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

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), ?-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.

SUBMITTER: Malhotra N

PROVIDER: S-EPMC4940232 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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

Malhotra Nikhil N Sood Hemant H Chauhan Rajinder Singh RS

3 Biotech 20160711 2

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 (SR ...[more]

PMID: 28330224

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Project description:BackgroundPueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting.ResultsObservations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated.ConclusionOur findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.

Project description:BACKGROUND:Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. RESULTS:Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9563 contigs. A total of 4510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from -?0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. CONCLUSIONS:The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability.

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

Publications

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

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