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Yang Z, Ni Y, Lin Z, Yang L, Chen G, Nijiati N, Hu Y, Chen X. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC PLANT BIOLOGY 2022; 22:285. [PMID: 35681138 PMCID: PMC9185937 DOI: 10.1186/s12870-022-03665-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 05/27/2023]
Abstract
Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding.
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Affiliation(s)
- Zhijian Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zebin Lin
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Liubin Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Guotai Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Nuerla Nijiati
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Yunzhuo Hu
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Xuanyang Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian China
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2
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Ren L, Zhang T, Wu H, Ge X, Wan H, Chen S, Li Z, Ma D, Wang A. Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato. Genes (Basel) 2022; 13:genes13030404. [PMID: 35327958 PMCID: PMC8953241 DOI: 10.3390/genes13030404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 01/15/2023] Open
Abstract
MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.
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Affiliation(s)
- Lei Ren
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Tingting Zhang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Haixia Wu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xinyu Ge
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Huihui Wan
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Shengyong Chen
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang 524094, China;
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Daifu Ma
- Key Laboratory for Biology and Genetic Breeding of Sweetpotato (Xuzhou), Ministry of Agriculture/Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou Institute of Agricultural Sciences, Xuzhou 221131, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
| | - Aimin Wang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
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3
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Sun L, Yang Y, Pan H, Zhu J, Zhu M, Xu T, Li Z, Dong T. Molecular Characterization and Target Prediction of Candidate miRNAs Related to Abiotic Stress Responses and/or Storage Root Development in Sweet Potato. Genes (Basel) 2022; 13:110. [PMID: 35052451 PMCID: PMC8774570 DOI: 10.3390/genes13010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 02/01/2023] Open
Abstract
Sweet potato is a tuberous root crop with strong environmental stress resistance. It is beneficial to study its storage root formation and stress responses to identify sweet potato stress- and storage-root-thickening-related regulators. Here, six conserved miRNAs (miR156g, miR157d, miR158a-3p, miR161.1, miR167d and miR397a) and six novel miRNAs (novel 104, novel 120, novel 140, novel 214, novel 359 and novel 522) were isolated and characterized in sweet potato. Tissue-specific expression patterns suggested that miR156g, miR157d, miR158a-3p, miR167d, novel 359 and novel 522 exhibited high expression in fibrous roots or storage roots and were all upregulated in response to storage-root-related hormones (indole acetic acid, IAA; zeaxanthin, ZT; abscisic acid, ABA; and gibberellin, GAs). The expression of miR156g, miR158a-3p, miR167d, novel 120 and novel 214 was induced or reduced dramatically by salt, dehydration and cold or heat stresses. Moreover, these miRNAs were all upregulated by ABA, a crucial hormone modulator in regulating abiotic stresses. Additionally, the potential targets of the twelve miRNAs were predicted and analyzed. Above all, these results indicated that these miRNAs might play roles in storage root development and/or stress responses in sweet potato as well as provided valuable information for the further investigation of the roles of miRNA in storage root development and stress responses.
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Affiliation(s)
- Li Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Yiyu Yang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Hong Pan
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Jiahao Zhu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
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Ren L, Wu H, Zhang T, Ge X, Wang T, Zhou W, Zhang L, Ma D, Wang A. Genome-Wide Identification of TCP Transcription Factors Family in Sweet Potato Reveals Significant Roles of miR319-Targeted TCPs in Leaf Anatomical Morphology. FRONTIERS IN PLANT SCIENCE 2021; 12:686698. [PMID: 34426735 PMCID: PMC8379018 DOI: 10.3389/fpls.2021.686698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/21/2021] [Indexed: 05/08/2023]
Abstract
Plant-specific TCP transcription factors play vital roles in the controlling of growth, development, and the stress response processes. Extensive researches have been carried out in numerous species, however, there hasn't been any information available about TCP genes in sweet potato (Ipomoea batatas L.). In this study, a genome-wide analysis of TCP genes was carried out to explore the evolution and function in sweet potato. Altogether, 18 IbTCPs were identified and cloned. The expression profiles of the IbTCPs differed dramatically in different organs or different stages of leaf development. Furthermore, four CIN-clade IbTCP genes contained miR319-binding sites. Blocking IbmiR319 significantly increased the expression level of IbTCP11/17 and resulted in a decreased photosynthetic rate due to the change in leaf submicroscopic structure, indicating the significance of IbmiR319-targeted IbTCPs in leaf anatomical morphology. A systematic analyzation on the characterization of the IbTCPs together with the primary functions in leaf anatomical morphology were conducted to afford a basis for further study of the IbmiR319/IbTCP module in association with leaf anatomical morphology in sweet potato.
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Affiliation(s)
- Lei Ren
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Haixia Wu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xinyu Ge
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tianlong Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wuyu Zhou
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Daifu Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory for Biology and Genetic Breeding of Sweetpotato (Xuzhou), Ministry of Agriculture/Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Aimin Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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5
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Nokihara K, Okada Y, Ohata S, Monden Y. Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato. PLANTS 2021; 10:plants10081535. [PMID: 34451581 PMCID: PMC8398197 DOI: 10.3390/plants10081535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022]
Abstract
Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato.
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Affiliation(s)
- Kanoko Nokihara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama 700-8530, Japan; (K.N.); (S.O.)
| | - Yoshihiro Okada
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Itoman, Okinawa 901-0336, Japan;
| | - Shinichiro Ohata
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama 700-8530, Japan; (K.N.); (S.O.)
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama 700-8530, Japan; (K.N.); (S.O.)
- Correspondence:
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6
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Huang X, Liang Y, Zhang B, Song X, Li Y, Qin Z, Li D, Chen R, Zhou Z, Deng Y, Wei J, Wu J. Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress. Front Genet 2021; 11:581993. [PMID: 33569078 PMCID: PMC7868625 DOI: 10.3389/fgene.2020.581993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022] Open
Abstract
Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.
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Affiliation(s)
- Xing Huang
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | | | - Baoqing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Xiupeng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Yangrui Li
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Zhengqiang Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Dewei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Rongfa Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Zhongfeng Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Yuchi Deng
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Jianming Wu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Ministry of Agriculture, Nanning, China
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Liu Y, Su W, Wang L, Lei J, Chai S, Zhang W, Yang X. Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid biosynthesis in leafy sweet potato. PLoS One 2021; 16:e0245266. [PMID: 33481815 PMCID: PMC7822329 DOI: 10.1371/journal.pone.0245266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/26/2020] [Indexed: 12/22/2022] Open
Abstract
Leafy sweet potato is rich in total phenolics (TP) which play key roles in health protection, the chlorogenic acid (CGA) constitutes the major components of phenolic compounds in leafy sweet potato. Unfortunately, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. To dissect the mechanisms of CGA biosynthesis, we performed transcriptome, small RNA (sRNA) and degradome sequencing of one low-CGA content and one high-CGA content genotype at two stages. A total of 2,333 common differentially expressed genes (DEGs) were identified, and the enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. The functional genes, such as CCR, CCoAOMT and HCT in the CGA biosynthetic pathway were down-regulated, indicating that the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. A total of 38 DE miRNAs were identified, and 1,799 targets were predicated for 38 DE miRNAs by using in silico approaches. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2/ethylene response factor (AP2/ERF) and Squamosa promoter binding protein-like (SPL) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family negatively targeted AP2/ERF and SPL. Six mRNAs and six miRNAs were validated by qRT-PCR, and the results showed that the expression levels of the mRNAs and miRNAs were consistent with the sequencing data. This study established comprehensive functional genomic resources for the CGA biosynthesis, and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs, and offered candidate genes for leafy sweet potato improvements.
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Affiliation(s)
- Yi Liu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenjin Su
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Lianjun Wang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Jian Lei
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Shasha Chai
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenying Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Xinsun Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
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8
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Liu X, Liu S, Zhang J, Wu Y, Wu W, Zhang Y, Liu B, Tang R, He L, Li R, Jia X. Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:379-386. [PMID: 32623093 DOI: 10.1016/j.plaphy.2020.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Sweetpotato (Ipomoea batatas. L) is an important food crop, harvested for its nutrient-rich tuberous roots. Drought and salt stresses are two major factors limiting the sweetpotato production. Since microRNAs (miRNAs) are well known to play crucial roles in regulation of plant stress responses, quantitative profiling of miRNA expression under stress conditions will facilitate identification and genetic manipulation of novel miRNAs to improve stress tolerance. Real-time quantitative reverse transcription PCR (qRT-PCR) is a commonly used tool for this purpose, but not without challenges. Although stem-loop and poly(A)-tail modified qRT-PCR methods were developed for characterizing miRNA expression, accurate profiling of miRNAs is still difficult in many plant species because of a lack of reliable reference genes for normalizing miRNA transcripts. To identify reference genes that are suitable for normalizing miRNA expression in sweetpotato, the expression stability of eight candidate miRNAs and two commonly used reference genes were tested in 96 samples involving four tissues and two cultivars under drought and salt stress treatments. Data analysis using the geNorm, NormFinder and Bestkeeper algorithms demonstrated that miRn60, miR482, and their combination were reliable references. We further validated the reference genes by expression analysis of the well-characterized miR319 and miR156 that regulate drought and salt stress responses, respectively. The reference genes identified in this study will facilitate future miRNA analysis under abiotic stress conditions in sweetpotato.
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Affiliation(s)
- Xiayu Liu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Shifang Liu
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jie Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yuhao Wu
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, Shanxi, China
| | - Wanyi Wu
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yi Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Baoling Liu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Ruimin Tang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Liheng He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Runzhi Li
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xiaoyun Jia
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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Tang C, Han R, Zhou Z, Yang Y, Zhu M, Xu T, Wang A, Li Z, Dong T. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153224. [PMID: 32634748 DOI: 10.1016/j.jplph.2020.153224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.
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Affiliation(s)
- Cheng Tang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Rongpeng Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zhengkun Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Yiyu Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Aimin Wang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
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10
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Yu J, Su Y, Sun J, Liu J, Li Z, Zhang B. Selection of stable reference genes for gene expression analysis in sweet potato (Ipomoea batatas L.). Mol Cell Probes 2020; 53:101610. [PMID: 32522510 DOI: 10.1016/j.mcp.2020.101610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/06/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022]
Abstract
Gene expression analysis is one of the most common and important studies in biology and biomedicine. No matter for traditional blotting analysis or currently commonly used PCR strategy, all need a stable reference gene for normalizing the gene expression. To screen and select housekeeping genes as the most stable reference genes, quantitative real-time PCR (qRT-PCR) was employed to analyze the expression of sixteen commonly used reference genes (IbelF, Ibα-tubulin, IbHIS, IbCOX, IbGAPDH, IbH2B1, IbARF, IbCYC, Ibβ-tubulin, IbACT, IbEFl-a, IbG14, IbPLD, IbRPL2, IbUBQ, IbUBI) in five different tissues under two different temperature stresses in sweet potato. Data analysis by the Delta CT, geNorm, NormFinder, and BestKeeper programs revealed that IbelF is the most stable gene and IbUBI is the least stable gene as reference. Our study also shows that combination of two or more genes as reference is a better choice, rendering more substantiated expression data for comparison. This study provides evidence for selecting reference genes in sweet potato gene expression analysis.
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Affiliation(s)
- Jingjing Yu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Yu Su
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Jianying Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Jingran Liu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Tseng KC, Chiang-Hsieh YF, Pai H, Wu NY, Zheng HQ, Chow CN, Lee TY, Chang SB, Lin NS, Chang WC. sRIS: A Small RNA Illustration System for Plant Next-Generation Sequencing Data Analysis. PLANT & CELL PHYSIOLOGY 2020; 61:1204-1212. [PMID: 32181856 DOI: 10.1093/pcp/pcaa034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/08/2020] [Indexed: 06/10/2023]
Abstract
Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/.
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Affiliation(s)
- Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Fan Chiang-Hsieh
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsuan Pai
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Nai-Yun Wu
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Qin Zheng
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Nga Chow
- College of Biosciences and Biotechnology, NCKU-AS Graduate Program in Translational Agricultural Sciences, National Cheng Kung University, Tainan 70101, Taiwan
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Tzong-Yi Lee
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Wen-Chi Chang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
- College of Biosciences and Biotechnology, NCKU-AS Graduate Program in Translational Agricultural Sciences, National Cheng Kung University, Tainan 70101, Taiwan
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12
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Yu J, Su D, Yang D, Dong T, Tang Z, Li H, Han Y, Li Z, Zhang B. Chilling and Heat Stress-Induced Physiological Changes and MicroRNA-Related Mechanism in Sweetpotato ( Ipomoea batatas L.). FRONTIERS IN PLANT SCIENCE 2020; 11:687. [PMID: 32528515 PMCID: PMC7264270 DOI: 10.3389/fpls.2020.00687] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/30/2020] [Indexed: 05/09/2023]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) is an important industrial and food crop. Both chilling and heat stress inhibits sweetpotato growth and development and then affects yield. However, the physiological and molecular mechanisms of sweetpotato response to chilling and heat stress is unclear. In this study, we investigated the effect of extreme temperature on sweetpotato physiological response, with a focus on oxidative stress and the potential microRNA (miRNA)-mediated molecular mechanism. Our results showed that both chilling and heat stress resulted in accumulation of reactive oxygen species (ROS), including H2O2 and O2 -, and caused oxidative stress in sweetpotato. This further affected the activities of oxidative stress-related enzymes and products, including SOD, POD, and MDA. Both chilling and heat stress inhibited POD activities but induced the enzyme activities of SOD and MDA. This suggests that sweetpotato cells initiated its own defense mechanism to handle extreme temperature-caused oxidative damage. Oxidative damage and repair are one mechanism that sweetpotato plants respond to extreme temperatures. Another potential mechanism is miRNA-mediated gene response. Chilling and heat stress altered the expression of stress-responsive miRNAs in sweetpotato seedlings. These miRNAs regulate sweetpotato response to extreme stress through targeting individual protein-coding genes.
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Affiliation(s)
- Jingjing Yu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Dan Su
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Dongjing Yang
- Xuzhou Institute of Agricultural Sciences in Xuhuai District, Jiangsu Xuzhou Sweetpotato Research Center, Sweet Potato Research Institute, CAAS, Xuzhou, China
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Xuzhou, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Zhonghou Tang
- Xuzhou Institute of Agricultural Sciences in Xuhuai District, Jiangsu Xuzhou Sweetpotato Research Center, Sweet Potato Research Institute, CAAS, Xuzhou, China
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Xuzhou, China
| | - Hongmin Li
- Xuzhou Institute of Agricultural Sciences in Xuhuai District, Jiangsu Xuzhou Sweetpotato Research Center, Sweet Potato Research Institute, CAAS, Xuzhou, China
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Xuzhou, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Zongyun Li,
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
- Baohong Zhang,
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13
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Antioxidative capacity is highly associated with the storage property of tuberous roots in different sweetpotato cultivars. Sci Rep 2019; 9:11141. [PMID: 31366974 PMCID: PMC6668466 DOI: 10.1038/s41598-019-47604-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 07/15/2019] [Indexed: 02/05/2023] Open
Abstract
The activities and gene expression of antioxidative enzymes and the ROS content were analyzed in two typical storage-tolerant cultivars (Xushu 32 and Shangshu 19) and another two storage-sensitive cultivars (Yanshu 25 and Sushu 16) to explore the association between the storage capacity of sweetpotato (Ipomoea batatas (L.) Lam) and ROS scavenging capability. The storage roots of the storage-tolerant cultivars maintained higher activities and expression levels of antioxidative enzymes, including ascorbate peroxidase (APX), peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD); lower activity and expression of lipoxygenase (LOX); and lower accumulation of ROS metabolites compared with the storage-sensitive cultivars. The antioxidative capability and ROS parameters of leaves were positively correlated with those of storage roots. Our results provide valuable insight for evaluating the storability of sweetpotato cultivars by analyzing the capabilities of the antioxidative system and the contents of ROS metabolites.
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14
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He L, Tang R, Shi X, Wang W, Cao Q, Liu X, Wang T, Sun Y, Zhang H, Li R, Jia X. Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato. BMC PLANT BIOLOGY 2019; 19:232. [PMID: 31159725 PMCID: PMC6547535 DOI: 10.1186/s12870-019-1790-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known. RESULTS In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed. CONCLUSIONS The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.
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Affiliation(s)
- Liheng He
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ruimin Tang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Xiaowen Shi
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Wenbing Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Xiayu Liu
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ting Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Yan Sun
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Hongmei Zhang
- Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, China
| | - Runzhi Li
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
| | - Xiaoyun Jia
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
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15
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Wang SQ, Tang J, Hu KD, Huang ZQ, Yang F, Zhang HY, Hu LY, Li YH, Yao GF, Zhang H. Antioxidative system in sweet potato root is activated by low-temperature storage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:3824-3833. [PMID: 30677132 DOI: 10.1002/jsfa.9604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/09/2019] [Accepted: 01/20/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sweet potato is susceptible to chilling injury during low-temperature storage. To explore the correlation between chilling injury and reactive oxygen species (ROS) metabolism, the content of ROS and the activities and gene expression of antioxidant enzymes were analyzed in the typical storage-tolerant cultivar Xushu 32 and storage-sensitive cultivar Yanshu 25. RESULTS The activities of antioxidant enzymes including ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) were enhanced rapidly in the early period of storage in response to chilling stress. Thereafter, the content of ROS metabolites increased consistently due to gradual decrease in ROS scavenging enzymes. Storage-tolerant cultivar Xushu 32 had higher antioxidant enzyme activities and gene expressions as well as higher content of antioxidant metabolites and lower content of ROS metabolites compared with storage-sensitive cultivar Yanshu 25, suggesting that the capacity of ROS scavenging by antioxidant enzymes and antioxidants is highly associated with the tolerance of sweet potato to chilling stress. CONCLUSION These results indicated that the antioxidative system is activated in the storage root of sweet potato and the antioxidative capacity is positively associated with better storage performance in the storage-tolerant cultivar. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Si-Qi Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jun Tang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou, China
| | - Kang-Di Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Zhong-Qin Huang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou, China
| | - Feng Yang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou, China
| | - Hui-Yun Zhang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou, China
| | - Lan-Ying Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
- Anhui Province Key Laboratory of Functional Compound Seasoning, Anhui Qiangwang Seasoning Food Co., Ltd., Jieshou, China
| | - Yan-Hong Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Gai-Fang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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