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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.


Cluster analysis of tuberous root development-related genes in A. heterophyllum through aK-means clustering, b agglomerative hierarchical clustering. K-means clustering indicated increased profiles for R4 and R5 stages while AHC reflected close proximity between R1–R3 stages using dissimilarities. Broken line in AHC marks the level of truncation during clustering
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Fig3: Cluster analysis of tuberous root development-related genes in A. heterophyllum through aK-means clustering, b agglomerative hierarchical clustering. K-means clustering indicated increased profiles for R4 and R5 stages while AHC reflected close proximity between R1–R3 stages using dissimilarities. Broken line in AHC marks the level of truncation during clustering

Mentions: For complete corroboration of the current findings, the data set was subjected to statistical analysis. The study showed positive correlation with the gene expression data for different stages (R1–R5) of tuberous root development in A. heterophyllum. Clustering of the whole data set revealed close relationship between R1, R2 and R3 stages showing more or less similar expression pattern while R4 and R5 stages exhibited increase in transcript abundance as plant attained maturity. The observed profiles of eight genes viz. GMPase, SHAGGY, NOP10, Expansin, RBX1, SRF, β-amylase and AGPase were found to be distinct and well separated from each other in R5 stage compared to R4 stage. The results obtained by K-means clustering and agglomerative hierarchical clustering (AHC) demonstrate this scenario very well (Fig. 3). Profile plot through K-means clustering indicated increased profiles for R4 and R5 stages while bottom up approach for clustering in AHC clearly reflected the close proximity of R1–R3 stages. Additionally, the Gaussian mixture models (GMM) for eight genes with high expression levels have ascertained their importance in the formation of tuberous roots (Supplementary Fig. 1). Overall, multiple genes of different families exhibited an important role in tuberous root architecture for biosynthesis and storage of primary metabolites, thus paving the way towards increasing the biomass yield through genetic modification in A. heterophyllum.Fig. 3


Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall
Cluster analysis of tuberous root development-related genes in A. heterophyllum through aK-means clustering, b agglomerative hierarchical clustering. K-means clustering indicated increased profiles for R4 and R5 stages while AHC reflected close proximity between R1–R3 stages using dissimilarities. Broken line in AHC marks the level of truncation during clustering
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940232&req=5

Fig3: Cluster analysis of tuberous root development-related genes in A. heterophyllum through aK-means clustering, b agglomerative hierarchical clustering. K-means clustering indicated increased profiles for R4 and R5 stages while AHC reflected close proximity between R1–R3 stages using dissimilarities. Broken line in AHC marks the level of truncation during clustering
Mentions: For complete corroboration of the current findings, the data set was subjected to statistical analysis. The study showed positive correlation with the gene expression data for different stages (R1–R5) of tuberous root development in A. heterophyllum. Clustering of the whole data set revealed close relationship between R1, R2 and R3 stages showing more or less similar expression pattern while R4 and R5 stages exhibited increase in transcript abundance as plant attained maturity. The observed profiles of eight genes viz. GMPase, SHAGGY, NOP10, Expansin, RBX1, SRF, β-amylase and AGPase were found to be distinct and well separated from each other in R5 stage compared to R4 stage. The results obtained by K-means clustering and agglomerative hierarchical clustering (AHC) demonstrate this scenario very well (Fig. 3). Profile plot through K-means clustering indicated increased profiles for R4 and R5 stages while bottom up approach for clustering in AHC clearly reflected the close proximity of R1–R3 stages. Additionally, the Gaussian mixture models (GMM) for eight genes with high expression levels have ascertained their importance in the formation of tuberous roots (Supplementary Fig. 1). Overall, multiple genes of different families exhibited an important role in tuberous root architecture for biosynthesis and storage of primary metabolites, thus paving the way towards increasing the biomass yield through genetic modification in A. heterophyllum.Fig. 3

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.