Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation

Kim, Su-Jung; Nie, Hualin; Jun, Byung-Ki; Kim, Jiseong; Lee, Jeongeun; Kim, Seungill; Kim, Ekyune

doi:10.1007/s13258-020-00927-7

Cited by 8 publications

(8 citation statements)

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“…On the other hand, few studies have addressed AR development from cutting stems in sweetpotato. However, recently Kim et al (2020) conducted transcriptome analysis to investigate AR formation by sweet-potatoes and they indicated the characteristics of DEGs in AR formation of sweetpotato. In the present study, cut stems grown for 3 days were used to determine hormonerelated genes and their regulation involving in AR formation by sweetpotato.…”

Section: Discussionmentioning

confidence: 99%

“…Total RNA was extracted from cutting stems by using a modified CTAB method, and treated with DNase I (Takara Bio, Japan) to remove genomic DNA (Kim and Hamada 2005). RNA sequencing was performed as previously described Kim et al (2020).…”

Section: Methodsmentioning

confidence: 99%

“…We performed transcriptome analysis on data obtained from cuttings stems grown for 0 and 3 days to investigate the hormones involved in AR formation. The RNA-seq showed 42,459 representative transcripts and 2,092 DEGs including genes involved in single-organism metabolic process, cell periphery, and the biosynthesis of secondary metabolites (Kim et al 2020). Hormone-related genes were selected from DEGs (≥ 2-fold change) and their regulations were confirmed ( Fig.…”

Section: Regulations Of Hormone-related Genes During Ar Formationmentioning

confidence: 99%

“…Ma et al (2015) revealed a relationship between stem node number and AR formation, and presented the morphologies AR development and emergence as observed under an optical microscope. In addition, Kim et al (2020) performed RNA-seq analysis using stems cuttings to identify the transcriptome involved in AR formation by sweetpotatoes.…”

Section: Introductionmentioning

confidence: 99%

“…However, research on AR formation by sweetpotatoes has been limited, and thus, little is known of hormonal regulation during the process. Therefore, in this study, we investigated the regulation of hormone-related genes involved in AR formation through RNA-seq data obtained from the stem cuttings of sweetpotato (Bioproject: PRJNA610478, SRA: SRR11241425, SRR11241427) (Kim et al 2020). The genes annotated with hormone-related genes were divided by function, and their expression patterns during AR formation were clustered.…”

Section: Introductionmentioning

confidence: 99%

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Regulation of hormone-related genes involved in adventitious root formation in sweetpotato

et al. 2020

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The sweetpotatoes (Ipomoea batatas) generate adventitious roots (ARs) from cut stems that develop into storage roots and make for an important means of propagation. However, few studies have investigated the hormones involved in AR development in sweetpotato. In this study, the expression patterns of hormone-related genes involved in AR formation were identified using the transcriptome data. RNA-seq data from stems grown for 0 and 3 days after cutting were analyzed. In addition, hormone-related genes were identified among differentially expressed genes (DEGs) and filtered genes, and cluster analysis was used to characterize expression patterns by function. Most hormone-related regulated genes expressed 3 days after growing the cut stems were abscisic acid (ABA)related genes, followed by ethylene-and auxin-related genes. For ABA, the biosynthesis genes (including genes annotated to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3)) and signal transduction and perception genes (including genes annotated to PROTEIN PHOSPHATASE 2Cs (PP2Cs)) tended to decrease. Expression patterns of auxin-and ethylene-related genes differed by function. These results suggest that ABA, auxin, and ethylene genes are involved in AR formation and that they may be regulated in a hormone function-dependent manner. These results contribute to the identification of hormone functions during AR formation and may contribute to understanding the mechanism of AR formation in the sweetpotato.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Regulations Of Hormone-related Genes During Ar Formationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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