roots was further validated on different developmental stages of tuberous root formation in A. heterophyllum. This was done to ascertain their significance in root biomass increase by screening all stages, from young rootlet to fully developed tuberous roots. Comparative expression analysis of tuberous root development stages (see “Materials and methods”) revealed that almost all genes showed increase in transcript abundance in R4 and R5 stages compared to R1, R2 and R3 stages. The results showed nonsignificant changes in the expression levels of eight genes coding for GMPase, SHAGGY, NOP10, Expansin, RBX1, AGPase, β-amylase and SRF enzymes from stages R1–R3, significant increase in intermediate R4 stage (6–39 folds) and dramatic increase in their transcript levels in fully developed mature tuberous roots of R5 stage (11–97 folds) in A. heterophyllum (Fig. 2). The precise reasons for variations in transcript abundance of these genes are not clear; however, the capacity of sink organ to biosynthesize and accumulate primary metabolites have been known to increase with age of the plant. For example, carbohydrate metabolism and starch accumulation were found to increase with tuberous root development in R. sativus (Mitsui et al. 2015) and I. batatas (Wang et al. 2015), respectively. The transcript of AGPase gene showed 97-fold expression in R5 stage compared to R1 stage. This could be related to the formation of fully developed sink tissue with increased storage ability for the accumulation of starch and other sugars (Saithong et al. 2013). Being a rate-limiting enzyme of starch biosynthesis, the expression pattern of AGPase gene was consistent with the published reports (Yu et al. 2010). Similarly, the 28-fold increase in transcript abundance of gene coding for β-amylase enzyme corresponds to its regulatory role in starch biosynthetic pathway (Buléon et al. 1998). The expression of SRF gene showed 28-fold increase in R5 stage compared to R1 stage. Previous reports have suggested that the mature storage roots of I. batatas (Tanaka et al. 2005) accumulate carotenoids, therefore, it was observed that the expression of SRF gene increases with the formation of fully developed tuberous roots having utmost rate of primary metabolism. Interestingly, the change in expression pattern of Expansin transcript was indeed an unforeseen finding. It showed 39-fold increase in R5 stage than R1 stage while its expression remained 24-fold in roots compared to shoots. The increase in its transcript level is attributed to its involvement in various biochemical and physiological processes for tuberous root development including root hair formation for rapid cell proliferation in various plant species (Huang et al. 2001; Li et al. 2003). The transcripts coding for SHAGGY and NOP10 genes showed 24- and 18-fold increase in expression level in R5 stage compared to R1 stage. SHAGGY has been known to be involved in plant developmental processes (Li et al. 2001) while NOP10 regulates mRNA splicing and ribosome biogenesis (Meier 2005), but its exact role in plant processes remains to be elucidated. Further, NAC1 and ANT are known for the biosynthesis and accumulation of primary metabolites towards biomass production in plants, but surprisingly, their transcripts did not showed significant increase in expression with increase in the root biomass. This could be attributed to their role in regulating cell proliferation and organ growth by maintaining the meristematic competence of organ cells (Xie et al. 2000; Hu et al. 2003), although molecular mechanism behind such developmental signals is largely undefined and can be fully ascertained through gene function approaches.Fig. 2


Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall
Expression status of tuberous root development genes in tuberous root developmental stages (R1–R5) of A. heterophyllum. Error bars represent mean ± SD for data recorded in triplicates (repeated thrice)
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Related In: Results  -  Collection

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Fig2: Expression status of tuberous root development genes in tuberous root developmental stages (R1–R5) of A. heterophyllum. Error bars represent mean ± SD for data recorded in triplicates (repeated thrice)
Mentions: The relative role of 15 genes showing higher expression in roots was further validated on different developmental stages of tuberous root formation in A. heterophyllum. This was done to ascertain their significance in root biomass increase by screening all stages, from young rootlet to fully developed tuberous roots. Comparative expression analysis of tuberous root development stages (see “Materials and methods”) revealed that almost all genes showed increase in transcript abundance in R4 and R5 stages compared to R1, R2 and R3 stages. The results showed nonsignificant changes in the expression levels of eight genes coding for GMPase, SHAGGY, NOP10, Expansin, RBX1, AGPase, β-amylase and SRF enzymes from stages R1–R3, significant increase in intermediate R4 stage (6–39 folds) and dramatic increase in their transcript levels in fully developed mature tuberous roots of R5 stage (11–97 folds) in A. heterophyllum (Fig. 2). The precise reasons for variations in transcript abundance of these genes are not clear; however, the capacity of sink organ to biosynthesize and accumulate primary metabolites have been known to increase with age of the plant. For example, carbohydrate metabolism and starch accumulation were found to increase with tuberous root development in R. sativus (Mitsui et al. 2015) and I. batatas (Wang et al. 2015), respectively. The transcript of AGPase gene showed 97-fold expression in R5 stage compared to R1 stage. This could be related to the formation of fully developed sink tissue with increased storage ability for the accumulation of starch and other sugars (Saithong et al. 2013). Being a rate-limiting enzyme of starch biosynthesis, the expression pattern of AGPase gene was consistent with the published reports (Yu et al. 2010). Similarly, the 28-fold increase in transcript abundance of gene coding for β-amylase enzyme corresponds to its regulatory role in starch biosynthetic pathway (Buléon et al. 1998). The expression of SRF gene showed 28-fold increase in R5 stage compared to R1 stage. Previous reports have suggested that the mature storage roots of I. batatas (Tanaka et al. 2005) accumulate carotenoids, therefore, it was observed that the expression of SRF gene increases with the formation of fully developed tuberous roots having utmost rate of primary metabolism. Interestingly, the change in expression pattern of Expansin transcript was indeed an unforeseen finding. It showed 39-fold increase in R5 stage than R1 stage while its expression remained 24-fold in roots compared to shoots. The increase in its transcript level is attributed to its involvement in various biochemical and physiological processes for tuberous root development including root hair formation for rapid cell proliferation in various plant species (Huang et al. 2001; Li et al. 2003). The transcripts coding for SHAGGY and NOP10 genes showed 24- and 18-fold increase in expression level in R5 stage compared to R1 stage. SHAGGY has been known to be involved in plant developmental processes (Li et al. 2001) while NOP10 regulates mRNA splicing and ribosome biogenesis (Meier 2005), but its exact role in plant processes remains to be elucidated. Further, NAC1 and ANT are known for the biosynthesis and accumulation of primary metabolites towards biomass production in plants, but surprisingly, their transcripts did not showed significant increase in expression with increase in the root biomass. This could be attributed to their role in regulating cell proliferation and organ growth by maintaining the meristematic competence of organ cells (Xie et al. 2000; Hu et al. 2003), although molecular mechanism behind such developmental signals is largely undefined and can be fully ascertained through gene function approaches.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13–171 folds) compared to shoots. Comparative expression analysis of those genes between tuberous root developmental stages showed 11–97 folds increase in transcripts in fully developed roots compared to young rootlets, thereby implying their association in biosynthesis, accumulation and storage of primary metabolites towards root biomass. Cluster analysis revealed a positive correlation with the gene expression data for different stages of tuberous root formation in A. heterophyllum. The outcome of this study can be useful in genetic improvement of A. heterophyllum for root biomass yield.

Electronic supplementary material: The online version of this article (doi:10.1007/s13205-016-0466-y) contains supplementary material, which is available to authorized users.

No MeSH data available.