1
|
Nie H, Zhao N, Li B, Jiang K, Li H, Zhang J, Guo A, Hua J. Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39376043 DOI: 10.1111/tpj.17058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/23/2024] [Accepted: 09/12/2024] [Indexed: 10/09/2024]
Abstract
Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.
Collapse
Affiliation(s)
- Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Bin Li
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Kaiyun Jiang
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Jingrou Zhang
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd., Haidian District, Beijing, 100193, China
| |
Collapse
|
2
|
Nikhil S, Mohideen HS, Sella RN. Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis. J Mol Evol 2024:10.1007/s00239-024-10198-5. [PMID: 39261311 DOI: 10.1007/s00239-024-10198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a multipurpose crop grown for food, fodder, and bioenergy production. Its cultivated varieties, along with their wild counterparts, contribute to the core genetic pool. Despite the availability of several re-sequenced sorghum genomes, a variable portion of sorghum genomes is not reported during reference genome assembly and annotation. The present analysis used 223 publicly available RNA-seq datasets from seven sweet sorghum cultivars to construct superTranscriptome. This approach yielded 45,864 Representative Transcript Assemblies (RTAs) that showcased intriguing Presence/Absence Variation (PAV) across 15 published sorghum genomes. We found 301 superTranscripts were exclusive to sweet sorghum, including 58 de novo genes encoded core and linker histones, zinc finger domains, glucosyl transferases, cellulose synthase, etc. The superTranscriptome added 2,802 new protein-coding genes to the Sweet Sorghum Reference Genome (SSRG), of which 559 code for different transcription factors (TFs). Our analysis revealed that MULE-like transposases were abundant in the sweet sorghum genome and could play a hidden role in the evolution of sweet sorghum. We observed large deletions in the D locus and terminal deletions in four other NAC encoding loci in the SSRG compared to its wild progenitor (353) suggesting non-functional NAC genes contributed to trait development in sweet sorghum. Moreover, superTranscript-based methods for Differential Exon Usage (DEU) and Differential Gene Expression (DGE) analyses were more accurate than those based on the SSRG. This study demonstrates that the superTranscriptome can enhance our understanding of fundamental sorghum mechanisms, improve genome annotations, and potentially even replace the reference genome.
Collapse
Affiliation(s)
- Shinde Nikhil
- Membrane Protein Interaction Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India
| | - Habeeb Shaikh Mohideen
- Entomoinformatics Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India
| | - Raja Natesan Sella
- Membrane Protein Interaction Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India.
| |
Collapse
|
3
|
Lai J, Liu B, Xiong G, Luo Q, Song S, Jiang J, Wei H, Wang J. Inhibitory mechanism of 4-ethyl-1,2-dimethoxybenzene produced by Streptomyces albidoflavus strain ML27 against Colletotrichum gloeosporioides. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 204:106086. [PMID: 39277399 DOI: 10.1016/j.pestbp.2024.106086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/17/2024]
Abstract
Actinomycetes have emerged as significant biocontrol resources due to their rich array of bioactive natural products. While much research has historically focused on secondary metabolites isolated from their fermentation broth, there remains a dearth of reports on their volatile organic compounds (VOCs). Here, strain ML27, isolated from soil, was identified as Streptomyces albidoflavus based on morphological features, physiological, biochemical, and molecular characteristics (16S rRNA, atpD, recA, and rpoB gene sequences). VOCs from S. albidoflavus strain ML27 were effectively captured using solid-phase microextraction (SPME) and tentatively identified through gas chromatography-mass spectrometry (GC/MS). Among these compounds, 4-ethyl-1,2-dimethoxybenzene exhibited broad-spectrum antifungal activity and demonstrated efficacy in controlling citrus anthracnose, with a control efficacy of 86.67%. Furthermore, the inhibitory mechanism of 4-ethyl-1,2-dimethoxybenzene against Colletotrichum gloeosporioides was revealed. Results indicated that 4-ethyl-1,2-dimethoxybenzene induced swelling, deformity, and breakage in C. gloeosporioides mycelia, and significantly inhibited spore germination. Transcriptome analysis revealed that 4-ethyl-1,2-dimethoxybenzene inhibited the growth and development of C. gloeosporioides primarily by disrupting energy metabolism and the integrity of the cell wall and membrane. Based on these results, it is promising to develop 4-ethyl-1,2-dimethoxybenzene as a novel biopesticide for controlling citrus anthracnose.
Collapse
Affiliation(s)
- Jiahao Lai
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045; Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Bing Liu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045.
| | - Guihong Xiong
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Qian Luo
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Shuilin Song
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Junxi Jiang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045; Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Hongyi Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045; Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China 330045
| | - Junwen Wang
- Economic Crops Research Institute of Jiangxi Province, Nanchang, Jiangxi, China, 330202
| |
Collapse
|
4
|
Wang X, Yan L, Li T, Zhang J, Zhang Y, Zhang J, Lian X, Zhang H, Zheng X, Hou N, Cheng J, Wang W, Zhang L, Ye X, Li J, Feng J, Tan B. The lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branch number by affecting brassinosteroid biosynthesis. THE NEW PHYTOLOGIST 2024; 243:1050-1064. [PMID: 38872462 DOI: 10.1111/nph.19903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Branch number is one of the most important agronomic traits of fruit trees such as peach. Little is known about how LncRNA and/or miRNA modules regulate branching through transcription factors. Here, we used molecular and genetic tools to clarify the molecular mechanisms underlying brassinosteroid (BR) altering plant branching. We found that the number of sylleptic branch and BR content in pillar peach ('Zhaoshouhong') was lower than those of standard type ('Okubo'), and exogenous BR application could significantly promote branching. PpTCP4 expressed great differentially comparing 'Zhaoshouhong' with 'Okubo'. PpTCP4 could directly bind to DWARF2 (PpD2) and inhibited its expression. PpD2 was the only one differentially expressed key gene in the path of BR biosynthesis. At the same time, PpTCP4 was identified as a target of miR6288b-3p. LncRNA1 could act as the endogenous target mimic of miR6288b-3p and repress expression of miR6288b-3p. Three deletions and five SNP sites of lncRNA1 promoter were found in 'Zhaoshouhong', which was an important cause of different mRNA level of PpTCP4 and BR content. Moreover, overexpressed PpTCP4 significantly inhibited branching. A novel mechanism in which the lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branching number was proposed.
Collapse
Affiliation(s)
- Xiaobei Wang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Lixia Yan
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Tianhao Li
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Jie Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Yajia Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Junjie Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Xiaodong Lian
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Haipeng Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Nan Hou
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Langlang Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Jidong Li
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- College of Forestry, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| |
Collapse
|
5
|
Pang Y, Zheng K, Min Q, Wang Y, Xue X, Li W, Zhao H, Qiao F, Han S. Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots. Int J Mol Sci 2024; 25:6226. [PMID: 38892412 PMCID: PMC11172603 DOI: 10.3390/ijms25116226] [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: 05/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.
Collapse
Affiliation(s)
- Yanrong Pang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Qinyue Min
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Yinxing Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Feng Qiao
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
| |
Collapse
|
6
|
Yu H, Teng Z, Liu B, Lv J, Chen Y, Qin Z, Peng Y, Meng S, He Y, Duan M, Zhang J, Ye N. Transcription factor OsMYB30 increases trehalose content to inhibit α-amylase and seed germination at low temperature. PLANT PHYSIOLOGY 2024; 194:1815-1833. [PMID: 38057158 DOI: 10.1093/plphys/kiad650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023]
Abstract
Low-temperature germination (LTG) is an important agronomic trait for direct-seeding cultivation of rice (Oryza sativa). Both OsMYB30 and OsTPP1 regulate the cold stress response in rice, but the function of OsMYB30 and OsTPP1 in regulating LTG and the underlying molecular mechanism remains unknown. Employing transcriptomics and functional studies revealed a sugar signaling pathway that regulates seed germination in response to low temperature (LT). Expression of OsMYB30 and OsTPP1 was induced by LT during seed germination, and overexpressing either OsMYB30 or OsTPP1 delayed seed germination and increased sensitivity to LT during seed germination. Transcriptomics and qPCR revealed that expression of OsTPP1 was upregulated in OsMYB30-overexpressing lines but downregulated in OsMYB30-knockout lines. In vitro and in vivo experiments revealed that OsMYB30 bound to the promoter of OsTPP1 and regulated the abundance of OsTPP1 transcripts. Overaccumulation of trehalose (Tre) was found in both OsMYB30- and OsTPP1-overexpressing lines, resulting in inhibition of α-amylase 1a (OsAMY1a) gene during seed germination. Both LT and exogenous Tre treatments suppressed the expression of OsAMY1a, and the osamy1a mutant was not sensitive to exogenous Tre during seed germination. Overall, we concluded that OsMYB30 expression was induced by LT to activate the expression of OsTPP1 and increase Tre content, which thus inhibited α-amylase activity and seed germination. This study identified a phytohormone-independent pathway that integrates environmental cues with internal factors to control seed germination.
Collapse
Affiliation(s)
- Huihui Yu
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Zhenning Teng
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Bohan Liu
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Jiahan Lv
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yinke Chen
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhonge Qin
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yan Peng
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shuan Meng
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yuchi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430000, China
| | - Meijuan Duan
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong 999077, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
| | - Nenghui Ye
- Hunan Provincial Key Laboratory of Rice Stress Biology, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
| |
Collapse
|
7
|
Guo S, Zhang M, Feng M, Liu G, Torregrosa L, Tao X, Ren R, Fang Y, Zhang Z, Meng J, Xu T. miR156b-targeted VvSBP8/13 functions downstream of the abscisic acid signal to regulate anthocyanins biosynthesis in grapevine fruit under drought. HORTICULTURE RESEARCH 2024; 11:uhad293. [PMID: 38371638 PMCID: PMC10873574 DOI: 10.1093/hr/uhad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/20/2023] [Indexed: 02/20/2024]
Abstract
Anthocyanins are the primary color components of grapevine berries and wines. In cultivation practices, a moderate water deficit can promote anthocyanin accumulation in red grape skins. Our previous study showed that abscisic acid (ABA) plays a key role in this process. Herein, we identified a microRNA, vv-miR156b, that is generated in grapevine berries in response to drought stress, along with increasing anthocyanin content and biosynthetic structural gene transcripts. In contrast, vv-miR156b short tandem target mimic (STTM) function-loss callus exhibits the opposite phenotype. Results from in vivo and in vitro experiments revealed that the ABA-signaling-regulated transcription factor VvAREB2 binds directly to the ABA-responsive element (ABRE) of the MIR156b promoter and activates miR156b expression. Furthermore, two miR156b downstream targets, VvSBP8 and VvSBP13, exhibited reduced grape anthocyanin content in their overexpressors but there was a contrary result in their CRISPR-edited lines, the decrease in anthocyanin content was rescued in miR156b and SBP8/13 double overexpressors. We further demonstrated that both VvSBP8 and VvSBP13, encoding transcriptional repressors, displayed sufficient ability to interact with VvMYC1 and VvMYBA1, thereby interfering with MYB-bHLH-WD (MBW) repeat transcriptional complex formation, resulting in the repression of anthocyanin biosynthesis. Our findings demonstrate a direct functional relationship between ABA signaling and the miR156-SBP-MBW complex regulatory module in driving drought-induced anthocyanin accumulation in grape berries.
Collapse
Affiliation(s)
- Shuihuan Guo
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Meng Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxin Feng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guipeng Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Laurent Torregrosa
- UMR LEPSE, Université de Montpellier , CIRAD, INRAE, Institut Agro, 34060 Montpellier, France
| | - Xiaoqing Tao
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Ren
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Fang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiangfei Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tengfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
8
|
Luo L, Molthoff J, Li Q, Liu Y, Luo S, Li N, Xuan S, Wang Y, Shen S, Bovy AG, Zhao J, Chen X. Identification of candidate genes associated with less-photosensitive anthocyanin phenotype using an EMS mutant ( pind) in eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1282661. [PMID: 38169942 PMCID: PMC10758619 DOI: 10.3389/fpls.2023.1282661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Eggplant (Solanum melongena L.) is a highly nutritious and economically important vegetable crop. However, the fruit peel of eggplant often shows poor coloration owing to low-light intensity during cultivation, especially in the winter. The less-photosensitive varieties produce anthocyanin in low light or even dark conditions, making them valuable breeding materials. Nevertheless, genes responsible for anthocyanin biosynthesis in less-photosensitive eggplant varieties are not characterized. In this study, an EMS mutant, named purple in the dark (pind), was used to identify the key genes responsible for less-photosensitive coloration. Under natural conditions, the peel color and anthocyanin content in pind fruits were similar to that of wildtype '14-345'. The bagged pind fruits were light purple, whereas those of '14-345' were white; and the anthocyanin content in the pind fruit peel was significantly higher than that in '14-345'. Genetic analysis revealed that the less-photosensitive trait was controlled by a single dominant gene. The candidate gene was mapped on chromosome 10 in the region 7.72 Mb to 11.71 Mb. Thirty-five differentially expressed genes, including 12 structural genes, such as CHS, CHI, F3H, DFR, ANS, and UFGT, and three transcription factors MYB113, GL3, and TTG2, were identified in pind using RNA-seq. Four candidate genes EGP21875 (myb domain protein 113), EGP21950 (unknown protein), EGP21953 (CAAX amino-terminal protease family protein), and EGP21961 (CAAX amino-terminal protease family protein) were identified as putative genes associated with less-photosensitive anthocyanin biosynthesis in pind. These findings may clarify the molecular mechanisms underlying less-photosensitive anthocyanin biosynthesis in eggplant.
Collapse
Affiliation(s)
- Lei Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jos Molthoff
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Ying Liu
- Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| |
Collapse
|
9
|
Liu L, Heidecker M, Depuydt T, Manosalva Perez N, Crespi M, Blein T, Vandepoele K. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots. PLANT PHYSIOLOGY 2023; 193:1933-1953. [PMID: 37345955 DOI: 10.1093/plphys/kiad360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.
Collapse
Affiliation(s)
- Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michel Heidecker
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Nicolas Manosalva Perez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Martin Crespi
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Thomas Blein
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| |
Collapse
|
10
|
Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
Collapse
Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
| |
Collapse
|
11
|
Pinky, Jain R, Yadav A, Sharma R, Dhaka N. Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108019. [PMID: 37714026 DOI: 10.1016/j.plaphy.2023.108019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.
Collapse
Affiliation(s)
- Pinky
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
| |
Collapse
|
12
|
Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey A. Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107940. [PMID: 37738864 DOI: 10.1016/j.plaphy.2023.107940] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
Collapse
Affiliation(s)
- Swati Hazra
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | | | - Synudeen Sahib
- S. S. Cottage, Njarackal, P.O.: Perinad, Kollam, 691601, Kerala, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh 792103, India.
| | - Arnab Majumdar
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, West Bengal 741246, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Priyabrata Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, West Bengal 741235, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Sayanti Mandal
- Department of Biotechnology, Dr. D. Y. Patil Arts, Commerce & Science College (affiliated to Savitribai Phule Pune University), Sant Tukaram Nagar, Pimpri, Pune, Maharashtra-411018, India.
| | - Samapika Nandy
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India; Department of Botany, Vedanta College, 33A Shiv Krishna Daw Lane, Kolkata-700054, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India.
| |
Collapse
|
13
|
Feng S, Long X, Gao M, Zhao Y, Guan X. Global identification of natural antisense transcripts in Gossypium hirsutum and Gossypium barbadense under chilling stress. iScience 2023; 26:107362. [PMID: 37554457 PMCID: PMC10405317 DOI: 10.1016/j.isci.2023.107362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
Natural antisense transcripts (NATs) in model plants have been recognized as important regulators of gene expression under abiotic stresses. However, the functional roles of NATs in crops under low temperature are still unclear. Here, we identified 815 and 689 NATs from leaves of Gossypium hirsutum and G. barbadense under chilling stress. Among those, 224 NATs were identified as interspecific homologs between the two species. The correlation coefficients for expression of NATs and their cognate sense genes (CSG) were 0.43 and 0.37 in G. hirsutum and G. barbadense, respectively. Furthermore, expression of interspecific NATs and CSGs alike was highly consistent under chilling stress with correlation coefficients of 0.90-0.91. Four cold-associated NATs were selected for functional validation using virus-induced gene silencing (VIGS). Our results suggest that CAN1 engage in the molecular regulation of chilling stress by regulating SnRK2.8 expression. This highly conserved NAT have valuable potential for applications in breeding cold-tolerant cotton.
Collapse
Affiliation(s)
- Shouli Feng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 300058, China
- Xianghu Laboratory, Hangzhou 311231, China
| | - Xuan Long
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 300058, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongyan Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan 572025, China
- Hainan Yazhou Bay Seed Lab, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan 572025, China
| |
Collapse
|
14
|
Meng J, Wang H, Chi R, Qiao Y, Wei J, Zhang Y, Han M, Wang Y, Li H. The eTM-miR858-MYB62-like module regulates anthocyanin biosynthesis under low-nitrogen conditions in Malus spectabilis. THE NEW PHYTOLOGIST 2023; 238:2524-2544. [PMID: 36942952 DOI: 10.1111/nph.18894] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/09/2023] [Indexed: 05/19/2023]
Abstract
The anthocyanin content increases in Malus spectabilis leaves under low-nitrogen conditions. Noncoding RNAs are indicated to play key regulatory roles in anthocyanin biosynthesis. However, the functional roles of noncoding RNAs in anthocyanin biosynthesis under low-nitrogen conditions remain elusive. In this study, miR858 was screened as a key regulator of anthocyanin biosynthesis under low-nitrogen conditions through whole-transcriptome sequencing. Then, we used miR858 as an entry point to explore the regulatory network of lncRNA-miRNA-mRNA by dual-luciferase reporter assays and GUS histochemical staining assays, as well as to identify the mechanism of this regulatory network in anthocyanin biosynthesis by both transient and stable transformation experiments in Malus. MiR858 overexpression increased total anthocyanin content. MiR858 acted by negatively regulating its target gene, MsMYB62-like, under the low-nitrogen condition. MsMYB62-like inhibited the expression of MsF3'H, thereby negatively regulating anthocyanin biosynthesis. In addition, eTM858-1 and eTM858-2 were identified as endogenous target mimics of miR858 that bind to miR858 to prevent cleavage of MsMYB62-like and thereby negatively regulate anthocyanin biosynthesis. The results clarify the mechanism through which the eTM-miR858-MYB62-like module regulates anthocyanin biosynthesis in Malus under low-nitrogen conditions.
Collapse
Affiliation(s)
- Jiaxin Meng
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Han Wang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rufei Chi
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuhang Qiao
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Wei
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuqin Zhang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Meiling Han
- Colloge of Urban and Rural Construction, Shanxi Agricultural University, Taigu, Shaanxi, 030801, China
| | - Yu Wang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Houhua Li
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
15
|
Wimalagunasekara SS, Weeraman JWJK, Tirimanne S, Fernando PC. Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa). J Genet Eng Biotechnol 2023; 21:69. [PMID: 37246172 DOI: 10.1186/s43141-023-00515-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/06/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance. RESULTS Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs. CONCLUSIONS These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
Collapse
Affiliation(s)
| | - Janith W J K Weeraman
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
| | - Shamala Tirimanne
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Pasan C Fernando
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| |
Collapse
|
16
|
Li G, Chen Q, Bai Q, Feng Y, Mao K, Yang M, He L, Liu M, Liu J, Wan D. LncRNA expression analysis by comparative transcriptomics among closely related poplars and their regulatory roles in response to salt stress. TREE PHYSIOLOGY 2023:tpad041. [PMID: 37017317 DOI: 10.1093/treephys/tpad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in regulating key biological processes; however, our knowledge of lncRNAs' roles in plant adaptive evolution is still limited. Here, we determined the divergence of conserved lncRNAs in closely related poplar species that were either tolerant or sensitive to salt stress by comparative transcriptome analysis. Among the 34,363 identified lncRNAs, approximately 3% were shared among poplar species with conserved sequences but diversified in their function, copy number, originating genomic region and expression patterns. Further cluster analysis revealed that the conserved lncRNAs showed more similar expression patterns within salt-tolerant poplars (P. euphratica and P. pruinosa) than between salt-tolerant and salt-sensitive poplars. Among these lncRNAs, the antisense lncRNA lncERF024 was induced by salt and differentiated expression between salt-sensitive and salt-tolerant poplars. Overexpression of lncERF024 in P. alba var. pyramidalis enhanced poplar tolerance to salt stress. Furthermore, RNA pull-down and RNA-seq analysis showed that numerous candidate genes or proteins associated with stress response and photosynthesis might be involved in salt resistance in PeulncERF024-OE poplars. Altogether, our study provided novel insight into how the diversification of lncRNA expression contributes to plant adaptation traits and showed that lncERF024 may be involved in the regulation both of gene expression and protein function conferring salt tolerance in Populus.
Collapse
Affiliation(s)
- Guiting Li
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Qingyuan Chen
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qiuxian Bai
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Department of Pharmacology, Ningxia Medical University, Yinchuan,750004, China
| | - Yannan Feng
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Kaili Mao
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mengran Yang
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ling He
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Meijun Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jianquan Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dongshi Wan
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
17
|
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
Collapse
|
18
|
Xie X, Jin J, Wang C, Lu P, Li Z, Tao J, Cao P, Xu Y. Investigating nicotine pathway-related long non-coding RNAs in tobacco. Front Genet 2023; 13:1102183. [PMID: 36744176 PMCID: PMC9892058 DOI: 10.3389/fgene.2022.1102183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with low or no protein-coding ability, which play essential roles in various biological processes in plants. Tobacco is an ideal model plant for studying nicotine biosynthesis and metabolism, and there is little research on lncRNAs in this field. Therefore, how to take advantage of the mature tobacco system to profoundly investigate the lncRNAs involved in the nicotine pathway is intriguing. By exploiting 549 public RNA-Seq datasets of tobacco, 30,212 lncRNA candidates were identified, including 24,084 large intervening non-coding RNAs (lincRNAs), 5,778 natural antisense transcripts (NATs) and 350 intronic non-coding RNAs (incRNAs). Compared with protein-coding genes, lncRNAs have distinct properties in terms of exon number, sequence length, A/U content, and tissue-specific expression pattern. lincRNAs showed an asymmetric evolutionary pattern, with a higher proportion (68.71%) expressed from the Nicotiana sylvestris (S) subgenome. We predicted the potential cis/trans-regulatory effects on protein-coding genes. One hundred four lncRNAs were detected as precursors of 30 known microRNA (miRNA) family members, and 110 lncRNAs were expected to be the potential endogenous target mimics for 39 miRNAs. By combining the results of weighted gene co-expression network analysis with the differentially expressed gene analysis of topping RNA-seq data, we constructed a sub-network containing eight lncRNAs and 25 nicotine-related coding genes. We confirmed that the expression of seven lncRNAs could be affected by MeJA treatment and may be controlled by the transcription factor NtMYC2 using a quantitative PCR assay and gene editing. The results suggested that lncRNAs are involved in the nicotine pathway. Our findings further deepened the understanding of the features and functions of lncRNAs and provided new candidates for regulating nicotine biosynthesis in tobacco.
Collapse
|
19
|
Lu J, Zhen S, Zhang J, Xie Y, He C, Wang X, Wang Z, Zhang S, Li Y, Cui Y, Wang G, Wang J, Liu J, Li L, Gu R, Zheng X, Fu J. Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:16. [PMID: 36662257 DOI: 10.1007/s00122-023-04293-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Long intergenic non-coding RNA (lincRNA), cis-acting expression quantitative trait locus (cis-eQTL), maize, regulatory evolution. The law of genetic variation during domestication explains the evolutionary mechanism and provides a theoretical basis for improving existing varieties of maize. Previous studies focused on exploiting regulatory variations controlling the expression of protein-coding genes rather than of non-protein-coding genes. Here, we examined the genetic and evolutionary features of long non-coding RNAs from intergenic regions (long intergenic non-coding RNAs, lincRNAs) using population-scale transcriptome data and identified 1168 lincRNAs with cis-acting expression quantitative trait loci (cis-eQTLs). We found that lincRNAs are more likely to be regulated by cis-eQTLs, which exert stronger effects than the protein-coding genes. During maize domestication and improvement, upregulated alleles of lincRNAs, which originated from both standing variation and new mutation, accumulate more frequently and show larger effect sizes than the coding genes. A stronger signature of genetic differentiation was observed in their regulatory regions compared to those of randomly sampled lincRNAs. In addition, we found that cis-regulatory differentiation of lincRNAs is related to the sequence conservation of lincRNA transcripts. Non-conserved lincRNAs more tend to gain upregulated alleles and show a stronger relationship with selected traits than conserved lincRNAs between maize and its wild relatives. Our findings in maize improve the understanding of cis-regulatory variation in lincRNA genes during domestication and improvement and provide an effective approach for prioritizing candidates for further investigation.
Collapse
Affiliation(s)
- Jiawen Lu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sihan Zhen
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng He
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheyuan Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Song Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
20
|
Feng X, Zhou L, Sheng A, Lin L, Liu H. Comparative transcriptome analysis on drought stress-induced floral formation of Curcuma kwangsiensis. PLANT SIGNALING & BEHAVIOR 2022; 17:2114642. [PMID: 36189888 PMCID: PMC9542783 DOI: 10.1080/15592324.2022.2114642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
The rhizomes and tubers of Curcuma kwangsiensis have extensive medicinal value in China. However, the inflorescences of C. kwangsiensis are rarely known in horticulture, because of its low field flowering rate. In order to improve the flowering rate of C. kwangsiensis, we conducted drought stress treatment on the rhizome of C. kwangsiensis. The flowering rate of rhizome was the highest after 4d of drought stress treatment, and the buds on the rhizome could be obviously swell on the 4th day of rehydration culture. In order to identify the genes regulating the flowering time of Curcuma kwangsiensis, comparative transcriptome analysis was performed on the buds on rhizomes before drought stress treatment, 4 d after drought stress treatment and 4 d after rehydration culture. During this process, a total of 20 DEGs controlling flowering time and 23 DEGs involved in ABA synthesis and signal transduction were identified, which might regulate the flowering of C. kwangsiensis under drought stress. Some floral integration factors, such as SOC1 and FTIP, were up-regulated under drought stress for 4 d, indicating that C. kwangsiensis had flowering trend under drought stress. The results of the present study will provide theoretical support for the application of Curcuma kwangsiensis in gardening.
Collapse
Affiliation(s)
- Xin Feng
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Liying Zhou
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Aiwu Sheng
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ling Lin
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huicheng Liu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
21
|
Zhang Y, Fan F, Zhang Q, Luo Y, Liu Q, Gao J, Liu J, Chen G, Zhang H. Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:3223. [PMID: 36501265 PMCID: PMC9737669 DOI: 10.3390/plants11233223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant-pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5' end, and a non-conserved 3' end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.
Collapse
Affiliation(s)
- Yixin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fan Fan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qunjie Zhang
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yongjian Luo
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinjian Liu
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jiadong Gao
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jun Liu
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guanghui Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
22
|
Jian G, Mo Y, Hu Y, Huang Y, Ren L, Zhang Y, Hu H, Zhou S, Liu G, Guo J, Ling Y. Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress. RICE (NEW YORK, N.Y.) 2022; 15:56. [PMID: 36326968 PMCID: PMC9633917 DOI: 10.1186/s12284-022-00599-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.
Collapse
Affiliation(s)
- Guihua Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Shuangxi Zhou
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2019, Australia
| | - Gang Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| |
Collapse
|
23
|
Shi S, Zhang S, Wu J, Liu X, Zhang Z. Identification of long non-coding RNAs involved in floral scent of Rosa hybrida. FRONTIERS IN PLANT SCIENCE 2022; 13:996474. [PMID: 36267940 PMCID: PMC9577252 DOI: 10.3389/fpls.2022.996474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) were found to play important roles in transcriptional, post-transcriptional, and epigenetic gene regulation in various biological processes. However, lncRNAs and their regulatory roles remain poorly studied in horticultural plants. Rose is economically important not only for their wide use as garden and cut flowers but also as important sources of natural fragrance for perfume and cosmetics industry, but presently little was known about the regulatory mechanism of the floral scent production. In this paper, a RNA-Seq analysis with strand-specific libraries, was performed to rose flowers in different flowering stages. The scented variety 'Tianmidemeng' (Rosa hybrida) was used as plant material. A total of 13,957 lncRNAs were identified by mining the RNA-Seq data, including 10,887 annotated lncRNAs and 3070 novel lncRNAs. Among them, 10,075 lncRNAs were predicted to possess a total of 29,622 target genes, including 54 synthase genes and 24 transcription factors related to floral scent synthesis. 425 lncRNAs were differentially expressed during the flowering process, among which 19 were differentially expressed among all the three flowering stages. Using weighted correlation network analysis (WGCNA), we correlate the differentially-expressed lncRNAs to synthesis of individual floral scent compounds. Furthermore, regulatory function of one of candidate lncRNAs for floral scent synthesis was verified using VIGS method in the rose. In this study, we were able to show that lncRNAs may play important roles in floral scent production in the rose. This study also improves our understanding of how plants regulate their secondary metabolism by lncRNAs.
Collapse
Affiliation(s)
- Shaochuan Shi
- Vegetable Research Institute, Shandong Academy of Agricultural Science, Jinan, China
| | - Shiya Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jie Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| |
Collapse
|
24
|
Cao P, Zhan C, Yin J, Gong S, Ma D, Li Y. Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato ( Solanum lycopersicum). FRONTIERS IN PLANT SCIENCE 2022; 13:981281. [PMID: 36186038 PMCID: PMC9523475 DOI: 10.3389/fpls.2022.981281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 05/26/2023]
Abstract
There is growing evidences indicating that long intergenic ncRNAs (lincRNAs) play key roles in plant development and stress responses. To research tomato lincRNA functions during the interaction between tomato and Ralstonia solanacearum, RNA-seq data of tomato plants inoculated with R. solanacearum was analyzed. In this study, 315 possible lincRNAs were identified from RNA-seq data. Then 23 differentially expressed lincRNAs between tomato plants inoculated with R. solanacearum and control were identified and a total of 171 possible target genes for these differentially expressed lincRNAs were predicted. Through GO and KEGG analysis, we found that lincRNA might be involved in jasmonic acid and ethylene signaling pathways to respond to tomato bacterial wilt infection. Furthermore, lincRNA may also be involved in regulating the expression of AGO protein. Subsequently, analysis of expression patterns between differentially expressed lincRNAs and adjacent mRNAs by qRT-PCR revealed that part of lincRNAs and their possible target genes exhibited positive correlation. Taken together, these results suggest that lincRNAs play potential roles in tomato against R. solanacearum infection and will provide fundamental information about the lincRNA-based plant defense mechanisms.
Collapse
Affiliation(s)
- Peina Cao
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yan Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
25
|
Khemka N, Rajkumar MS, Garg R, Jain M. Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea. PLANTA 2022; 256:79. [PMID: 36094579 DOI: 10.1007/s00425-022-03986-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.
Collapse
Affiliation(s)
- Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
26
|
Zhang F, Yang L, Huang W, Luo X, Xie J, Hu B, Chen Y. Flavonoid Metabolic Profiles and Gene Mapping of Rice (Oryza sativa L.) Purple Gradient Grain Hulls. RICE (NEW YORK, N.Y.) 2022; 15:43. [PMID: 35934754 PMCID: PMC9357590 DOI: 10.1186/s12284-022-00589-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) grain hull color is an easily observable trait and regarded as a crucial morphological marker in rice breeding. Here, a purple gradient grain hull mutant (pg) was found from natural mutations of a straw-white grain hull rice variety IARI 6184B (Orzya sativa L. subsp. indica). The color of the mutant grain hulls changed from straw-white to pink, then purple, and finally brownish-yellow. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified 217 flavonoids, including 18 anthocyanins, among which cyanidin O-syringic acid had the highest concentration in pink (66.2 × 106) and purple (68.0 × 106) grain hulls. The relative contents of hesperetin O-malonyl-hexoside, apigenin derivatives, genistein derivatives, and kaempferol 3-O derivatives were consistently downregulated during pg grain hull development. Conversely, 12 anthocyanins were upregulated in colored hulls, and cyanidin 3-O-malonylhexoside was abundant only in pink and purple grain hulls. Moreover, the candidate gene was mapped into a 1.38 Mb region on chromosome 4 through bulked segregant analysis based on deep sequencing (BSA-seq) and gene mapping approaches. These results increased our understanding of anthocyanin biosynthesis in rice grains, helping rice breeders to select new rice varieties with desirable grain traits.
Collapse
Affiliation(s)
- Fantao Zhang
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Limin Yang
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Wenxue Huang
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Xiangdong Luo
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Jiankun Xie
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Biaolin Hu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences/National Engineering Laboratory for Rice (Nanchang), No 1738, Liangtangbei Road, Nanchang, 330200, Jiangxi, China.
| | - Yaling Chen
- Laboratory of Plant Genetic Improvement and Biotechnology, College of Life Sciences, Jiangxi Normal University, No 99, Ziyang Road, Nanchang, 330022, Jiangxi, China.
| |
Collapse
|
27
|
Chen L, Shen E, Zhao Y, Wang H, Wilson I, Zhu QH. The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton. Int J Mol Sci 2022; 23:ijms23158594. [PMID: 35955726 PMCID: PMC9368808 DOI: 10.3390/ijms23158594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the repositories and conservativeness of lincRNAs in different cotton species or about their role in responding to biotic stresses. Here, by using publicly available RNA-seq datasets from diverse sources, including experiments of Verticillium dahliae (Vd) infection, we identified 24,425 and 17,713 lincRNAs, respectively, in Gossypium hirsutum (Ghr) and G. barbadense (Gba), the two cultivated allotetraploid cotton species, and 6933 and 5911 lincRNAs, respectively, in G. arboreum (Gar) and G. raimondii (Gra), the two extant diploid progenitors of the allotetraploid cotton. While closely related subgenomes, such as Ghr_At and Gba_At, tend to have more conserved lincRNAs, most lincRNAs are species-specific. The majority of the synthetic and transcribed lincRNAs (78.2%) have a one-to-one orthologous relationship between different (sub)genomes, although a few of them (0.7%) are retained in all (sub)genomes of the four species. The Vd responsiveness of lincRNAs seems to be positively associated with their conservation level. The major functionalities of the Vd-responsive lincRNAs seem to be largely conserved amongst Gra, Ghr, and Gba. Many Vd-responsive Ghr-lincRNAs overlap with Vd-responsive QTL, and several lincRNAs were predicted to be endogenous target mimicries of miR482/2118, with a pair being highly conserved between Ghr and Gba. On top of the confirmation of the feature characteristics of the lincRNAs previously reported in cotton and other species, our study provided new insights into the conservativeness and divergence of lincRNAs during cotton evolution and into the relationship between the conservativeness and Vd responsiveness of lincRNAs. The study also identified candidate lincRNAs with a potential role in disease response for functional characterization.
Collapse
Affiliation(s)
- Li Chen
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
| | - Enhui Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China;
| | - Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- Correspondence:
| |
Collapse
|
28
|
Li J, Liu Z, Gao C, Miao Y, Cui K. Overexpression of DsEXLA2 gene from Dendrocalamus sinicus accelerates the plant growth rate of Arabidopsis. PHYTOCHEMISTRY 2022; 199:113178. [PMID: 35385712 DOI: 10.1016/j.phytochem.2022.113178] [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: 12/02/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Expansins play crucial roles in cell wall loosening and a range of life activities involving cell wall modification. Nevertheless, the biological functions of expansin genes during fast growth of bamboo remain unclear. In this study, Dendrocalamus sinicus, the largest and fastest growing bamboo species in the world, was used as the research material, and the full length of DsEXLA2 was cloned. Bioinformatics analysis revealed that DsEXLA2 contained expansin family typical domains (DPBB_1 and Pollen_allerg_1, CDRC motif) and amino acid sequence was highly conserved among different species. The expression level of DsEXLA2 increased from top section to basal section in different internodes. Subcellular localization verified that DsEXLA2 protein was located in the cell wall. Further genetic transformation studies in Arabidopsis indicated that compared with the wild type, DsEXLA2 overexpressed transgenic plants exhibited higher plant height, thicker stem, larger leaf, and less epidermal hair number and smaller stomatal aperture in the prophase and metaphase of growth. In addition, the cellulose content in the stem of transgenic plants was increased, and cell wall was thickened significantly. Moreover, a total of 1656 differentially expressed genes (DEGs) were identified by RNA-seq. The upregulated genes were predominantly enriched in the plant-pathogen interaction, MAPK signaling pathway-plant, plant hormone signal transduction, lipid metabolism and amino acid metabolism, while the downregulated genes were mainly enriched in energy metabolism, carbohydrate metabolism, plant hormone signal transduction and ribosome. These data implied that overexpression of DsEXLA2 gene accelerates the plant growth rate of Arabidopsis. This study is helpful to reveal the molecular mechanism of DsEXLA2 in culm growth and development of D. sinicus, and to understand the rapid growth of bamboos.
Collapse
Affiliation(s)
- Jin Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Zirui Liu
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Chengjie Gao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Yingchun Miao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Kai Cui
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China.
| |
Collapse
|
29
|
Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening. Sci Rep 2022; 12:11044. [PMID: 35773470 PMCID: PMC9247041 DOI: 10.1038/s41598-022-15330-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.
Collapse
|
30
|
Yu L, Huang T, Qi X, Yu J, Wu T, Luo Z, Zhou L, Li Y. Genome-Wide Analysis of Long Non-coding RNAs Involved in Nodule Senescence in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:917840. [PMID: 35707611 PMCID: PMC9189404 DOI: 10.3389/fpls.2022.917840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Plant long non-coding RNAs (lncRNAs) are widely accepted to play crucial roles during diverse biological processes. In recent years, thousands of lncRNAs related to the establishment of symbiosis, root nodule organogenesis and nodule development have been identified in legumes. However, lncRNAs involved in nodule senescence have not been reported. In this study, senescence-related lncRNAs were investigated in Medicago truncatula nodules by high-throughput strand-specific RNA-seq. A total of 4576 lncRNAs and 126 differentially expressed lncRNAs (DElncRNAs) were identified. We found that more than 60% lncRNAs were associated with transposable elements, especially TIR/Mutator and Helitron DNA transposons families. In addition, 49 DElncRNAs were predicted to be the targets of micro RNAs. Functional analysis showed that the largest sub-set of differently expressed target genes of DElncRNAs were associated with the membrane component. Of these, nearly half genes were related to material transport, suggesting that an important function of DElncRNAs during nodule senescence is the regulation of substance transport across membranes. Our findings will be helpful for understanding the functions of lncRNAs in nodule senescence and provide candidate lncRNAs for further research.
Collapse
|
31
|
Zhu Y, Chen L, Hong X, Shi H, Li X. Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. BMC Genomics 2022; 23:381. [PMID: 35590257 PMCID: PMC9118565 DOI: 10.1186/s12864-022-08602-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts’ direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique. Results A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes. Conclusion The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08602-9.
Collapse
Affiliation(s)
- Yan Zhu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangna Hong
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Henan University, Kaifeng, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
32
|
Liu YN, Liu CC, Guo R, Tian L, Cheng JF, Wu YN, Wang D, Wang B. The Rice Qa-SNAREs in SYP13 Subfamily Are Involved in Regulating Arbuscular Mycorrhizal Symbiosis and Seed Fertility. FRONTIERS IN PLANT SCIENCE 2022; 13:898286. [PMID: 35665185 PMCID: PMC9158536 DOI: 10.3389/fpls.2022.898286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Qa-SNARE gene SYP132 (isoform α) was previously reported to affect arbuscular mycorrhizal (AM) symbiosis in the legume species Medicago truncatula. In non-legumes especially monocots, it remains unknown whether certain SNARE genes are also involved in AM symbiosis. In this work, we studied a rice orthologous gene OsSYP132, which showed induced expression in mycorrhizal roots and two paralogous genes OsSYP131a and OsSYP131b, which were not induced by the AM fungus Rhizophagus irregularis. After employing CRISPR/Cas9 technique to generate their mutants, the Ossyp131a homozygous mutant T0 plants exhibited a dwarf phenotype and produced no fertile seeds, indicating a required role of this gene in seed fertility. Unlike the case in legume, the Ossyp132 mutants exhibited normal mycorrhizal phenotype, so did the Ossyp131b mutants. In the Ossyp131b Ossyp132 double mutants, however, the colonization rate and arbuscule abundance level decreased markedly, indicating an impaired fungal proliferation ability in rice roots. Such a defect was further confirmed by the reduced expression levels of AM marker genes. Our results in rice therefore demonstrated that while SYP13II members showed evolutionary and induction patterns specific to symbiosis, AM symbiosis is in fact controlled by the combined action of both SYP13I and SYP13II clades, revealing a functional redundancy among SYNTAXIN genes in mutualism.
Collapse
Affiliation(s)
- Ying-Na Liu
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Cheng-Chen Liu
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Rui Guo
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Li Tian
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jian-Fei Cheng
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ya-Nan Wu
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dong Wang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Bin Wang
- Department of Biology, School of Life Sciences, Nanjing University, Nanjing, China
| |
Collapse
|
33
|
Wu LB, Eom JS, Isoda R, Li C, Char SN, Luo D, Schepler-Luu V, Nakamura M, Yang B, Frommer WB. OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility. THE NEW PHYTOLOGIST 2022; 234:975-989. [PMID: 35211968 DOI: 10.1111/nph.18054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.
Collapse
Affiliation(s)
- Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding I, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Joon-Seob Eom
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Reika Isoda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Chenhao Li
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dangping Luo
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| |
Collapse
|
34
|
Ye X, Wang S, Zhao X, Gao N, Wang Y, Yang Y, Wu E, Jiang C, Cheng Y, Wu W, Liu S. Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:978-993. [PMID: 35218100 DOI: 10.1111/tpj.15714] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 06/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.
Collapse
Affiliation(s)
- Xiaoxue Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ni Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yao Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ernest Wu
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| |
Collapse
|
35
|
Tissue specificity and responses to abiotic stresses and hormones of PIN genes in rice. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01031-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
36
|
An JP, Xu RR, Liu X, Su L, Yang K, Wang XF, Wang GL, You CX. Abscisic acid insensitive 4 interacts with ICE1 and JAZ proteins to regulate ABA signaling-mediated cold tolerance in apple. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:980-997. [PMID: 34555166 DOI: 10.1093/jxb/erab433] [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: 07/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid is involved in the regulation of cold stress response, but its molecular mechanism remains to be elucidated. In this study, we demonstrated that the APETALA2/ethylene responsive factor (AP2/ERF) family protein MdABI4 positively regulates abscisic acid-mediated cold tolerance in apple. We found that MdABI4 interacts with MdICE1, a key regulatory protein involved in the cold stress response, and enhances the transcriptional regulatory function of MdICE1 on its downstream target gene MdCBF1, thus improving abscisic acid-mediated cold tolerance. The jasmonate-ZIM domain (JAZ) proteins MdJAZ1 and MdJAZ2 negatively modulate MdABI4-improved cold tolerance in apple by interacting with the MdABI4 protein. Further investigation showed that MdJAZ1 and MdJAZ2 interfere with the interaction between the MdABI4 and MdICE1 proteins. Together, our data revealed that MdABI4 integrates jasmonic acid and abscisic acid signals to precisely modulate cold tolerance in apple through the JAZ-ABI4-ICE1-CBF regulatory cascade. These findings provide insights into the crosstalk between jasmonic acid and abscisic acid signals in response to cold stress.
Collapse
Affiliation(s)
- Jian-Ping An
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Rui-Rui Xu
- Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong, College of Biological and Agricultural Engineering, Weifang University, Weifang, Shandong, China
| | - Xin Liu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, China
| | - Ling Su
- Shandong Academy of Grape, Jinan, Shandong, China
| | - Kuo Yang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| |
Collapse
|
37
|
Liu P, Zhang Y, Zou C, Yang C, Pan G, Ma L, Shen Y. Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress. BMC Genomics 2022; 23:50. [PMID: 35026983 PMCID: PMC8756644 DOI: 10.1186/s12864-021-08286-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/29/2021] [Indexed: 01/10/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. Results The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF. Conclusions The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08286-7.
Collapse
|
38
|
Wang X, Wu R, Shen T, Li Z, Li C, Wu B, Jiang H, Zhao G. An R2R3-MYB Transcription Factor OsMYBAS1 Promotes Seed Germination under Different Sowing Depths in Transgenic Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:139. [PMID: 35009142 PMCID: PMC8747419 DOI: 10.3390/plants11010139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
MYB-type transcription factors play essential regulatory roles in seed germination and the response to seedling establishment stress. This study isolated a rice R2R3-MYB gene, OsMYBAS1, and functionally characterized its role in seed germination by generating transgenic rice plants with the overexpression and knockout of OsMYBAS1. Gene expression analysis suggested that OsMYBAS1 was highly expressed in brown rice and root, respectively. Subcellular localization analysis determined that OsMYBAS1 was localized in the nucleus. No significant differences in seed germination rate were observed among wild-type (WT) and transgenic rice plants at the 0-cm sowing depth. However, when sown at a depth of 4 cm, higher germination rates, root lengths and seedling heights were obtained in OsMYBAS1-overexpressing plants than in WT. Furthermore, the opposite results were recorded between the osmybas1 mutants and WT. Moreover, OsMYBAS1-overexpressing plants significantly enhanced superoxide dismutase (SOD) enzyme activity and suppressed the accumulation of malondialdehyde (MDA) content at the 4-cm sowing depth. These results indicate that the MYB transcription factor OsMYBAS1 may promote rice seed germination and subsequent seedling establishment under deep-sowing conditions. These findings can provide valuable insight into rice seed-quality breeding to facilitate the development of a dry, direct-seeding production system.
Collapse
Affiliation(s)
- Xiaomin Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Rong Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Tongshu Shen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Zhenan Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Chengyong Li
- The Agro-Tech Extension Center of Quzhou, 139 Fushi Road, Quzhou 324000, China;
| | - Bangkui Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Hongye Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| | - Guangwu Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.W.); (R.W.); (T.S.); (Z.L.); (B.W.); (H.J.)
| |
Collapse
|
39
|
Chen L, Zhu QH. The evolutionary landscape and expression pattern of plant lincRNAs. RNA Biol 2022; 19:1190-1207. [PMID: 36382947 PMCID: PMC9673970 DOI: 10.1080/15476286.2022.2144609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular processes, including development and stress response. Many lincRNAs have been bioinformatically identified in plants, but their evolutionary dynamics and expression characteristics are still elusive. Here, we systematically identified thousands of lincRNAs in 26 plant species, including 6 non-flowering plants, investigated the conservation of the identified lincRNAs in different levels of plant lineages based on sequence and/or synteny homology and explored characteristics of the conserved lincRNAs during plant evolution and their co-expression relationship with protein-coding genes (PCGs). In addition to confirmation of the features well documented in literature for lincRNAs, such as species-specific, fewer exons, tissue-specific expression patterns and less abundantly expressed, we revealed that histone modification signals and/or binding sites of transcription factors were enriched in the conserved lincRNAs, implying their biological functionalities, as demonstrated by identifying conserved lincRNAs related to flower development in both the Brassicaceae and grass families and ancient lincRNAs potentially functioning in meristem development of non-flowering plants. Compared to PCGs, lincRNAs are more likely to be associated with transposable elements (TEs), but with different characteristics in different evolutionary lineages, for instance, the types of TEs and the variable level of association in lincRNAs with different conservativeness. Together, these results provide a comprehensive view on the evolutionary landscape of plant lincRNAs and shed new insights on the conservation and functionality of plant lincRNAs.
Collapse
Affiliation(s)
- Li Chen
- School of Life Sciences, Westlake University, Hangzhou, China
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität Zu Berlin, Berlin, Germany
| | | |
Collapse
|
40
|
Golicz AA. Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data. Methods Mol Biol 2022; 2443:465-482. [PMID: 35037221 DOI: 10.1007/978-1-0716-2067-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length without discernible protein coding potential. Long intergenic noncoding RNAs (lincRNAs) constitute a subset of lncRNAs, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincRNA discovery from publicly available non-stranded RNA-Seq datasets. The pipeline presented can be applied to any plant species for which RNA-Seq data and a reference genome sequence are available.
Collapse
Affiliation(s)
- A A Golicz
- Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany.
| |
Collapse
|
41
|
Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc.
Collapse
|
42
|
Yin J, Yan J, Hou L, Jiang L, Xian W, Guo Q. Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici. BMC Genomics 2021; 22:868. [PMID: 34856924 PMCID: PMC8638555 DOI: 10.1186/s12864-021-08183-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. RESULTS In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. CONCLUSIONS This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.
Collapse
Affiliation(s)
- Junliang Yin
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, 434000 Jingzhou, Hubei China
| | - Jiahui Yan
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Liling Jiang
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Wenrong Xian
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Qinghai Academy of Agriculture and Forestry Science, Qinghai University, 810016 Xining, China
| |
Collapse
|
43
|
Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.
Collapse
|
44
|
Gao HN, Jiang H, Cui JY, You CX, Li YY. Review: The effects of hormones and environmental factors on anthocyanin biosynthesis in apple. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111024. [PMID: 34620429 DOI: 10.1016/j.plantsci.2021.111024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/22/2021] [Accepted: 08/12/2021] [Indexed: 05/24/2023]
Abstract
Fruit coloration is an appearance trait that directly affects the commercial value and market competitiveness of apples. The red color of apple fruit is mainly affected by anthocyanin accumulation, and the synthesis of anthocyanin is affected by various factors. The critical roles of hormones and environmental factors during apple anthocyanin biosynthesis are described. This review also elaborates the specific mechanisms of the responses of internal genes to stress and changes in anthocyanin when apples are exposed to different environmental stressors. This study provides direction for future research on apple anthocyanin and is a reference for anthocyanin studies in other species.
Collapse
Affiliation(s)
- Huai-Na Gao
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Han Jiang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Jian-Ying Cui
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Yuan-Yuan Li
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| |
Collapse
|
45
|
Kandpal M, Dhaka N, Sharma R. Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2389-2406. [PMID: 34744373 PMCID: PMC8526681 DOI: 10.1007/s12298-021-01059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01059-2.
Collapse
Affiliation(s)
- Manu Kandpal
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana India
| | - Rita Sharma
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| |
Collapse
|
46
|
Miculan M, Nelissen H, Ben Hassen M, Marroni F, Inzé D, Pè ME, Dell’Acqua M. A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1056-1071. [PMID: 34087008 PMCID: PMC8519057 DOI: 10.1111/tpj.15364] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/31/2021] [Indexed: 05/13/2023]
Abstract
The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.
Collapse
Affiliation(s)
- Mara Miculan
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Manel Ben Hassen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Fabio Marroni
- IGA Technology ServicesUdine33100Italy
- Department of Agricultural, FoodAT, Environmental and Animal Sciences (DI4A)University of UdineUdine33100Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Mario Enrico Pè
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | | |
Collapse
|
47
|
Ma B, Zhang A, Zhao Q, Li Z, Lamboro A, He H, Li Y, Jiao S, Guan S, Liu S, Yao D, Zhang J. Genome-wide identification and analysis of long non-coding RNAs involved in fatty acid biosynthesis in young soybean pods. Sci Rep 2021; 11:7603. [PMID: 33828134 PMCID: PMC8027399 DOI: 10.1038/s41598-021-87048-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs of more than 200 nucleotides. To date, the roles of lncRNAs in soybean fatty acid synthesis have not been fully studied. Here, the low-linolenic acid mutant 'MT72' and the wild-type control 'JN18' were used as materials. The lncRNAs in young pods at 30 and 40 days (d) after flowering were systematically identified and analyzed using transcriptome sequencing technology combined with bioinformatics tools. A total of 39,324 lncRNAs and 561 differentially expressed lncRNAs were identified. A lncRNAs-miRNAs-protein-coding genes (mRNAs) network was constructed, and 46 lncRNAs, 46 miRNAs and 137 mRNAs were found to be correlated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 12 targeted mRNAs in the competing endogenous RNA network showed that these lncRNAs may be involved in the biological processes of fatty acid transport, lipid synthesis and cell division. Finally, the expression levels of differentially expressed lncRNAs, miRNAs and mRNAs were verified using qRT-PCR. The expression patterns of most genes were consistent with the sequencing results. In conclusion, new information was provided for the study of fatty acid synthesis by lncRNAs in young soybean pods.
Collapse
Affiliation(s)
- Bohan Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Zeyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Abraham Lamboro
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Suqi Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| |
Collapse
|
48
|
Zhang Y, Li P, She G, Xu Y, Peng A, Wan X, Zhao J. Molecular Basis of the Distinct Metabolic Features in Shoot Tips and Roots of Tea Plants ( Camellia sinensis): Characterization of MYB Regulator for Root Theanine Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3415-3429. [PMID: 33719427 DOI: 10.1021/acs.jafc.0c07572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The physiological and metabolic differences between shoot tips and roots of tea plants are significant, and understanding them is required for improvement of tea quality and plant growth. A high-quality full-length transcriptome sequencing on tea plant roots and shoot tips by PacBio SMRT technology was done to gain a further understanding. Approximately 160699 and 166120 full-length transcripts were recovered in roots and shoots, respectively, including 31232 and 41068 novel isoforms and 16960 and 26029 alternative splicing (AS) isoforms. These supported 21699 full-length reads and 31232 and 41068 novel transcripts from root and shoot, respectively, including 1679 long noncoding RNAs (lncRNAs) and 2772 fusion transcripts, which significantly upgrade the Camellia sinensis genome annotation. The respective 6475 and 6981 transcripts in roots and shoots differ in 3'-untranslated regions. Meanwhile, extensive analyses of novel transcripts, ASs, and lncRNAs also revealed a large number of ASs and lincRNAs closely related to the regulation of characteristic secondary metabolites including catechins, theanine, and caffeine. Finally, a root-specific CsMYB6 was characterized to regulate theanine biosynthesis by genetic and molecular analyses. CsMYB6 directly bound to and activate the promoter of theanine synthetase gene (CsTSI). The study lays a foundation for the further investigation of metabolic genomics and regulation in tea plants.
Collapse
Affiliation(s)
- Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Anqi Peng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| |
Collapse
|
49
|
Zheng W, Hu H, Lu Q, Jin P, Cai L, Hu C, Yang J, Dai L, Chen J. Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana. BIOLOGY 2021; 10:biology10030232. [PMID: 33802832 PMCID: PMC8002735 DOI: 10.3390/biology10030232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection. Abstract Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.
Collapse
Affiliation(s)
- Weiran Zheng
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
| | - Haichao Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Peng Jin
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- Correspondence: (L.D.); (J.C.)
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Correspondence: (L.D.); (J.C.)
| |
Collapse
|
50
|
Song X, Hu J, Wu T, Yang Q, Feng X, Lin H, Feng S, Cui C, Yu Y, Zhou R, Gong K, Yu T, Pei Q, Li N. Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage. HORTICULTURE RESEARCH 2021; 8:48. [PMID: 33642591 PMCID: PMC7917108 DOI: 10.1038/s41438-021-00484-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/30/2020] [Accepted: 12/13/2020] [Indexed: 05/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the "protein processing in endoplasmic reticulum" and "plant hormone signal transduction" pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.
Collapse
Affiliation(s)
- Xiaoming Song
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China.
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA.
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
| | - Jingjing Hu
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Tong Wu
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qihang Yang
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Xuehuan Feng
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Hao Lin
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shuyan Feng
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Chunlin Cui
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Ying Yu
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, Denmark
| | - Ke Gong
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Tong Yu
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qiaoying Pei
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Nan Li
- College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China.
| |
Collapse
|