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Li J, Wen X, Zhang Q, Tian Y, Pu Y, Wang J, Liu B, Du Y, Dai S. cla-miR164- NO APICAL MERISTEM ( ClNAM) regulates the inflorescence architecture development of Chrysanthemum lavandulifolium. HORTICULTURE RESEARCH 2024; 11:uhae039. [PMID: 38623074 PMCID: PMC11017518 DOI: 10.1093/hr/uhae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/28/2024] [Indexed: 04/17/2024]
Abstract
Chrysanthemum × morifolium has great ornamental and economic value on account of its exquisite capitulum. However, previous studies have mainly focused on the corolla morphology of the capitulum. Such an approach cannot explain the variable inflorescence architecture of the chrysanthemum. Previous research from our group has shown that NO APICAL MERISTEM (ClNAM) is likely to function as a hub gene in capitulum architecture in the early development stage. In the present study, ClNAM was used to investigate the function of these boundary genes in the capitulum architecture of Chrysanthemum lavandulifolium, a closely related species of C. × morifolium in the genus. Modification of ClNAM in C. lavandulifolium resulted in an advanced initiation of the floral primordium at the capitulum. As a result, the receptacle morphology was altered and the number of florets decreased. The ray floret corolla was shortened, but the disc floret was elongated. The number of capitula increased significantly, arranged in more densely compounded corymbose synflorescences. The yeast and luciferase reporter system revealed that ClAP1, ClRCD2, and ClLBD18 target and activate ClNAM. Subsequently, ClNAM targets and activates ClCUC2a/c, which regulates the initiation of floral and inflorescence in C. lavandulifolium. ClNAM was also targeted and cleaved by cla-miR164 in this process. In conclusion, this study established a boundary gene regulatory network with cla-miR164-ClNAM as the hub. This network not only influences the architecture of capitulum, but also affects compound corymbose synflorescences of the C. lavandulifolium. These results provide new insights into the mechanisms regulating inflorescence architecture in chrysanthemum.
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Affiliation(s)
- Junzhuo Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Xiaohui Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
- Flower Research and Development Center, Zhejiang Academy of Agricultural Sciences, Hangzhou 311202, China
| | - Qiuling Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Yuankai Tian
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Ya Pu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Jiaying Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Bo Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Yihan Du
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
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Zhu P, Li H, Lu T, Liang R, Wan B. Combined analysis of mRNA and miRNA transcriptomes reveals the regulatory mechanism of Xanthomonas arboricola pv pruni resistance in Prunus persica. BMC Genomics 2024; 25:214. [PMID: 38413907 PMCID: PMC10898114 DOI: 10.1186/s12864-024-10113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica). RESULTS This study compared the mRNA and miRNA profiles of two peach varieties, 'Yanbao' (resistant) and 'Yingzui' (susceptible), after inoculation with Xap to identify miRNAs and target genes associated with peach tree resistance. mRNA sequencing results revealed that in the S0-vs-S3 comparison group, 1574 genes were upregulated and 3975 genes were downregulated. In the R0-vs-R3 comparison group, 1575 genes were upregulated and 3726 genes were downregulated. Through miRNA sequencing, a total of 112 known miRNAs belonging to 70 miRNA families and 111 new miRNAs were identified. Notably, some miRNAs were exclusively expressed in either resistant or susceptible varieties. Additionally, 59 miRNAs were downregulated and 69 miRNAs were upregulated in the R0-vs-R3 comparison group, while 46 miRNAs were downregulated and 52 miRNAs were upregulated in the S0-vs-S3 comparison group. Joint analysis of mRNA and miRNA identified 79 relationship pairs in the S0-vs-S3 comparison group, consisting of 48 miRNAs and 51 target genes. In the R0-vs-R3 comparison group, there were 58 relationship pairs, comprising 28 miRNAs and 20 target genes. Several target genes related to resistance, such as SPL6, TIFY6B, and Prupe.4G041800_v2.0.a1 (PPO), were identified through literature reports and GO/KEGG enrichment analysis. CONCLUSION In conclusion, this study discovered several candidate genes involved in peach tree resistance by analyzing differential expression of mRNA and miRNA. These findings provide valuable insights into the mechanisms underlying resistance to Xap in peach trees.
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Affiliation(s)
- Pengxiang Zhu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Haiyan Li
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Tailiang Lu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Ruizheng Liang
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
| | - Baoxiong Wan
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
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Yuan H, Zheng Z, Bao Y, Zhao X, Lv J, Tang C, Wang N, Liang Z, Li H, Xiang J, Qian Y, Shi Y. Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice. Int J Mol Sci 2024; 25:2177. [PMID: 38396854 PMCID: PMC10889564 DOI: 10.3390/ijms25042177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.
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Affiliation(s)
- Hongyan Yuan
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhenzhen Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaling Bao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Xueyu Zhao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jiaqi Lv
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Chenghang Tang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Hua Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
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Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
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Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
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Du W, Ding J, Li J, Li H, Ruan C. Co-regulatory effects of hormone and mRNA-miRNA module on flower bud formation of Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1109603. [PMID: 37008468 PMCID: PMC10064061 DOI: 10.3389/fpls.2023.1109603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Few flower buds in a high-yield year are the main factors restricting the yield of Camellia oleifera in the next year. However, there are no relevant reports on the regulation mechanism of flower bud formation. In this study, hormones, mRNAs, and miRNAs were tested during flower bud formation in MY3 ("Min Yu 3," with stable yield in different years) and QY2 ("Qian Yu 2," with less flower bud formation in a high-yield year) cultivars. The results showed that except for IAA, the hormone contents of GA3, ABA, tZ, JA, and SA in the buds were higher than those in the fruit, and the contents of all hormones in the buds were higher than those in the adjacent tissues. This excluded the effect of hormones produced from the fruit on flower bud formation. The difference in hormones showed that 21-30 April was the critical period for flower bud formation in C. oleifera; the JA content in MY3 was higher than that in QY2, but a lower concentration of GA3 contributed to the formation of the C. oleifera flower bud. JA and GA3 might have different effects on flower bud formation. Comprehensive analysis of the RNA-seq data showed that differentially expressed genes were notably enriched in hormone signal transduction and the circadian system. Flower bud formation in MY3 was induced through the plant hormone receptor TIR1 (transport inhibitor response 1) of the IAA signaling pathway, the miR535-GID1c module of the GA signaling pathway, and the miR395-JAZ module of the JA signaling pathway. In addition, the expression of core clock components GI (GIGANTEA) and CO (CONSTANS) in MY3 increased 2.3-fold and 1.8-fold over that in QY2, respectively, indicating that the circadian system also played a role in promoting flower bud formation in MY3. Finally, the hormone signaling pathway and circadian system transmitted flowering signals to the floral meristem characteristic genes LFY (LEAFY) and AP1 (APETALA 1) via FT (FLOWERING LOCUS T) and SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO 1) to regulate flower bud formation. These data will provide the basis for understanding the mechanism of flower bud alternate formation and formulating high yield regulation measures for C. oleifera.
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Jiang J, Zhu H, Li N, Batley J, Wang Y. The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23169477. [PMID: 36012740 PMCID: PMC9409142 DOI: 10.3390/ijms23169477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Na Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: (J.B.); (Y.W.)
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (J.B.); (Y.W.)
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Lan T, Yang X, Chen J, Tian P, Shi L, Yu Y, Liu L, Gao L, Mo B, Chen X, Tang G. Mechanism for the genomic and functional evolution of the MIR2118 family in the grass lineage. THE NEW PHYTOLOGIST 2022; 233:1915-1930. [PMID: 34878652 DOI: 10.1111/nph.17910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
The MIR2118 family has undergone tremendous expansion in the grass lineage, in which the miRNA targets numerous noncoding PHAS loci to produce 21-nt phased small interfering RNAs (phasiRNAs) involved in male fertility. However, the evolutionary trajectory of the grass MIR2118 genes and the functions of phasiRNAs have not yet been fully elucidated. We conducted comparative genomic, molecular evolution, expression and parallel analysis of RNA ends (PARE) analyses of MIR2118 and the miR2118-mediated regulatory pathway in grasses, focusing on Oryza sativa. In total, 617 MIR2118 and eight MIR1859 novel members were identified. Phylogenetic analyses showed that grass MIR2118 genes form a distinct clade from the MIR482/2118 genes of nongrass species. We reconstructed hypothetical evolutionary histories of the grass MIR2118 clusters and its MIR1859 variants, and examined the polycistronic composition and the differential expression of the osa-MIR2118 clusters. PARE data showed that osa-miR2118 might also direct the cleavage of some protein-coding gene transcripts. Importantly, we found that PARE analysis is inherently prone to false-positive target predictions when a large number of small RNAs, such as phasiRNAs, are analysed. Our results revealed the evolution and diversification of the MIR2118 family, and provide new insights into the functions of phasiRNAs in the grasses.
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Affiliation(s)
- Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiwei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Lina Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI, 49931, USA
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Luo P, Di D, Wu L, Yang J, Lu Y, Shi W. MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling. Int J Mol Sci 2022; 23:ijms23010510. [PMID: 35008937 PMCID: PMC8745101 DOI: 10.3390/ijms23010510] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/30/2022] Open
Abstract
Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.
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Affiliation(s)
- Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Correspondence: (P.L.); (D.D.)
| | - Dongwei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
- Correspondence: (P.L.); (D.D.)
| | - Lei Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Jiangwei Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
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9
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Yadav A, Kumar S, Verma R, Lata C, Sanyal I, Rai SP. microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2471-2485. [PMID: 34924705 PMCID: PMC8639965 DOI: 10.1007/s12298-021-01096-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Sanoj Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005 India
| | - Rita Verma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067 India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashi Pandey Rai
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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10
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Dang T, Lavagi-Craddock I, Bodaghi S, Vidalakis G. Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings. Front Microbiol 2021; 12:646273. [PMID: 33995303 PMCID: PMC8121382 DOI: 10.3389/fmicb.2021.646273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.
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Affiliation(s)
| | | | | | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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11
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Yu J, Bennett D, Dardick C, Zhebentyayeva T, Abbott AG, Liu Z, Staton ME. Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. Front Mol Biosci 2021; 8:612881. [PMID: 33968979 PMCID: PMC8098804 DOI: 10.3389/fmolb.2021.612881] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Margaret E Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.,Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
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12
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Regulation of Fruit Growth in a Peach Slow Ripening Phenotype. Genes (Basel) 2021; 12:genes12040482. [PMID: 33810423 PMCID: PMC8066772 DOI: 10.3390/genes12040482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/25/2023] Open
Abstract
Consumers' choices are mainly based on fruit external characteristics such as the final size, weight, and shape. The majority of edible fruit are by tree fruit species, among which peach is the genomic and genetic reference for Prunus. In this research, we used a peach with a slow ripening (SR) phenotype, identified in the Fantasia (FAN) nectarine, associated with misregulation of genes involved in mesocarp identity and showing a reduction of final fruit size. By investigating the ploidy level, we observed a progressive increase in endoreduplication in mesocarp, which occurred in the late phases of FAN fruit development, but not in SR fruit. During fruit growth, we also detected that genes involved in endoreduplication were differentially modulated in FAN compared to SR. The differential transcriptional outputs were consistent with different chromatin states at loci of endoreduplication genes. The impaired expression of genes controlling cell cycle and endocycle as well as those claimed to play a role in fruit tissue identity result in the small final size of SR fruit.
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13
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Fenn MA, Giovannoni JJ. Phytohormones in fruit development and maturation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:446-458. [PMID: 33274492 DOI: 10.1111/tpj.15112] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 05/21/2023]
Abstract
Phytohormones are integral to the regulation of fruit development and maturation. This review expands upon current understanding of the relationship between hormone signaling and fruit development, emphasizing fleshy fruit and highlighting recent work in the model crop tomato (Solanum lycopersicum) and additional species. Fruit development comprises fruit set initiation, growth, and maturation and ripening. Fruit set transpires after fertilization and is associated with auxin and gibberellic acid (GA) signaling. Interaction between auxin and GAs, as well as other phytohormones, is mediated by auxin-responsive Aux/IAA and ARF proteins. Fruit growth consists of cell division and expansion, the former shown to be influenced by auxin signaling. While regulation of cell expansion is less thoroughly understood, evidence indicates synergistic regulation via both auxin and GAs, with input from additional hormones. Fruit maturation, a transitional phase that precipitates ripening, occurs when auxin and GA levels subside with a concurrent rise in abscisic acid (ABA) and ethylene. During fruit ripening, ethylene plays a clear role in climacteric fruits, whereas non-climacteric ripening is generally associated with ABA. Recent evidence indicates varying requirements for both hormones within both ripening physiologies, suggesting rebalancing and specification of roles for common regulators rather than reliance upon one. Numerous recent discoveries pertaining to the molecular basis of hormonal activity and crosstalk are discussed, while we also note that many questions remain such as the molecular basis of additional hormonal activities, the role of epigenome changes, and how prior discoveries translate to the plethora of angiosperm species.
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Affiliation(s)
- Matthew A Fenn
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - James J Giovannoni
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University campus, Ithaca, NY, 14853, USA
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14
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miRNA-mediated regulation of auxin signaling pathway during plant development and stress responses. J Biosci 2020. [DOI: 10.1007/s12038-020-00062-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Fu L, Ding Z, Tan D, Han B, Sun X, Zhang J. Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed. BMC Genomics 2020; 21:212. [PMID: 32138656 PMCID: PMC7059339 DOI: 10.1186/s12864-020-6633-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. Results In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. Conclusions This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. .,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. .,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.
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16
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Zhou Y, Luo S, Hameed S, Xiao D, Zhan J, Wang A, He L. Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita). BMC Genomics 2020; 21:117. [PMID: 32013881 DOI: 10.21203/rs.2.9777/v4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/14/2020] [Indexed: 05/24/2023] Open
Abstract
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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Affiliation(s)
- Yunyi Zhou
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Shuzhen Luo
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Saba Hameed
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Dong Xiao
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Jie Zhan
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China.
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China.
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
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17
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Zhou Y, Luo S, Hameed S, Xiao D, Zhan J, Wang A, He L. Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita). BMC Genomics 2020; 21:117. [PMID: 32013881 PMCID: PMC6998100 DOI: 10.1186/s12864-020-6492-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/14/2020] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
- Yunyi Zhou
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Shuzhen Luo
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Saba Hameed
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Dong Xiao
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.,Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Jie Zhan
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.,Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China. .,Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China. .,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China. .,Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, People's Republic of China. .,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
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18
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Lin Y, Liu T, Cui T, Wang Z, Zhang Y, Tan P, Huang Y, Yu J, Wang D. RNAInter in 2020: RNA interactome repository with increased coverage and annotation. Nucleic Acids Res 2020; 48:D189-D197. [PMID: 31906603 PMCID: PMC6943043 DOI: 10.1093/nar/gkz804] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.
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Affiliation(s)
- Yunqing Lin
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuncong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100730, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279; or
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19
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Sun M, Shen Y, Li H, Yang J, Cai X, Zheng G, Zhu Y, Jia B, Sun X. The multiple roles of OsmiR535 in modulating plant height, panicle branching and grain shape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:60-69. [PMID: 31128716 DOI: 10.1016/j.plantsci.2019.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 05/20/2023]
Abstract
The miR156/miR529-SPL module acts a vital role in regulating plant growth and development. Though miR535 shows very high sequence identity to miR156 and miR529, it is still unknown whether miR535 could control plant growth and development. In this study, we performed the evolutionary analyses of miR535s in land plants and found that miR535s were less conserved than miR156s during evolution. In rice, miR535 expressed at a very low level during the vegetative growth but highly accumulated in young panicles, which is similar with OsmiR529, but opposite to OsmiR156. Expectedly, OsmiR535 overexpression in rice reduced plant height by decreasing the 1st and 2nd internode length. Furthermore, OsmiR535 overexpression imposed great influence in panicle architecture, such as more but shorter panicles, and fewer primary/secondary panicle branches. Moreover, OsmiR535 overexpression increased the grain length, but did not affect grain width. Through quantitative real-time PCR analyses, we further revealed that OsmiR535 overexpression repressed the expression of OsSPL7/12/16, as well as the OsSPLs downstream panicle related genes, including OsPIN1B, OsDEP1, OsLOG and OsSLR1. Taken together, our findings suggest that OsmiR535 multiply modulates plant height, panicle architecture and grain shape possibly by regulating OsSPLs genes in rice.
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Affiliation(s)
- Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Hongyu Li
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Guiping Zheng
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yanming Zhu
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin, 150030, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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Wang Y, Li W, Chang H, Zhou J, Luo Y, Zhang K, Wang B. Sweet cherry fruit miRNAs and effect of high CO 2 on the profile associated with ripening. PLANTA 2019; 249:1799-1810. [PMID: 30840178 DOI: 10.1007/s00425-019-03110-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/12/2019] [Indexed: 05/11/2023]
Abstract
157 known and 55 novel miRNAs were found in sweet cherry fruit. MiRNA target genes involved in fruit ripening and the differentially expressed miRNAs under CO2 treatment were identified. MicroRNAs (miRNAs) are short non-coding RNAs and play important functions in many biological processes, including fruit ripening and senescence. In the current study, the high-throughput sequencing and bioinformatics methods were implemented to decipher the miRNAs landscape in sweet cherry fruit. A total of 157 known miRNAs belonging to 50 families and 55 putative novel miRNAs were found. Target genes of the miRNAs were predicted and genes involved in fruit ripening were found, including F-box proteins and TFs such as SPL, TCP, NAC, MYB, ARF and AP2/ERF. And these target genes were further confirmed by degradome sequencing. A regulatory network model was constructed to uncover the miRNAs and their targets involved in fruit ripening and senescence. Importantly, elevated carbon dioxide can significantly postpone the ripening and senescence of sweet cherry fruit and the differentially expressed miRNAs exposed to CO2 were identified. These miRNAs included miR482j, miR6275, miR164, miR166, miR171, miR393, miR858, miR3627a, miR6284, miR6289 and miR7122b, and some of their functions were linked to fruit ripening. This study was the first report to profile miRNAs in sweet cherry fruit and it would provide more information for further study of miRNA roles in the ripening processes and their regulation mechanism underlying the effects of high carbon dioxide treatment on fruit ripening.
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Affiliation(s)
- Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Wensheng Li
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Hong Chang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Jiahua Zhou
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kaichun Zhang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
- National R&D Center For Fruit Processing, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China.
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China.
| | - Baogang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
- National R&D Center For Fruit Processing, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China.
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China.
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