151
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Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H. Reassessment of the Four Yield-related Genes Gn1a, DEP1, GS3, and IPA1 in Rice Using a CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2016; 7:377. [PMID: 27066031 PMCID: PMC4811884 DOI: 10.3389/fpls.2016.00377] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/11/2016] [Indexed: 05/17/2023]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) systems have been successfully used as efficient tools for genome editing in a variety of species. We used the CRISPR/Cas9 system to mutate the Gn1a (Os01g0197700), DEP1 (Os09g0441900), GS3 (Os03g0407400), and IPA1 (Os08g0509600) genes of rice cultivar Zhonghua 11, genes which have been reported to function as regulators of grain number, panicle architecture, grain size and plant architecture, respectively. Analysis of the phenotypes and frequencies of edited genes in the first generation of transformed plants (T0) showed that the CRISPR/Cas9 system was highly efficient in inducing targeted gene editing, with the desired genes being edited in 42.5% (Gn1a), 67.5% (DEP1), 57.5% (GS3), and 27.5% (IPA1) of the transformed plants. The T2 generation of the gn1a, dep1, and gs3 mutants featured enhanced grain number, dense erect panicles, and larger grain size, respectively. Furthermore, semi-dwarf, and grain with long awn, phenotypes were observed in dep1 and gs3 mutants, respectively. The ipa1 mutants showed two contrasting phenotypes, having either fewer tillers or more tillers, depending on the changes induced in the OsmiR156 target region. In addition, we found that mutants with deletions occurred more frequently than previous reports had indicated and that off-targeting had taken place in highly similar target sequences. These results proved that multiple regulators of important traits can be modified in a single cultivar by CRISPR/Cas9, and thus facilitate the dissection of complex gene regulatory networks in the same genomic background and the stacking of important traits in cultivated varieties.
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Affiliation(s)
- Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xiaoxia Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Zejiao Zhou
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Maichun Fang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xiaoping Pan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Qiupeng Lin
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Wanbin Luo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Guojiang Wu, ; Hongqing Li,
| | - Hongqing Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
- *Correspondence: Guojiang Wu, ; Hongqing Li,
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152
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Koramutla MK, Bhatt D, Negi M, Venkatachalam P, Jain PK, Bhattacharya R. Strength, Stability, and cis-Motifs of In silico Identified Phloem-Specific Promoters in Brassica juncea (L.). FRONTIERS IN PLANT SCIENCE 2016; 7:457. [PMID: 27148290 PMCID: PMC4834444 DOI: 10.3389/fpls.2016.00457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/24/2016] [Indexed: 05/03/2023]
Abstract
Aphids, a hemipteran group of insects pose a serious threat to many of the major crop species including Brassica oilseeds. Transgenic strategies for developing aphid-resistant plant types necessitate phloem-bound expression of the insecticidal genes. A few known phloem-specific promoters, in spite of tissue-specific activity fail to confer high level gene-expression. Here, we identified seven orthologues of phloem-specific promoters in B. juncea (Indian mustard), and experimentally validated their strength of expression in phloem exudates. Significant cis-motifs, globally occurring in phloem-specific promoters showed variable distribution frequencies in these putative phloem-specific promoters of B. juncea. In RT-qPCR based gene-expression study promoter of Glutamine synthetase 3A (GS3A) showed multifold higher activity compared to others, across the different growth stages of B. juncea plants. A statistical method employing four softwares was devised for rapidly analysing stability of the promoter-activities across the plant developmental stages. Different statistical softwares ranked these B. juncea promoters differently in terms of their stability in promoter-activity. Nevertheless, the consensus in output empirically suggested consistency in promoter-activity of the six B. juncea phloem- specific promoters including GS3A. The study identified suitable endogenous promoters for high level and consistent gene-expression in B. juncea phloem exudate. The study also demonstrated a rapid method of assessing species-specific strength and stability in expression of the endogenous promoters.
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Affiliation(s)
- Murali Krishna Koramutla
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Deepa Bhatt
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Manisha Negi
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | | | - Pradeep K. Jain
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Ramcharan Bhattacharya
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
- *Correspondence: Ramcharan Bhattacharya ;
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153
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Khaldun ABM, Huang W, Lv H, Liao S, Zeng S, Wang Y. Comparative Profiling of miRNAs and Target Gene Identification in Distant-Grafting between Tomato and Lycium (Goji Berry). FRONTIERS IN PLANT SCIENCE 2016; 7:1475. [PMID: 27803702 PMCID: PMC5067468 DOI: 10.3389/fpls.2016.01475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/16/2016] [Indexed: 05/10/2023]
Abstract
Local translocation of small RNAs between cells is proved. Long distance translocation between rootstock and scion is also well documented in the homo-grafting system, but the process in distant-grafting is widely unexplored where rootstock and scion belonging to different genera. Micro RNAs are a class of small, endogenous, noncoding, gene silencing RNAs that regulate target genes of a wide range of important biological pathways in plants. In this study, tomato was grafted onto goji (Lycium chinense Mill.) to reveal the insight of miRNAs regulation and expression patterns within a distant-grafting system. Goji is an important traditional Chinese medicinal plant with enriched phytochemicals. Illumina sequencing technology has identified 68 evolutionary known miRNAs of 37 miRNA families. Moreover, 168 putative novel miRNAs were also identified. Compared with control tomato, 43 (11 known and 32 novels) and 163 (33 known and 130 novels) miRNAs were expressed significantly different in shoot and fruit of grafted tomato, respectively. The fruiting stage was identified as the most responsive in the distant-grafting approach and 123 miRNAs were found as up-regulating in the grafted fruit which is remarkably higher compare to the grafted shoot tip (28). Potential targets of differentially expressed miRNAs were found to be involved in diverse metabolic and regulatory pathways. ADP binding activities, molybdopterin synthase complex and RNA helicase activity were found as enriched terms in GO (Gene Ontology) analysis. Additionally, "metabolic pathways" was revealed as the most significant pathway in KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The information of the small RNA transcriptomes that are obtained from this study might be the first miRNAs elucidation for a distant-grafting system, particularly between goji and tomato. The results from this study will provide the insights into the molecular aspects of miRNA-mediated regulation in the medicinal plant goji, and in grafted tomato. Noteworthy, it would provide a basis how miRNA signals could exchange between rootstock and scion, and the relevance to diverse biological processes.
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Affiliation(s)
- A. B. M. Khaldun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- University of the Chinese Academy of SciencesBeijing, China
- Oilseed Research Center, Bangladesh Agricultural Research Institute (BARI)Joydebpur, Gazipur, Bangladesh
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
| | - Haiyan Lv
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
| | - Sihong Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- University of the Chinese Academy of SciencesBeijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden (CAS)Guangzhou, China
| | - Ying Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden (CAS)Guangzhou, China
- Northwest Center for Agrobiotechnology (Ningxia), CASBeijing, China
- *Correspondence: Ying Wang
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154
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Makhzoum A, Yousefzadi M, Malik S, Gantet P, Tremouillaux-Guiller J. Strigolactone biology: genes, functional genomics, epigenetics and applications. Crit Rev Biotechnol 2015; 37:151-162. [PMID: 26669271 DOI: 10.3109/07388551.2015.1121967] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Strigolactones (SLs) represent an important new plant hormone class marked by their multifunctional role in plant and rhizosphere interactions. These compounds stimulate hyphal branching in arbuscular mycorrhizal fungi (AMF) and seed germination of root parasitic plants. In addition, they are involved in the control of plant architecture by inhibiting bud outgrowth as well as many other morphological and developmental processes together with other plant hormones such as auxins and cytokinins. The biosynthetic pathway of SLs that are derived from carotenoids was partially decrypted based on the identification of mutants from a variety of plant species. Only a few SL biosynthetic and regulated genes and related regulatory transcription factors have been identified. However, functional genomics and epigenetic studies started to give first elements on the modality of the regulation of SLs related genes. Since they control plant architecture and plant-rhizosphere interaction, SLs start to be used for agronomical and biotechnological applications. Furthermore, the genes involved in the SL biosynthetic pathway and genes regulated by SL constitute interesting targets for plant breeding. Therefore, it is necessary to decipher and better understand the genetic determinants of their regulation at different levels.
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Affiliation(s)
- Abdullah Makhzoum
- a Department of Biology , University of Western Ontario , London , Ontario , Canada
| | - Morteza Yousefzadi
- b Department of Marine Biology , Faculty of Marine Sciences and Technology, Hormozgan University , Bandar Abbas , Iran
| | - Sonia Malik
- c Health Sciences Graduate Program, Biological and Health Sciences Centre, Federal University of Maranhão , São Luís, MA , Brazil
| | - Pascal Gantet
- d Faculté des Sciences , Université de Montpellier , UMR DIADE , Montpellier , France , and
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155
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Prakash P, Rajakani R, Gupta V. Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets. Comput Biol Chem 2015; 61:62-74. [PMID: 26815768 DOI: 10.1016/j.compbiolchem.2015.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants.
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Affiliation(s)
- Pravin Prakash
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
| | - Raja Rajakani
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
| | - Vikrant Gupta
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India.
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156
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Fan K, Fan D, Ding Z, Su Y, Wang X. Cs-miR156 is involved in the nitrogen form regulation of catechins accumulation in tea plant (Camellia sinensis L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:350-360. [PMID: 26520678 DOI: 10.1016/j.plaphy.2015.10.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/21/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
The nitrogen source affects the growth of tea plants and regulates the accumulation of catechins in the leaves. In this report, we assessed the influences of NH4(+) and NO3(-) on plant growth, catechins accumulation and associated gene expression. Compared with the preferential nitrogen source NH4(+), when NO3(-) was supplied as the sole nitrogen source, tea plants showed similar symptoms with the nitrogen-free treatments and showed lower nitrogen, free amino acid accumulation, chlorophyll content and biomass gain, indicating NO3(-) was not efficiently used by these plants. However, the total shoot catechins content was significantly higher for NO3(-) treatments than that for NH4(+) treatment or combined NH4(+)+NO3(-) treatment, suggesting that, in addition to its influence on plant growth, the nitrogen form regulated the accumulation of catechins in tea. The expression of catechins biosynthesis-related genes was associated with the regulation of catechins accumulation and composition changes mediated by nitrogen form. PAL, CHS, CHI, and DFR genes exhibited higher expression levels in plants supplied with NO3(-), in which the transcript level of DFR in the shoots was significantly correlated with the catechins content. In the end, we identified a new function for the Cs-miR156, which was drastically induced through NH4(+). Moreover, a potential mechanism of the Cs-miR156 pathway in regulating catechins biosynthesis in tea plants has been suggested, with particular respect to nitrogen forms. Cs-miR156 might repress the expression of the target gene SPL to regulate the DFR gene, which plays a vital role in catechins biosynthesis.
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Affiliation(s)
- Kai Fan
- Institute of Tea Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Dongmei Fan
- Institute of Tea Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Zhaotang Ding
- Institute of Tea Science, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Yanhua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | - Xiaochang Wang
- Institute of Tea Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
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157
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Cao D, Li Y, Wang J, Nan H, Wang Y, Lu S, Jiang Q, Li X, Shi D, Fang C, Yuan X, Zhao X, Li X, Liu B, Kong F. GmmiR156b overexpression delays flowering time in soybean. PLANT MOLECULAR BIOLOGY 2015; 89:353-63. [PMID: 26341865 DOI: 10.1007/s11103-015-0371-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 08/27/2015] [Indexed: 05/23/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is an important crop used for human consumption, animal feed and biodiesel fuel. Wering time and maturity significantly affect soybean grain yield. In Arabidopsis thaliana, miR156 has been proposed to regulate the transition from the juvenile to the adult phase of shoot development, which is accompanied by changes in vegetative morphology and an increase in reproductive potential. However, the molecular mechanisms underlying miR156 function in soybean flowering remain unknown. Here, we report that the overexpression of GmmiR156b delays flowering time in soybean. GmmiR156b may target SPL orthologs and negatively regulate GmSPLs, thereby delaying flowering in soybean under LD and natural conditions. GmmiR156b down-regulates several known flowering time regulators in soybean, such as GmAP1 (a, b, c), GmLFY2, GmLFY2, GmFULs, GmSOC1s, GmFT5a, and GmmiR172. These data show that a similar miR156-SPL regulatory module was conserved in the soybean flowering pathway. However, GmFULs, GmSOC1a and GmSOC1b were significantly suppressed under LD conditions but not under SD conditions, which is different in Arabidopsis that these genes were down-regulated irrespective of photoperiod. In addition, GmmiR156b was up-regulated by E1, E2 (GmGI), E3 and E4, which control flowering time and maturity in soybean, and suppressed E1 (E1-Like) and E2 (E2-Like) genes under LD conditions. These data indicated that the miR156-SPL regulatory module was also with some degree of divergent in soybean flowering pathway.
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Affiliation(s)
- Dong Cao
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
| | - Ying Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jialin Wang
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
| | - Haiyang Nan
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
| | - Youning Wang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Sijia Lu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Jiang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Xiaoming Li
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danning Shi
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Fang
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohui Yuan
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
| | - Xiaohui Zhao
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Li
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China.
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China.
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin, 150081, China.
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158
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Wei X, Zhang X, Yao Q, Yuan Y, Li X, Wei F, Zhao Y, Zhang Q, Wang Z, Jiang W, Zhang X. The miRNAs and their regulatory networks responsible for pollen abortion in Ogura-CMS Chinese cabbage revealed by high-throughput sequencing of miRNAs, degradomes, and transcriptomes. FRONTIERS IN PLANT SCIENCE 2015; 6:894. [PMID: 26557132 PMCID: PMC4617173 DOI: 10.3389/fpls.2015.00894] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/08/2015] [Indexed: 05/23/2023]
Abstract
Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetables in Asia and is cultivated across the world. Ogura-type cytoplasmic male sterility (Ogura-CMS) has been widely used in the hybrid breeding industry for Chinese cabbage and many other cruciferous vegetables. Although, the cause of Ogura-CMS has been localized to the orf138 locus in the mitochondrial genome, however, the mechanism by which nuclear genes respond to the mutation of the mitochondrial orf138 locus is unclear. In this study, a series of whole genome small RNA, degradome and transcriptome analyses were performed on both Ogura-CMS and its maintainer Chinese cabbage buds using deep sequencing technology. A total of 289 known miRNAs derived from 69 families (including 23 new families first reported in B. rapa) and 426 novel miRNAs were identified. Among these novel miRNAs, both 3-p and 5-p miRNAs were detected on the hairpin arms of 138 precursors. Ten known and 49 novel miRNAs were down-regulated, while one known and 27 novel miRNAs were up-regulated in Ogura-CMS buds compared to the fertile plants. Using degradome analysis, a total of 376 mRNAs were identified as targets of 30 known miRNA families and 100 novel miRNAs. A large fraction of the targets were annotated as reproductive development related. Our transcriptome profiling revealed that the expression of the targets was finely tuned by the miRNAs. Two novel miRNAs were identified that were specifically highly expressed in Ogura-CMS buds and sufficiently suppressed two pollen development essential genes: sucrose transporter SUC1 and H (+) -ATPase 6. These findings provide clues for the contribution of a potential miRNA regulatory network to bud development and pollen engenderation. This study contributes new insights to the communication between the mitochondria and chromosome and takes one step toward filling the gap in the regulatory network from the orf138 locus to pollen abortion in Ogura-CMS plants from a miRNA perspective.
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Affiliation(s)
- Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qiuju Yao
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fang Wei
- College of Life Science, Zhengzhou UniversityZhengzhou, China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Qiang Zhang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Wusheng Jiang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
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159
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Liu Q, Shen G, Peng K, Huang Z, Tong J, Kabir MH, Wang J, Zhang J, Qin G, Xiao L. The alteration in the architecture of a T-DNA insertion rice mutant osmtd1 is caused by up-regulation of MicroRNA156f. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:819-29. [PMID: 25677853 PMCID: PMC6681133 DOI: 10.1111/jipb.12340] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/09/2015] [Indexed: 05/18/2023]
Abstract
Plant architecture is an important factor for crop production. Some members of microRNA156 (miR156) and their target genes SQUAMOSA Promoter-Binding Protein-Like (SPL) were identified to play essential roles in the establishment of plant architecture. However, the roles and regulation of miR156 is not well understood yet. Here, we identified a T-DNA insertion mutant Osmtd1 (Oryza sativa multi-tillering and dwarf mutant). Osmtd1 produced more tillers and displayed short stature phenotype. We determined that the dramatic morphological changes were caused by a single T-DNA insertion in Osmtd1. Further analysis revealed that the T-DNA insertion was located in the gene Os08g34258 encoding a putative inhibitor I family protein. Os08g34258 was knocked out and OsmiR156f was significantly upregulated in Osmtd1. Overexpression of Os08g34258 in Osmtd1 complemented the defects of the mutant architecture, while overexpression of OsmiR156f in wild-type rice phenocopied Osmtd1. We showed that the expression of OsSPL3, OsSPL12, and OsSPL14 were significantly downregulated in Osmtd1 or OsmiR156f overexpressed lines, indicating that OsSPL3, OsSPL12, and OsSPL14 were possibly direct target genes of OsmiR156f. Our results suggested that OsmiR156f controlled plant architecture by mediating plant stature and tiller outgrowth and may be regulated by an unknown protease inhibitor I family protein.
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Affiliation(s)
- Qing Liu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Gezhi Shen
- Crop Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Keqin Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Mohammed Humayun Kabir
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jianhui Wang
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jingzhe Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
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160
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Aung B, Gruber MY, Hannoufa A. The MicroRNA156 system: A tool in plant biotechnology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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161
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Hayashi-Tsugane M, Maekawa M, Tsugane K. A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1. Sci Rep 2015; 5:14357. [PMID: 26403301 PMCID: PMC4585910 DOI: 10.1038/srep14357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/26/2015] [Indexed: 12/22/2022] Open
Abstract
A non-autonomous DNA transposon in rice, nDart1, is actively transposed in the presence of an autonomous element, aDart1, under natural conditions. The nDart1-promoted gene tagging line was developed using the endogenous nDart1/aDart1 system to generate various rice mutants effectively. While the dominant mutants were occasionally isolated from the tagging line, it was unclear what causes dominant mutations. A semidominant mutant, Bushy dwarf tiller1 (Bdt1), which has the valuable agronomic traits of multiple tillering and dwarfism, was obtained from the tagging line. Bdt1 mutant carried a newly inserted nDart1 at 38-bp upstream of transcription initiation site of a non-protein-coding gene, miR156d. This insertion caused an upstream shift of the miR156d transcription initiation site and, consequently, increased the functional transcripts producing mature microRNAs. These results indicate that the total amount of miR156d is controlled not only by transcript quantity but also by transcript quality. Furthermore, transgenic lines introduced an miR156d fragment that flanked the nDart1 sequence at the 5′ region, suggesting that insertion of nDart1 in the gene promoter region enhances gene expression as a cis-element. This study demonstrates the ability of nDart1 to produce gain-of-function mutants as well as further insights into the function of transposable elements in genome evolution.
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Affiliation(s)
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Kazuo Tsugane
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,The Graduate University for Advanced Studies [SOKENDAI], Okazaki 444-8585, Japan
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162
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Li J, Ding Q, Wang F, Zhang Y, Li H, Gao J. Integrative Analysis of mRNA and miRNA Expression Profiles of the Tuberous Root Development at Seedling Stages in Turnips. PLoS One 2015; 10:e0137983. [PMID: 26367742 PMCID: PMC4569476 DOI: 10.1371/journal.pone.0137983] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 08/24/2015] [Indexed: 11/18/2022] Open
Abstract
The tuberous root of Brassica rapa L. (turnip) is an important modified organ for nutrition storage. A better understanding of the molecular mechanisms involved in the process of tuberous root development is of great value in both economic and biological context. In this study, we analyzed the expression profiles of both mRNAs and miRNAs in tuberous roots at an early stage before cortex splitting (ES), cortex splitting stage (CSS), and secondary root thickening stage (RTS) in turnip based on high-throughput sequencing technology. A large number of differentially expressed genes (DEGs) and several differentially expressed miRNAs (DEMs) were identified. Based on the DEG analysis, we propose that metabolism is the dominant pathway in both tuberous root initiation and secondary thickening process. The plant hormone signal transduction pathway may play a predominant role in regulating tuberous root initiation, while the starch and sucrose metabolism may be more important for the secondary thickening process. These hypotheses were partially supported by sequential DEM analyses. Of all DEMs, miR156a, miR157a, and miR172a exhibited relatively high expression levels, and were differentially expressed in both tuberous root initiation and the secondary thickening process with the expression profiles negatively correlated with those of their target genes. Our results suggest that these miRNAs play important roles in tuberous root development in turnips.
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Affiliation(s)
- Jingjuan Li
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Qian Ding
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Fengde Wang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Yihui Zhang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Huayin Li
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Jianwei Gao
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
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163
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Li M, Yang Y, Li X, Gu L, Wang F, Feng F, Tian Y, Wang F, Wang X, Lin W, Chen X, Zhang Z. Analysis of integrated multiple 'omics' datasets reveals the mechanisms of initiation and determination in the formation of tuberous roots in Rehmannia glutinosa. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5837-51. [PMID: 26077835 DOI: 10.1093/jxb/erv288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
All tuberous roots in Rehmannia glutinosa originate from the expansion of fibrous roots (FRs), but not all FRs can successfully transform into tuberous roots. This study identified differentially expressed genes and proteins associated with the expansion of FRs, by comparing the tuberous root at expansion stages (initiated tuberous root, ITRs) and FRs at the seedling stage (initiated FRs, IFRs). The role of miRNAs in the expansion of FRs was also explored using the sRNA transcriptome and degradome to identify miRNAs and their target genes that were differentially expressed between ITRs and FRs at the mature stage (unexpanded FRs, UFRs, which are unable to expand into ITRs). A total of 6032 genes and 450 proteins were differentially expressed between ITRs and IFRs. Integrated analyses of these data revealed several genes and proteins involved in light signalling, hormone response, and signal transduction that might participate in the induction of tuberous root formation. Several genes related to cell division and cell wall metabolism were involved in initiating the expansion of IFRs. Of 135 miRNAs differentially expressed between ITRs and UFRs, there were 27 miRNAs whose targets were specifically identified in the degradome. Analysis of target genes showed that several miRNAs specifically expressed in UFRs were involved in the degradation of key genes required for the formation of tuberous roots. As far as could be ascertained, this is the first time that the miRNAs that control the transition of FRs to tuberous roots in R. glutinosa have been identified. This comprehensive analysis of 'omics' data sheds new light on the mechanisms involved in the regulation of tuberous roots formation.
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Affiliation(s)
- Mingjie Li
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Yanhui Yang
- College of Bioengineering, Henan University of Technology, Zhengzhou, China, 450001
| | - Xinyu Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002
| | - Li Gu
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Fengji Wang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Fajie Feng
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Yunhe Tian
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Fengqing Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002
| | - Xiaoran Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002
| | - Wenxiong Lin
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
| | - Xinjian Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002
| | - Zhongyi Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002
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164
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Aung B, Gruber MY, Amyot L, Omari K, Bertrand A, Hannoufa A. MicroRNA156 as a promising tool for alfalfa improvement. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:779-90. [PMID: 25532560 DOI: 10.1111/pbi.12308] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/17/2014] [Accepted: 11/04/2014] [Indexed: 05/20/2023]
Abstract
A precursor of miR156 (MsmiR156d) was cloned and overexpressed in alfalfa (Medicago sativa L.) as a means to enhance alfalfa biomass yield. Of the five predicted SPL genes encoded by the alfalfa genome, three (SPL6, SPL12 and SPL13) contain miR156 cleavage sites and their expression was down-regulated in transgenic alfalfa plants overexpressing miR156. These transgenic plants had reduced internode length and stem thickness, enhanced shoot branching, increased trichome density, a delay in flowering time and elevated biomass production. Minor effects on sugar, starch, lignin and cellulose contents were also observed. Moreover, transgenic alfalfa plants had increased root length, while nodulation was maintained. The multitude of traits affected by miR156 may be due to the network of genes regulated by the three target SPLs. Our results show that the miR156/SPL system has strong potential as a tool to substantially improve quality and yield traits in alfalfa.
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Affiliation(s)
- Banyar Aung
- Agriculture and Agri-Food Canada, London, ON, Canada
- Biology Department, Western University, London, ON, Canada
| | | | - Lisa Amyot
- Agriculture and Agri-Food Canada, London, ON, Canada
| | - Khaled Omari
- Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London, ON, Canada
- Biology Department, Western University, London, ON, Canada
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165
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Chen Z, Gao X, Zhang J. Alteration of osa-miR156e expression affects rice plant architecture and strigolactones (SLs) pathway. PLANT CELL REPORTS 2015; 34:767-81. [PMID: 25604991 DOI: 10.1007/s00299-015-1740-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/30/2014] [Accepted: 01/06/2015] [Indexed: 05/20/2023]
Abstract
Overexpressing osa--miR156e in rice produced a bushy mutant and osa--miR156e regulation of tillering may do this through the strigolactones (SLs) pathway. Appropriate downregulation of osa--miR156 expression contributed to the improvement of plant architecture. Tillering is one of the main determinants for rice architecture and yield. In this study, a bushy mutant of rice was identified with increased tiller number, reduced plant height, prolonged heading date, low seed setting, and small panicle size due to a T-DNA insertion which essentially elevated the expression of osa-miR156e. Transgenic plants with constitutive expression of osa-miR156e also had the bushy phenotype, which showed osa-miR156 may control apical dominance and tiller outgrowth via regulating the strigolactones signaling pathway. Furthermore, the extent of impaired morphology was correlated with the expression level of osa-miR156e. In an attempt to genetically improve rice architecture, ectopic expression of osa-miR156e under the GAL4-UAS system or OsTB1 promoter was conducted. According to agronomic trait analysis, pTB1:osa-miR156e transgenic plants significantly improved the grain yield per plant compared to plants overexpressing osa-miR156e, even though the yield was still inferior to the wild type, making it a very interesting albeit negative result. Our results suggested that osa-miR156 could serve as a potential tool for modifying rice plant architecture through genetic manipulation of the osa-miR156 expression level.
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Affiliation(s)
- Zhihui Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China,
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166
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Wang H, Wang H. The miR156/SPL Module, a Regulatory Hub and Versatile Toolbox, Gears up Crops for Enhanced Agronomic Traits. MOLECULAR PLANT 2015; 8:677-88. [PMID: 25617719 DOI: 10.1016/j.molp.2015.01.008] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/26/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
In the past two decades, members of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors, first identified in Antirrhinum majus, have emerged as pivotal regulators of diverse biological processes in plants, including the timing of vegetative and reproductive phase change, leaf development, tillering/branching, plastochron, panicle/tassel architecture, fruit ripening, fertility, and response to stresses. Transcripts of a subset of SPLs are targeted for cleavage and/or translational repression by microRNA156s (miR156s). The levels of miR156s are regulated by both endogenous developmental cues and various external stimuli. Accumulating evidence shows that the regulatory circuit around the miR156/SPL module is highly conserved among phylogenetically distinct plant species, and plays important roles in regulating plant fitness, biomass, and yield. With the expanding knowledge and a mechanistic understanding of their roles and regulatory relationship, we can now harness the miR156/SPL module as a plethora of tools to genetically manipulate crops for optimal parameters in growth and development, and ultimately to maximize yield by intelligent design of crops.
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Affiliation(s)
- Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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167
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An Y, Guo Y, Liu C, An H. BdVIL4 regulates flowering time and branching through repressing miR156 in ambient temperature dependent way in Brachypodium distachyon. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 89:92-9. [PMID: 25728135 DOI: 10.1016/j.plaphy.2015.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/18/2015] [Indexed: 05/11/2023]
Abstract
Responsing to environmental signals, Vernalization Insensitive 3 (VIN3) family proteins are involved in plant development control by repressing the target genes epigenecticly together with Polycomb Repressive Complex 2 (PRC2) complex. BdVIL4 is a VIN3 like gene in Brachypodium distachyon, preferentially expressed in young tissues spatially. The RNAi plants were constructed to study the function of BdVIL4 on the development process. The plants with BdVIL4 RNA interferenced (BdVIL4 RNAi plants) had no obvious difference from the wild at 23 °C, but flowered significantly later and had more branches than the control at l6 °C. In BdVIL4 RNAi plants the expression of miR156 were upregulated, and much more at low temperature (l6 °C). Coincidentally, similar to the BdVIL4 RNAi plants, the miR156 overexpressors also showed late flowering and more branches, and the late flowering phynotype just only performanced at lower temperature. The results suggested that BdVIL4 are involved in the regulation of branching and flowering responsing to the ambient temperature by repressing the expression of miR156.
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Affiliation(s)
- Yanrong An
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, PR China.
| | - Yuyu Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, PR China
| | - Chengcheng Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, PR China
| | - Hailong An
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, PR China.
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168
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Navarro C, Cruz-Oró E, Prat S. Conserved function of FLOWERING LOCUS T (FT) homologues as signals for storage organ differentiation. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:45-53. [PMID: 25449726 DOI: 10.1016/j.pbi.2014.10.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 05/24/2023]
Abstract
Due to their high carbohydrate content and relative low farming demands, tuber-bearing species are an important contribution to human dietary needs in many climatic zones, and interest in these staple crops for processed food and other industrial uses is increasing. Over the past years we have seen remarkable advances in our understanding of the signalling mechanisms involved in the differentiation of these organs, partly aided by their conservation with the well-characterized photoperiodic control of flowering in Arabidopsis. Recent studies have led to the identification of members of the FT gene family as major component of the tuber-inducing signal and the characterization of circadian and photoperiodic components involved in the regulation of these genes. A relevant role of microRNAs in the control of storage organ formation has been established, and hormonal balance requirements similar to those controlling shoot branching were shown to be implicated in the activation of stolon meristem cells. Hence, the recent finding that FT controls branching through direct interaction with the TCP factors holds great promise for the identification of genes acting as FT signal integrators in the stolon.
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Affiliation(s)
- Cristina Navarro
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Eduard Cruz-Oró
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Salomé Prat
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
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169
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Rameau C, Bertheloot J, Leduc N, Andrieu B, Foucher F, Sakr S. Multiple pathways regulate shoot branching. FRONTIERS IN PLANT SCIENCE 2015; 5:741. [PMID: 25628627 PMCID: PMC4292231 DOI: 10.3389/fpls.2014.00741] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.
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Affiliation(s)
- Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
- Institut Jean-Pierre Bourgin, AgroParisTech, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | | | - Nathalie Leduc
- UMR1345 IRHS, Université d’Angers, SFR 4207 QUASAV, Angers, France
| | - Bruno Andrieu
- UMR1091 EGC, INRA, Thiverval-Grignon, France
- UMR1091 EGC, AgroParisTech, Thiverval-Grignon, France
| | | | - Soulaiman Sakr
- UMR1345 IRHS, Agrocampus-Ouest, SFR 4207 QUASAV, Angers, France
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170
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Notaguchi M. Identification of phloem-mobile mRNA. JOURNAL OF PLANT RESEARCH 2015; 128:27-35. [PMID: 25516498 DOI: 10.1007/s10265-014-0675-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 10/06/2014] [Indexed: 05/07/2023]
Abstract
Signaling between cells, tissues and organs is essential for multicellular organisms to coordinate and adapt their development and growth to internal and environmental changes. Plants have evolved a plant-specific symplasmic pathway, called plasmodesmata, for efficient intercellular communication, in addition to the receptor-ligand-based apoplasmic pathway. Long-distance signaling between distant organs is enabled via the phloem tube system, where plasmodesmata contribute to phloem loading and unloading for photosynthate allocation. In addition to signaling by small molecules such as metabolites and phytohormones, the transport of proteins, small RNAs and mRNAs is also considered an important mechanism to achieve long-distance signaling in plants. Recent studies on phloem-mobile proteins and small RNAs have revealed their role in crucial physiological processes including flowering, systemic silencing and nutrient allocation. However, the biological role of mRNAs found in the phloem tube is not yet clear, though their mobility over long-distances has been well evidenced. To gain this knowledge, it is important to collect further information on mRNA profiles in the phloem translocation stream. In this review, I summarize the current approaches to identifying the mRNA population in the phloem translocation system, and discuss the possible role of short- and long-distance mRNA transport.
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Affiliation(s)
- Michitaka Notaguchi
- Graduate School of Science, Nagoya University, B-105, Bldg B, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan,
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171
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Notaguchi M, Okamoto S. Dynamics of long-distance signaling via plant vascular tissues. FRONTIERS IN PLANT SCIENCE 2015; 6:161. [PMID: 25852714 PMCID: PMC4364159 DOI: 10.3389/fpls.2015.00161] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/01/2015] [Indexed: 05/18/2023]
Abstract
Plant vascular systems are constructed by specific cell wall modifications through which cells are highly specialized to make conduits for water and nutrients. Xylem vessels are formed by thickened cell walls that remain after programmed cell death, and serve as water conduits from the root to the shoot. In contrast, phloem tissues consist of a complex of living cells, including sieve tube elements and their neighboring companion cells, and translocate photosynthetic assimilates from mature leaves to developing young tissues. Intensive studies on the content of vascular flow fluids have unveiled that plant vascular tissues transport various types of gene product, and the transport of some provides the molecular basis for the long-distance communications. Analysis of xylem sap has demonstrated the presence of proteins in the xylem transpiration stream. Recent studies have revealed that CLE and CEP peptides secreted in the roots are transported to above ground via the xylem in response to plant-microbe interaction and soil nitrogen starvation, respectively. Their leucine-rich repeat transmembrane receptors localized in the shoot phloem are required for relaying the signal from the shoot to the root. These findings well-fit to the current scenario of root-to-shoot-to-root feedback signaling, where peptide transport achieves the root-to-shoot signaling, the first half of the signaling process. Meanwhile, it is now well-evidenced that proteins and a range of RNAs are transported via the phloem translocation system, and some of those can exert their physiological functions at their destinations, including roots. Thus, plant vascular systems may serve not only as conduits for the translocation of essential substances but also as long-distance communication pathways that allow plants to adapt to changes in internal and external environments at the whole plant level.
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Affiliation(s)
- Michitaka Notaguchi
- Graduate School of Science, Nagoya University, NagoyaJapan
- ERATO Higashiyama Live-Holonics Project, NagoyaJapan
- *Correspondence: Michitaka Notaguchi and Satoru Okamoto, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan ;
| | - Satoru Okamoto
- Graduate School of Science, Nagoya University, NagoyaJapan
- Research Fellow of the Japan Society for the Promotion of Science, TokyoJapan
- *Correspondence: Michitaka Notaguchi and Satoru Okamoto, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan ;
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172
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Goldschmidt EE. Plant grafting: new mechanisms, evolutionary implications. FRONTIERS IN PLANT SCIENCE 2014; 5:727. [PMID: 25566298 PMCID: PMC4269114 DOI: 10.3389/fpls.2014.00727] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/01/2014] [Indexed: 05/18/2023]
Abstract
Grafting, an old plant propagation practice, is still widely used with fruit trees and in recent decades also with vegetables. Taxonomic proximity is a general prerequisite for successful graft-take and long-term survival of the grafted, composite plant. However, the mechanisms underlying interspecific graft incompatibility are as yet insufficiently understood. Hormonal signals, auxin in particular, are believed to play an important role in the wound healing and vascular regeneration within the graft union zone. Incomplete and convoluted vascular connections impede the vital upward and downward whole plant transfer routes. Long-distance protein, mRNA and small RNA graft-transmissible signals currently emerge as novel mechanisms which regulate nutritional and developmental root/top relations and may play a pivotal role in grafting physiology. Grafting also has significant pathogenic projections. On one hand, stock to scion mechanical contact enables the spread of diseases, even without a complete graft union. But, on the other hand, grafting onto resistant rootstocks serves as a principal tool in the management of fruit tree plagues and vegetable soil-borne diseases. The 'graft hybrid' historic controversy has not yet been resolved. Recent evidence suggests that epigenetic modification of DNA-methylation patterns may account for certain graft-transformation phenomena. Root grafting is a wide spread natural phenomenon; both intraspecific and interspecific root grafts have been recorded. Root grafts have an evolutionary role in the survival of storm-hit forest stands as well as in the spread of devastating diseases. A more fundamental evolutionary role is hinted by recent findings that demonstrate plastid and nuclear genome transfer between distinct Nicotiana species in the graft union zone, within a tissue culture system. This has led to the formation of alloploid cells that, under laboratory conditions, gave rise to a novel, alloploid Nicotiana species, indicating that natural grafts may play a role in plant speciation, under certain circumstances.
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Affiliation(s)
- Eliezer E. Goldschmidt
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
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173
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Wang JW. Regulation of flowering time by the miR156-mediated age pathway. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4723-30. [PMID: 24958896 DOI: 10.1093/jxb/eru246] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age pathway, which is controlled by microRNA156 (miR156) and its target SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors, ensures plants flower under non-inductive conditions. In this review, I summarize the recent advance in understanding of the age pathway, focusing on the regulatory basis of the developmental decline in miR156 level by age and the molecular mechanism by which the age pathway is integrated into other flowering time pathways.
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Affiliation(s)
- Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), Institute of Plant Physiology and Ecology (SIPPE), Shanghai Institutes for Biological Sciences (SIBS), Shanghai 200032, P. R. China
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