Molecular characterization of nine sweet potato (<i>Ipomoea batatas</i> Lam.) <scp>MADS</scp>‐box transcription factors during storage root development and following abiotic stress

Dong, Tingting; Song, Weihan; ChuanTing, Tan; Zhou, Zhiguang; Yu, Jiawen; Han, Rongpeng; Zhu, Mingku; Li, Zongyun

doi:10.1111/pbr.12613

Cited by 20 publications

(11 citation statements)

References 54 publications

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“…DELLA can interact with PIF3, PIF4 to impact the expansion genes expression in hypocotyl elongation [71]. In sweet potato, MADS were preferentially expressed in root at the initiation of tuber, and in the vascular cambium region where the active cell proliferation regulated by jasmonic acid, cytokinins, and stress response [53,54]. Among auxin signal-related genes, Aux/IAA, ARFs were enriched and expressed in tuber enlargement stage in this study.…”

Section: Regulatory Network Associated With Tuber Expansionmentioning

confidence: 66%

Integrated mRNA and miRNA transcriptome analysis reveals regulatory network of yam tuber expansion

Zhou¹,

Zhan²,

Hameed³

et al. 2019

Preprint

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Yam tuber is a storage organ, derived from modified stem. Tuber expansion is a complex process, it depends on the expression of genes that can be influenced by environmental and endogenous factors. However, little is known about the mechanism that regulates tuber expansion. In order to identify genes and miRNAs involved in tuber enlargement, we examined the transcriptome and small RNA in yam tuber during its initiation and expansion stages. A total of 14238 differentially expressed transcripts in yam tuber at its expansion stage were identified by using transcriptome technology. Among them, 5723 genes were up-regulated and 8515 genes were down-regulated, respectively. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these DEGs are somehow involved in response of tuber expansion. In addition, 536 transcription factor genes showed differential expression during the expansion stage at transcriptional level. REVEILLE 6-like was identified to be up-regulated in the circadian rhythm pathway. REVEILLE 6-like LHY protein, zinc finger CCCH domain-containing protein 14, and DELLA genes were up-regulated in expansion stage. Moreover, these genes were involved in circadian rhythm pathway, starch and sucrose metabolism pathway, and GA pathway by KEGG analysis respectively. Noteworthy, data analysis revealed that 23 known tuber miRNAs belong to 11 miRNA families, and 50 novel miRNAs were identified. miRNA160, miRNA396, and miRNA535 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage. The integrated analysis of miRNA-mRNA identified to be preferentially expressed in hormone signaling in expansion stage, miRNA160 was down-regulated in expansion stage, ARF18 and ARF17 were up-regulated in auxin signal transduction of tuber expansion in yam, highlighting the involvement of miRNA-mRNA in the regulation the hormone. The transcriptome and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, thus a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

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Section: Regulatory Network Associated With Tuber Expansionmentioning

confidence: 66%

Integrated mRNA and miRNA transcriptome analysis reveals regulatory network of yam tuber expansion

Zhou¹,

Zhan²,

Hameed³

et al. 2019

Preprint

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“…Most transcription factors have been identified to play critical roles in organogenesis, including MADS, bHLH, and GRAS. In sweet potato, MADS were preferentially expressed in root at initiation of tuberization, and in the vascular cambium region where the active cell proliferation regulated by jasmonic acid, cytokinins and stress response [53,54]. In Arabidopsis, bHLH family, such as PIF3, PIF4, and PIF5 are key regulators for cell elongation during seedling development, antagonistically regulated by light and gibberellins [55].…”

Section: Transcription Factors Regulationmentioning

confidence: 99%

“…DELLAs were significantly expressed in GAmediated rhizome development process, suggesting that these DELLAs can regulate rhizomatic expansion [37]. In sweet potato, MADS were preferentially expressed in root at the initiation of the tuber, and in the vascular cambium region where the active cell proliferation was regulated by jasmonic acid, cytokinins, and stress response [53,54]. Most Aux/IAA, ARFs and SAUR genes were enriched and expressed in the root cortex during splitting and expanding stage in radish, suggesting that these transcripts may be involved in cell expansion in the cambium [35].…”

Section: Regulatory Network Associated With Tuber Expansionmentioning

confidence: 99%

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

et al. 2020

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Background: Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages. Results: A total of 14,238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage. Conclusion: The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

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“…Adaptor sequences and low-quality reads were filtered to generate high-quality reads, whose quality were controlled by FASTQ format [33]. The de novo assembly and analysis of transcriptome was carried out using the superTranscripts function of Trinity software (v2.4.0) (release 2014-07- 17) according to the protocol [34], to construct the possible 'gene' sequences of C speciosa. To annotate the gene ontology (GO) and biology pathway, several public databases, including NCBI non-redundant (NR), Kyoto Encyclopedia of Genes and Genomes (KEGG) and UniProt were performed.…”

Section: De Novo Assembly and Annotation Of Transcriptomementioning

confidence: 99%

“…Many key genes regulating storage root formation, especially transcription factors (TFs), have been intensively studied. Several MADS-box genes (IbMADS1, 3,4,10,79;IbMBP1~9;IbAGL17,20;StMADS1,3,11,13,16,29;SRD1) have been found to significantly express in root tissues of sweet potato and potato, and their possible functions in tuber development have subsequently been studied [13,17]. Three sweet potato class 1 knotted1-like homeobox (KNOX1) genes (Ibkn1, Ibkn2 and Ibkn3) all expressed in the storage roots, but only Ibkn1 and Ibkn2 were obviously up-regulated in storage roots [18].…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis of roots at different development stages reveals the mechanism of root expansion of Callerya speciosa Champ.

Yao

Lan

Huang

et al. 2019

Preprint

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Background Callerya speciosa Champ., a perennial shrub medicinal plant of Fabaceae, is one of the most commonly used in traditional Chinese medicine and food that has been widely cultivated in South China. The tuberous roots of C. speciosa transferred from fibrous roots but few fibrous roots can transfer into tuberous roots. To date, the underlying mechanisms for tuberous root formation and development of C. speciosa have not yet been elucidated.

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Molecular characterization of nine sweet potato (Ipomoea batatas Lam.) MADS‐box transcription factors during storage root development and following abiotic stress

Cited by 20 publications

References 54 publications

Integrated mRNA and miRNA transcriptome analysis reveals regulatory network of yam tuber expansion

Integrated mRNA and miRNA transcriptome analysis reveals regulatory network of yam tuber expansion

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

Comparative transcriptome analysis of roots at different development stages reveals the mechanism of root expansion of Callerya speciosa Champ.

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