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Alisha A, Szweykowska-Kulinska Z, Sierocka I. Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes. Sci Rep 2024; 14:1611. [PMID: 38238367 PMCID: PMC10796333 DOI: 10.1038/s41598-024-51626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.
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Affiliation(s)
- Alisha Alisha
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Fan E, Liu C, Wang Z, Wang S, Ma W, Lu N, Liu Y, Fu P, Wang R, Lv S, Qu G, Wang J. Genome-Wide Identification and Expression Analysis of the SQUAMOSA Promoter-Binding Protein-like ( SPL) Transcription Factor Family in Catalpabungei. Int J Mol Sci 2023; 25:97. [PMID: 38203267 PMCID: PMC10779025 DOI: 10.3390/ijms25010097] [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: 10/31/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024] Open
Abstract
As a plant-specific transcription factor, the SPL gene family plays a critical role in plant growth and development. Although the SPL gene family has been identified in diverse plant species, there have been no genome-wide identification or systematic study reports on the SPL gene family in Catalpa bungei. In this study, we identified 19 putative SPL gene family members in the C. bungei genome. According to the phylogenetic relationship, they can be divided into eight groups, and the genes in the same group have a similar gene structure and conserved motifs. Synteny analysis showed that fragment duplication played an important role in the expansion of the CbuSPL gene family. At the same time, CbuSPL genes have cis-acting elements and functions related to light response, hormone response, growth and development, and stress response. Tissue-specific expression and developmental period-specific expression analysis showed that CbuSPL may be involved in flowering initiation and development, flowering transition, and leaf development. In addition, the ectopic expression of CbuSPL4 in Arabidopsis confirmed that it can promote early flowering and induce the expression of related flowering genes. These systematic research results will lay a foundation for further study on the functional analysis of SPL genes in C. bungei.
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Affiliation(s)
- Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Caixia Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Shanshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Yuhang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
| | - Pengyue Fu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Rui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Siyu Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (E.F.); (C.L.); (S.W.); (Y.L.); (P.F.); (R.W.); (S.L.); (G.Q.)
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Z.W.); (W.M.); (N.L.)
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Zhai X, Feng Y, Zhang X, Guo X. Comparative Analysis Based on Physiological and Transcriptomic Data between Juvenile and Adult Tree Peony ( Paeonia delavayi). Int J Mol Sci 2023; 24:10906. [PMID: 37446082 DOI: 10.3390/ijms241310906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
A long juvenile period limits the breeding process of many woody plants including tree peony. To investigate the physiological and transcriptomic differences between juvenile and adult plants of tree peony and to explore the key SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are vital in age-dependent pathways, 1-year-old and 3-year-old Paeonia delavayi plants were used to compare the relevant physiological parameters and transcriptomic profiles of the leaves in two phases of plants. The results of the physiological parameters showed that the starch content in the leaves of adult plants remained unchanged and that the soluble sugar content significantly increased compared with those in the juvenile plants. In terms of plant hormones, the contents of cytokinin-like hormone (N6-isopentenyladenine (iP)) and jasmonic acid (JA) significantly decreased, whereas the contents of auxin (indole-3-acetic acid, IAA), abscisic acid (ABA), cytokinin-like hormone (N6-isopentenyladenenosine (iPR)), and ethylene precursor (1-aminocyclopropane-1-carboxylic acid, ACC) showed no statistic difference. Transcriptome sequencing results showed that there were 194 differentially expressed genes (DEGs) between juvenile and adult plants, including 171 up-regulated DEGs and 23 down-regulated DEGs. Circadian rhythm, plant hormone signal transduction, and sugar metabolism were closely related to the juvenile-to-adult transition in P. delavayi, involving a total of 12 DEGs. In addition, a total of 13 SPL genes were identified in the transcriptome data, but only PdSPL10 (c71307.graph_c0) was differentially expressed. It was further validated via qRT-PCR analysis, indicating that PdSPL10 might be a key gene regulating the process of juvenile-to-adult in P. delavayi. Based on the above results, a hypothetical transcriptional network regulating juvenile-to-adult transition and flowering in P. delavayi was proposed. These findings provide a reference for understanding the mechanism of juvenile-to-adult transition in tree peony.
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Affiliation(s)
- Xiaoli Zhai
- College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yan Feng
- College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiuxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianfeng Guo
- College of Forestry, Shandong Agricultural University, Tai'an 271018, China
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Yu R, Xiong Z, Zhu X, Feng P, Hu Z, Fang R, Zhang Y, Liu Q. RcSPL1-RcTAF15b regulates the flowering time of rose ( Rosa chinensis). HORTICULTURE RESEARCH 2023; 10:uhad083. [PMID: 37323236 PMCID: PMC10266950 DOI: 10.1093/hr/uhad083] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Rose (Rosa chinensis), which is an economically valuable floral species worldwide, has three types, namely once-flowering (OF), occasional or re-blooming (OR), and recurrent or continuous flowering (CF). However, the mechanism underlying the effect of the age pathway on the duration of the CF or OF juvenile phase is largely unknown. In this study, we observed that the RcSPL1 transcript levels were substantially upregulated during the floral development period in CF and OF plants. Additionally, accumulation of RcSPL1 protein was controlled by rch-miR156. The ectopic expression of RcSPL1 in Arabidopsis thaliana accelerated the vegetative phase transition and flowering. Furthermore, the transient overexpression of RcSPL1 in rose plants accelerated flowering, whereas silencing of RcSPL1 had the opposite phenotype. Accordingly, the transcription levels of floral meristem identity genes (APETALA1, FRUITFULL, and LEAFY) were significantly affected by the changes in RcSPL1 expression. RcTAF15b protein, which is an autonomous pathway protein, was revealed to interact with RcSPL1. The silencing and overexpression of RcTAF15b in rose plants led to delayed and accelerated flowering, respectively. Collectively, the study findings imply that RcSPL1-RcTAF15b modulates the flowering time of rose plants.
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Affiliation(s)
- Rui Yu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhiying Xiong
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinhui Zhu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Panpan Feng
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ziyi Hu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Rongxiang Fang
- National Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [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: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach. Genes (Basel) 2023; 14:genes14030661. [PMID: 36980934 PMCID: PMC10048520 DOI: 10.3390/genes14030661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.
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Cao L, Li T, Geng S, Zhang Y, Pan Y, Zhang X, Wang F, Hao C. TaSPL14-7A is a conserved regulator controlling plant architecture and yield traits in common wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1178624. [PMID: 37089636 PMCID: PMC10113487 DOI: 10.3389/fpls.2023.1178624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Plant architecture is a crucial influencing factor of wheat yield and adaptation. In this study, we cloned and characterized TaSPL14, a homologous gene of the rice ideal plant architecture gene OsSPL14 in wheat. TaSPL14 homoeologs (TaSPL14-7A, TaSPL14-7B and TaSPL14-7D) exhibited similar expression patterns, and they were all preferentially expressed in stems at the elongation stage and in young spikes. Moreover, the expression level of TaSPL14-7A was higher than that of TaSPL14-7B and TaSPL14-7D. Overexpression of TaSPL14-7A in wheat resulted in significant changes in plant architecture and yield traits, including decreased tiller number and increased kernel size and weight. Three TaSPL14-7A haplotypes were identified in Chinese wheat core collection, and haplotype-based association analysis showed that TaSPL14-7A-Hap1/2 were significantly correlated with fewer tillers, larger kernels and higher kernel weights in modern cultivars. The haplotype effect resulted from a difference in TaSPL14-7A expression levels among genotypes, with TaSPL14-7A-Hap1/2 leading to higher expression levels than TaSPL14-7A-Hap3. As favorable haplotypes, TaSPL14-7A-Hap1/2 underwent positive selection during global wheat breeding over the last century. Together, the findings of our study provide insight into the function and genetic effects of TaSPL14 and provide a useful molecular marker for wheat breeding.
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Affiliation(s)
- Lina Cao
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Tian Li, ; Fang Wang, ; Chenyang Hao,
| | - Shuaifeng Geng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinhui Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxue Pan
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Tian Li, ; Fang Wang, ; Chenyang Hao,
| | - Chenyang Hao
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Tian Li, ; Fang Wang, ; Chenyang Hao,
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Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit ( Passiflora edulis Sims). Int J Mol Sci 2022; 23:ijms232214153. [PMID: 36430627 PMCID: PMC9695787 DOI: 10.3390/ijms232214153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The SQUAMOSA promoter binding proteins (SBPs) gene family plays important roles in plant growth and development. The SBP gene family has been identified and reported in many species, but it has not been well studied in passion fruit. In this study, a total of 14 SBP genes were identified in passion fruit and named from PeSBP1 to PeSBP14 based on their chromosomal distribution. The phylogenetic tree, gene structure, conserved motifs, collinearity analysis, and expression patterns of the identified SBP members were analyzed. We classified the PeSBP genes into eight groups (I to VIII) according to the phylogenetic tree, gene structure, and conserved motifs. Synteny analysis found that 5 homologous gene pairs existed in PeSBP genes and 11 orthologous gene pairs existed between passion fruit and Arabidopsis. Synonymous nucleotide substitution analysis showed that the PeSBP genes were under strong negative selection. The expression pattern of PeSBP genes in seed, root, leaf, and flower showed that nine of the PeSBP genes displayed high expression in the leaf and the flower. The expression patterns of PeSBP3/6/8/9/10 were further detected by qRT-PCR. In addition, differences in the expression levels occurred for each gene in the different flower organs and at the different developmental stages. There were large differences among SBPs based on transcriptional levels under cold, heat, salt, and osmotic stress conditions. Altogether, this study provides an overview of SBP genes in passion fruit and lays the foundation for further functional analysis.
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Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE ( SPL) Gene Family between Wheat and Rice. Int J Mol Sci 2022; 23:ijms23042099. [PMID: 35216210 PMCID: PMC8874652 DOI: 10.3390/ijms23042099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022] Open
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs’ functions in rice to facilitate the functional genomics of TaSPL genes. To achieve these goals, we combined several approaches, including genome-wide analysis of TaSPLs, comparative genomic analysis, expression profiling, and functional study of TaSPL3 in rice. We established the orthologous relationships of 56 TaSPL genes with the corresponding OsSPLs, laying a foundation for the comparison of known SPL functions between wheat and rice. Some TaSPLs exhibited different spatial–temporal expression patterns when compared to their rice orthologs, thus implicating functional divergence. TaSPL2/6/8/10 were identified to respond to different abiotic stresses through the combination of RNA-seq and qPCR expression analysis. Additionally, ectopic expression of TaSPL3 in rice promotes heading dates, affects leaf and stem development, and leads to smaller panicles and decreased yields per panicle. In conclusion, our work provides useful information toward cataloging of the functions of TaSPLs, emphasized the conservation and divergence between TaSPLs and OsSPLs, and identified the important SPL genes for wheat improvement.
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Madzima TF, Vendramin S, Lynn JS, Lemert P, Lu KC, McGinnis KM. Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation. FRONTIERS IN PLANT SCIENCE 2021; 12:694289. [PMID: 34489998 PMCID: PMC8418275 DOI: 10.3389/fpls.2021.694289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Plants respond to abiotic stress stimuli, such as water deprivation, through a hierarchical cascade that includes detection and signaling to mediate transcriptional and physiological changes. The phytohormone abscisic acid (ABA) is well-characterized for its regulatory role in these processes in response to specific environmental cues. ABA-mediated changes in gene expression have been demonstrated to be temporally-dependent, however, the genome-wide timing of these responses are not well-characterized in the agronomically important crop plant Zea mays (maize). ABA-mediated responses are synergistic with other regulatory mechanisms, including the plant-specific RNA-directed DNA methylation (RdDM) epigenetic pathway. Our prior work demonstrated that after relatively long-term ABA induction (8 h), maize plants homozygous for the mop1-1 mutation, defective in a component of the RdDM pathway, exhibit enhanced transcriptional sensitivity to the phytohormone. At this time-point, many hierarchically positioned transcription factors are differentially expressed resulting in primary (direct) and secondary (indirect) transcriptional outcomes. To identify more immediate and direct MOP1-dependent responses to ABA, we conducted a transcriptomic analysis using mop1-1 mutant and wild type plants treated with ABA for 1 h. One h of ABA treatment was sufficient to induce unique categories of differentially expressed genes (DEGs) in mop1-1. A comparative analysis between the two time-points revealed that distinct epigenetically-regulated changes in gene expression occur within the early stages of ABA induction, and that these changes are predicted to influence less immediate, indirect transcriptional responses. Homology with MOP1-dependent siRNAs and a gene regulatory network (GRN) were used to identify putative immediate and indirect targets, respectively. By manipulating two key regulatory networks in a temporal dependent manner, we identified genes and biological processes regulated by RdDM and ABA-mediated stress responses. Consistent with mis-regulation of gene expression, mop1-1 homozygous plants are compromised in their ability to recover from water deprivation. Collectively, these results indicate transcriptionally and physiologically relevant roles for MOP1-mediated regulation of gene expression of plant responses to environmental stress.
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Affiliation(s)
- Thelma F. Madzima
- Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, United States
| | - Stefania Vendramin
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Jason S. Lynn
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Phebe Lemert
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Katherine C. Lu
- Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, United States
| | - Karen M. McGinnis
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
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RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genet 2021; 17:e1009326. [PMID: 34125827 PMCID: PMC8224964 DOI: 10.1371/journal.pgen.1009326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/24/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on Mediator of Paramutation1 (Mop1), a gene encoding a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silenced MuDR transposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via histone H3 lysine 9 dimethylation (H3K9me2), and histone H3 lysine 27 dimethylation (H3K27me2), even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by histone H3 lysine 27 trimethylation (H3K27me3), a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in a mop1 mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in mop1 wild-type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in a mop1 mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements. Most plant genomes are mostly transposable elements (TEs), most of which are held in check by modifications of both DNA and histones. The bulk of silenced TEs are associated with methylated DNA and histone H3 lysine 9 dimethylation (H3K9me2). In contrast, epigenetically silenced genes are often associated with histone lysine 27 trimethylation (H3K27me3). Although stress can affect each of these modifications, plants are generally competent to rapidly reset them following that stress. Here we demonstrate that although DNA methylation is not required to maintain silencing of the MuDR element, it is essential for preventing heat-induced, stable and heritable changes in both H3K9me2 and H3K27me3 at this element, and for concomitant changes in transcriptional activity. These finding suggest that RdDM acts to buffer the effects of heat on silenced transposable elements, and that a loss of DNA methylation under conditions of stress can have profound and long-lasting effects on epigenetic silencing in maize.
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12
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Xie Z, Su Z, Wang W, Guan L, Bai Y, Zhu X, Wang X, Jia H, Fang J, Wang C. Characterization of VvSPL18 and Its Expression in Response to Exogenous Hormones during Grape Berry Development and Ripening. Cytogenet Genome Res 2019; 159:97-108. [PMID: 31760391 DOI: 10.1159/000503912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 11/19/2022] Open
Abstract
The sequence and structure of grape SBP-box-like18 (VvSPL18) were identified and characterized to explore its regulatory roles during grape berry development and ripening. Homologous conservation across diverse plant species was observed, and its potential function and modulated roles in grapes were investigated. The results showed that VvSPL18 has an ORF sequence of 1,137 bp, encodes 378 amino acids, and is located on chromosome 14 of grapevine. VvSPL18 has the closest relationship with its homolog in soybeans. The promoter of VvSPL18 contains cis-elements responsive to gibberellins (GA) and salicylic acid (SA), indicating that this gene might respond to these hormones involved in the modulation of grape berry. VvSPL18 is mainly distributed in the nucleus. Expression profiles showed that VvSPL18 is highly expressed only at the veraison stage of the grape berry and is slightly expressed in other phases. RNA-seq data also revealed that VvSPL18 might participate in the modulation of grape berry development and ripening. Treatment with diverse hormones demonstrated that abscisic acid (ABA) had almost no effect on its expression, whereas naphthalene acetic acid (NAA) significantly upregulated its expression at the veraison stage. We also found that VvSPL18 has a GA-responsive cis-element but no NAA-responsive cis-element. GA could promote the expression of VvSPL18 with a peak at an earlier stage than NAA, suggesting that VvSPL18 responds faster to GA than to NAA. This result indicates that VvSPL18 might modulate berry development at this phase through an ABA-independent pathway, and it might directly respond to GA, but indirectly to NAA. Our findings provide insights into the functions of VvSPL18 in mediating grape berry development and ripening.
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13
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Xiong J, Bai Y, Ma C, Zhu H, Zheng D, Cheng Z. Molecular Cloning and Characterization of SQUAMOSA-Promoter Binding Protein-Like Gene FvSPL10 from Woodland Strawberry ( Fragaria vesca). PLANTS 2019; 8:plants8090342. [PMID: 31514279 PMCID: PMC6784255 DOI: 10.3390/plants8090342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022]
Abstract
SQUAMOSA-promoter binding protein-like (SPL) proteins are plant-specific transcript factors that play essential roles in plant growth and development. Although many SPL genes have been well characterized in model plants like Arabidopsis, rice and tomato, the functions of SPLs in strawberry are still largely elusive. In the present study, we cloned and characterized FvSPL10, the ortholog of AtSPL9, from woodland strawberry. Subcellular localization shows FvSPL10 localizes in the cell nucleus. The luciferase system assay indicates FvSPL10 is a transcriptional activator, and both in vitro and in vivo assays indicate FvSPL10 could bind to the promoter of FvAP1 and activate its expression. Ectopic expression of FvSPL10 in Arabidopsis promotes early flowering and increases organs size. These results demonstrate the multiple regulatory roles of FvSPL10 in plant growth and development and lay a foundation for investigating the biological functions of FvSPL10 in strawberry.
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Affiliation(s)
- Jinsong Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yibo Bai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuangju Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongyu Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongming Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
- Department of Plant Science, University of Tennessee, Knoxville, TN 37996, USA.
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14
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Peng X, Wang Q, Zhao Y, Li X, Ma Q. Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. Genet Mol Biol 2019; 42:380-394. [PMID: 31271590 PMCID: PMC6726161 DOI: 10.1590/1678-4685-gmb-2017-0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2018] [Indexed: 11/21/2022] Open
Abstract
SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six groups according to phylogeny. We found that most of the SPL-containing regions in maize showed extensive conservation with duplicated regions of rice and sorghum. A gene duplication analysis in maize indicated that ZmSPLs showed a significant excess of segmental duplication. The Ka/Ks analysis indicated that 9 out of 18 duplicated pairs in maize experienced positive selection, while SPL gene pairs of rice and sorghum mainly evolved under purifying selection, suggesting novel evolutionary features for ZmSPLs. The 31 ZmSPLs were further analyzed by describing their gene structure, phylogenetic relationships, chromosomal location, and expression, Among the ZmSPLs, 13 were predicated to be targeted by miR156s and involved in drought stress response. These results provide the foundation for future functional analyses of ZmSPLs.
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Affiliation(s)
- Xiaojian Peng
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qianqian Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
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15
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Perspectives on microRNAs and Phased Small Interfering RNAs in Maize ( Zea mays L.): Functions and Big Impact on Agronomic Traits Enhancement. PLANTS 2019; 8:plants8060170. [PMID: 31212808 PMCID: PMC6630462 DOI: 10.3390/plants8060170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023]
Abstract
Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed.
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16
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Selection pressure causes differentiation of the SPL gene family in the Juglandaceae. Mol Genet Genomics 2019; 294:1037-1048. [DOI: 10.1007/s00438-019-01562-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
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17
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Zeng RF, Zhou JJ, Liu SR, Gan ZM, Zhang JZ, Hu CG. Genome-Wide Identification and Characterization of SQUAMOSA-Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina. Biomolecules 2019; 9:biom9020066. [PMID: 30769909 PMCID: PMC6407117 DOI: 10.3390/biom9020066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 12/02/2022] Open
Abstract
SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.
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Affiliation(s)
- Ren-Fang Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing-Jing Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sheng-Rui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230000, China.
| | - Zhi-Meng Gan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
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18
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Stephenson E, Estrada S, Meng X, Ourada J, Muszynski MG, Habben JE, Danilevskaya ON. Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize. PLoS One 2019; 14:e0203728. [PMID: 30726207 PMCID: PMC6364868 DOI: 10.1371/journal.pone.0203728] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 11/19/2022] Open
Abstract
Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.
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Affiliation(s)
- Elizabeth Stephenson
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Stacey Estrada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Xin Meng
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Jesse Ourada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Michael G. Muszynski
- University of Hawaii at Manoa, Tropical Plant and Soil Sciences, Honolulu, Hawaii; United States of America
| | - Jeffrey E. Habben
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Olga N. Danilevskaya
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
- * E-mail:
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19
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Cao R, Guo L, Ma M, Zhang W, Liu X, Zhao H. Identification and Functional Characterization of Squamosa Promoter Binding Protein-Like Gene TaSPL16 in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:212. [PMID: 30873195 PMCID: PMC6401658 DOI: 10.3389/fpls.2019.00212] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa promoter binding protein-like (SPL) proteins are plant-specific transcript factors and play critical roles in plant growth and development. The functions of many SPL gene family members were well characterized in Arabidopsis and rice, in contrast, research on wheat SPL genes is lagging behind. In this study, we cloned and characterized TaSPL16, an orthologous gene of rice OsSPL16, in wheat. Three TaSPL16 homoeologs are located on the short arms of chromosome 7A, 7B, and 7D, and share more than 96% sequence identity with each other. All the TaSPL16 homoeologs have three exons and two introns, with a miR156 binding site in their last exons. They encode putative proteins of 407, 409, and 414 amino acid residues, respectively. Subcellular localization showed TaSPL16 distribution in the cell nucleus, and transcription activity of TaSPL16 was validated in yeast. Analysis of the spatiotemporal expression profile showed that TaSPL16 is highly expressed in young developing panicles, lowly expressed in developing seeds and almost undetectable in vegetative tissues. Ectopic expression of TaSPL16 in Arabidopsis causes a delay in the emergence of vegetative leaves (3-4 days late), promotes early flowering (5-7 days early), increases organ size, and affects yield-related traits. These results demonstrated the regulatory roles of TaSPL16 in plant growth and development as well as seed yield. Our findings enrich the existing knowledge on SPL genes in wheat and provide valuable information for further investigating the effects of TaSPL16 on plant architecture and yield-related traits of wheat.
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Affiliation(s)
- Rufei Cao
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Lijian Guo
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Meng Ma
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wenjing Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiangli Liu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronmy, Northwest A&F University, Yangling, China
- *Correspondence: Huixian Zhao,
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20
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Xiong JS, Zheng D, Zhu HY, Chen JQ, Na R, Cheng ZM. Genome-wide identification and expression analysis of the SPL gene family in woodland strawberry Fragaria vesca. Genome 2018; 61:675-683. [PMID: 30067072 DOI: 10.1139/gen-2018-0014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
SQUAMOSA promoter-binding protein-like (SPL) is a class of plant-specific transcription factors that play critical roles in regulating plant growth and development. However, little systematic research on SPL genes has been conducted in strawberry. In this study, 14 SPL genes were identified in the genome of woodland strawberry (Fragaria vesca), one of the model plants of the family Rosaceae. Chromosome localization analysis indicated that the 14 FvSPL genes were unevenly distributed on six chromosomes. Phylogenetic analysis indicated that the FvSPL proteins could be clustered into six groups (G1 to G6). Genes with similar structure were classified into the same group, implying their functional redundancy. In addition, nine out of the 14 FvSPL genes, belonging to G1, G2, and G5, were found to be the putative targets of FvmiR156 genes. Expression analysis indicated FvSPL genes exhibited highly diverse expression patterns in the tissues and organs examined. The transcript levels of most FvmiR156-targeted FvSPL genes in fruit were lower than those non-miR156-targeted genes. In addition, the expression of the FvmiR156-targeted FvSPL genes decreased during fruit ripening, whereas the expression of FvmiR156 genes increased in fruit during this process. The results provide a foundation for future functional analysis of FvSPL genes in strawberry growth and development.
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Affiliation(s)
- Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong-Yu Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Qiu Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ran Na
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zong-Ming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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21
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Zhao Y, Zhang Y, Wang L, Wang X, Xu W, Gao X, Liu B. Mapping and Functional Analysis of a Maize Silkless Mutant sk-A7110. FRONTIERS IN PLANT SCIENCE 2018; 9:1227. [PMID: 30186299 PMCID: PMC6111845 DOI: 10.3389/fpls.2018.01227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/31/2018] [Indexed: 05/03/2023]
Abstract
The maize (Zea mays) stigma, which is commonly known as silk, is indispensable for reproduction and thus for grain yield. Here, we isolated a spontaneous mutant sk-A7110, which completely lacks silk; scanning electron microscopy showed that the sk-A7110 pistils degenerated during late floret differentiation. Genetic analysis confirmed that this trait was controlled by a recessive nuclear gene and sk-A7110 was mapped to a 74.13-kb region on chromosome 2 between the simple sequence repeat markers LA714 and L277. Sequence analysis of candidate genes in this interval identified a single-nucleotide insertion at position 569 downstream of the transcriptional start site in Zm00001d002970, which encodes a UDP-glycosyltransferase; this insertion produces a frameshift and premature translational termination. RNA-sequencing analysis of young ears identified 258 differentially expressed genes (DEGs) between sk-A7110 and the wild type (WT), including 119 up- and 139 down-regulated genes. Interestingly, most DEGs related to jasmonic acid (JA) synthesis were up-regulated in the mutant compared to WT. Consistent with this, the JA and JA-Isoleucine (JA-Ile) contents were significantly higher in sk-A7110 ears than in WT. At the same time, RNA-sequencing analysis of tassels showed that sk-A7110 could reduce the number of tassel branches in maize by down-regulating the expression of UB2 and UB3 genes. Our identification of the sk-A7110 mutant and the responsible gene will facilitate further studies on female infertility research or maize breeding.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yongzhong Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Lijing Wang
- Agricultural Technology Promotion Center of Yanzhou, Jining, China
| | - Xueran Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Wei Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Xianyu Gao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Baoshen Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- *Correspondence: Baoshen Liu,
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22
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Detecting the Candidate Gender Determinants by Bioinformatic Prediction of miRNAs and Their Targets from Transcriptome Sequences of the Male and Female Flowers in Salix suchowensis. BIOMED RESEARCH INTERNATIONAL 2017. [PMID: 28638836 PMCID: PMC5468582 DOI: 10.1155/2017/9614596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female S. suchowensis to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male. Analyzing sequence complementarity led to identification of 124 and 55 miRNA targets in the male and female flower buds, respectively. By mapping the target genes of the predicted miRNAs to the sequence assemblies of S. suchowensis, a miR156 mediated gene was detected at the gender locus of willow, which was a transcription factor involved in flower development. It is noteworthy that this target is not expressed in male flower, while it is expressed fairly highly in female flower based on the transcriptome data derived from the alternate sexes of willows. This study provides new bioinformatic clue for further exploring the genetic mechanism underlying gender determination in willows.
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23
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Shao F, Lu Q, Wilson IW, Qiu D. Genome-wide identification and characterization of the SPL gene family in Ziziphus jujuba. Gene 2017; 627:315-321. [PMID: 28652183 DOI: 10.1016/j.gene.2017.06.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/05/2017] [Accepted: 06/22/2017] [Indexed: 01/23/2023]
Abstract
SQUAMOSA Promoter-Binding Protein-Likes (SPLs) are plant specific transcription factors playing important roles in plant growth and development. The SPL gene family has been studied in various plant species; however, there is no report about SPLs in Zizyphus jujuba. In this study, we identified 18 putative ZjSPL genes in Z. jujuba using a genome-wide analysis. Sequence features, gene structures, conserved domains and motifs were analyzed. The phylogenetic relationships of SPLs in Z. jujuba and A. thaliana were revealed. A total of 5 pairs of ZjSPLs were identified, suggesting the importance of gene duplication in SPL gene expansion in Z. jujuba. In addition, 11 of the 18 ZjSPLs, belonging to G1, G2 and G5 subgroups, were found to be targets of miR156, suggesting the conservation of miR156-mediated posttranscriptional regulation in plants. Expression analysis revealed that eight ZjSPL genes were responsive to the infection of witches'-broom phytoplasma. Our results provide a basis for the further elucidation of the biological function of ZjSPLs and their regulation in witches'-broom disease.
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Affiliation(s)
- Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Qiang Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Iain W Wilson
- CSIRO Agriculture & Food, PO Box 1600, Canberra, ACT 2601, Australia.
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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24
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Manzano S, Megías Z, Martínez C, García A, Aguado E, Chileh T, López-Alonso D, García-Maroto F, Kejnovský E, Široký J, Kubát Z, Králová T, Vyskot B, Jamilena M. Overexpression of a flower-specific aerolysin-like protein from the dioecious plant Rumex acetosa alters flower development and induces male sterility in transgenic tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:58-72. [PMID: 27599169 DOI: 10.1111/tpj.13322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 05/07/2023]
Abstract
Sex determination in Rumex acetosa, a dioecious plant with a complex XY1 Y2 sex chromosome system (females are XX and males are XY1 Y2 ), is not controlled by an active Y chromosome but depends on the ratio between the number of X chromosomes and autosomes. To gain insight into the molecular mechanisms of sex determination, we generated a subtracted cDNA library enriched in genes specifically or predominantly expressed in female floral buds in early stages of development, when sex determination mechanisms come into play. In the present paper, we report the molecular and functional characterization of FEM32, a gene encoding a protein that shares a common architecture with proteins in different plants, animals, bacteria and fungi of the aerolysin superfamily; many of these function as β pore-forming toxins. The expression analysis, assessed by northern blot, RT-PCR and in situ hybridization, demonstrates that this gene is specifically expressed in flowers in both early and late stages of development, although its transcripts accumulate much more in female flowers than in male flowers. The ectopic expression of FEM32 under both the constitutive promoter 35S and the flower-specific promoter AP3 in transgenic tobacco showed no obvious alteration in vegetative development but was able to alter floral organ growth and pollen fertility. The 35S::FEM32 and AP3::FEM32 transgenic lines showed a reduction in stamen development and pollen viability, as well as a diminution in fruit set, fruit development and seed production. Compared with other floral organs, pistil development was, however, enhanced in plants overexpressing FEM32. According to these effects, it is likely that FEM32 functions in Rumex by arresting stamen and pollen development during female flower development. The aerolysin-like pore-forming proteins of eukaryotes are mainly involved in defence mechanisms against bacteria, fungi and insects and are also involved in apoptosis and programmed cell death (PCD), a mechanism that could explain the role of FEM32 in Rumex sex determination.
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Affiliation(s)
- Susana Manzano
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
| | - Zoraida Megías
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
| | - Cecilia Martínez
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
| | - Alicia García
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
| | - Encarnación Aguado
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
| | - Tarik Chileh
- Grupo de investigación 'Biotecnología de productos naturales', BITAL, CeiA3, Universidad de Almería, 04120, Almería, Spain
| | - Diego López-Alonso
- Grupo de investigación 'Biotecnología de productos naturales', BITAL, CeiA3, Universidad de Almería, 04120, Almería, Spain
| | - Federico García-Maroto
- Grupo de investigación 'Biotecnología de productos naturales', BITAL, CeiA3, Universidad de Almería, 04120, Almería, Spain
| | - Eduard Kejnovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jiří Široký
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Zdeněk Kubát
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Tereza Králová
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Manuel Jamilena
- Grupo de investigación 'Genética de hortícolas' (BIO293), Centro de Investigación en Biotencología Agroalimentaria (BITAL), Agrifood Campus of International Excellence (CeiA3), Universidad de Almería, 04120, Almería, Spain
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25
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Hayward AP, Moreno MA, Howard TP, Hague J, Nelson K, Heffelfinger C, Romero S, Kausch AP, Glauser G, Acosta IF, Mottinger JP, Dellaporta SL. Control of sexuality by the sk1-encoded UDP-glycosyltransferase of maize. SCIENCE ADVANCES 2016; 2:e1600991. [PMID: 27819048 PMCID: PMC5091354 DOI: 10.1126/sciadv.1600991] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/27/2016] [Indexed: 05/05/2023]
Abstract
Sex determination in maize involves the production of staminate and pistillate florets from an initially bisexual floral meristem. Pistil elimination in staminate florets requires jasmonic acid signaling, and functional pistils are protected by the action of the silkless 1 (sk1) gene. The sk1 gene was identified and found to encode a previously uncharacterized family 1 uridine diphosphate glycosyltransferase that localized to the plant peroxisomes. Constitutive expression of an sk1 transgene protected all pistils in the plant, causing complete feminization, a gain-of-function phenotype that operates by blocking the accumulation of jasmonates. The segregation of an sk1 transgene was used to effectively control the production of pistillate and staminate inflorescences in maize plants.
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Affiliation(s)
- Andrew P. Hayward
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
| | - Maria A. Moreno
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
| | - Thomas P. Howard
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
| | - Joel Hague
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02892, USA
| | - Kimberly Nelson
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02892, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
| | - Sandra Romero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
| | - Albert P. Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02892, USA
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Ivan F. Acosta
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - John P. Mottinger
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02892, USA
| | - Stephen L. Dellaporta
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520–8104, USA
- Corresponding author.
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26
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Cheng H, Hao M, Wang W, Mei D, Tong C, Wang H, Liu J, Fu L, Hu Q. Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus. BMC PLANT BIOLOGY 2016; 16:196. [PMID: 27608922 PMCID: PMC5017063 DOI: 10.1186/s12870-016-0852-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/11/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. RESULTS In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3'UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. CONCLUSIONS Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.
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Affiliation(s)
- Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Chaobo Tong
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
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27
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Wu X, Li Y, Shi Y, Song Y, Zhang D, Li C, Buckler ES, Li Y, Zhang Z, Wang T. Joint-linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1551-62. [PMID: 26801971 PMCID: PMC5066742 DOI: 10.1111/pbi.12519] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/31/2015] [Accepted: 11/22/2015] [Indexed: 05/18/2023]
Abstract
Both insufficient and excessive male inflorescence size leads to a reduction in maize yield. Knowledge of the genetic architecture of male inflorescence is essential to achieve the optimum inflorescence size for maize breeding. In this study, we used approximately eight thousand inbreds, including both linkage populations and association populations, to dissect the genetic architecture of male inflorescence. The linkage populations include 25 families developed in the U.S. and 11 families developed in China. Each family contains approximately 200 recombinant inbred lines (RILs). The association populations include approximately 1000 diverse lines from the U.S. and China. All inbreds were genotyped by either sequencing or microarray. Inflorescence size was measured as the tassel primary branch number (TBN) and tassel length (TL). A total of 125 quantitative trait loci (QTLs) were identified (63 for TBN, 62 for TL) through linkage analyses. In addition, 965 quantitative trait nucleotides (QTNs) were identified through genomewide study (GWAS) at a bootstrap posterior probability (BPP) above a 5% threshold. These QTLs/QTNs include 24 known genes that were cloned using mutants, for example Ramosa3 (ra3), Thick tassel dwarf1 (td1), tasselseed2 (ts2), liguleless2 (lg2), ramosa1 (ra1), barren stalk1 (ba1), branch silkless1 (bd1) and tasselseed6 (ts6). The newly identified genes encode a zinc transporter (e.g. GRMZM5G838098 and GRMZM2G047762), the adapt in terminal region protein (e.g. GRMZM5G885628), O-methyl-transferase (e.g. GRMZM2G147491), helix-loop-helix (HLH) DNA-binding proteins (e.g. GRMZM2G414252 and GRMZM2G042895) and an SBP-box protein (e.g. GRMZM2G058588). These results provide extensive genetic information to dissect the genetic architecture of inflorescence size for the improvement of maize yield.
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Affiliation(s)
- Xun Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Nanchong Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- USA Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiwu Zhang
- Department of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Mao HD, Yu LJ, Li ZJ, Yan Y, Han R, Liu H, Ma M. Genome-wide analysis of the SPL family transcription factors and their responses to abiotic stresses in maize. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Du S, Sang Y, Liu X, Xing S, Li J, Tang H, Sun L. Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L. FRONTIERS IN PLANT SCIENCE 2016; 7:871. [PMID: 27379148 PMCID: PMC4910463 DOI: 10.3389/fpls.2016.00871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/02/2016] [Indexed: 05/21/2023]
Abstract
In plants, sex determination is a comprehensive process of correlated events, which involves genes that are differentially and/or specifically expressed in distinct developmental phases. Exploring gene expression profiles from different sex types will contribute to fully understanding sex determination in plants. In this study, we conducted RNA-sequencing of female and male buds (FB and MB) as well as ovulate strobilus and staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the genes potentially related to sex determination in this species. Approximately 60 Gb of clean reads were obtained from eight cDNA libraries. De novo assembly of the clean reads generated 108,307 unigenes with an average length of 796 bp. Among these unigenes, 51,953 (47.97%) had at least one significant match with a gene sequence in the public databases searched. A total of 4709 and 9802 differentially expressed genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively. Genes involved in plant hormone signal and transduction as well as those encoding DNA methyltransferase were found to be differentially expressed between different sex types. Their potential roles in sex determination of G. biloba were discussed. Pistil-related genes were expressed in male buds while anther-specific genes were identified in female buds, suggesting that dioecism in G. biloba was resulted from the selective arrest of reproductive primordia. High correlation of expression level was found between the RNA-Seq and quantitative real-time PCR results. The transcriptome resources that we generated allowed us to characterize gene expression profiles and examine differential expression profiles, which provided foundations for identifying functional genes associated with sex determination in G. biloba.
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30
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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: 187] [Impact Index Per Article: 23.4] [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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Li ZF, Zhang YC, Chen YQ. miRNAs and lncRNAs in reproductive development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:46-52. [PMID: 26259173 DOI: 10.1016/j.plantsci.2015.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/24/2015] [Accepted: 05/25/2015] [Indexed: 05/14/2023]
Abstract
Non-coding RNAs (ncRNAs) regulate gene expression at the transcriptional and post-transcriptional levels. Many ncRNAs have been identified in the past decade, including small ncRNAs, such as microRNAs (miRNAs), and long ncRNAs (lncRNAs). These novel molecules have important roles in a wide range of biological processes such as the regulation of reproduction and sex determination. Due to their ability to regulate specific genes or entire gene families, these molecules have the potential for uses in the development of breeding strategies as well as in the genetic modification of agronomic traits. In this review, we summarize recent progress on the understanding of plant miRNAs and lncRNAs in male and female development. We also discuss future challenges of using these molecules in agricultural applications, including transgenic plants in hybrid breeding, for novel genetic trait selection, for rapid character screening, and genetic modification for crop improvement.
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Affiliation(s)
- Zhe-Feng Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Chan Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China.
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32
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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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33
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Liu H, Yang X, Liao X, Zuo T, Qin C, Cao S, Dong L, Zhou H, Zhang Y, Liu S, Shen Y, Lin H, Lübberstedt T, Zhang Z, Pan G. Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development. Genomics 2015; 106:52-60. [PMID: 25847872 DOI: 10.1016/j.ygeno.2015.03.005] [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] [Received: 02/21/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
Abstract
The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.
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Affiliation(s)
- Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Xuerong Yang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | | | - Tao Zuo
- Interdepartmental Genetics Program, Iowa State University, Ames 50011, USA
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China; Zunyi Academy of Agricultural Sciences, Zunyi 563102, China
| | - Shiliang Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China
| | - Ling Dong
- Department of Agronomy, Northeast Agricultural University, 150030 Harbin, China
| | | | - Yongzhong Zhang
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Sisi Liu
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | | | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
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Klein-Cosson C, Chambrier P, Rogowsky PM, Vernoud V. Regulation of a maize HD-ZIP IV transcription factor by a non-conventional RDR2-dependent small RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:747-758. [PMID: 25619590 DOI: 10.1111/tpj.12771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Small non-coding RNAs are versatile riboregulators that control gene expression at the transcriptional or post-transcriptional level, governing many facets of plant development. Here we present evidence for the existence of a 24 nt small RNA (named small1) that is complementary to the 3' UTR of OCL1 (Outer Cell Layer1), the founding member of the maize HD-ZIP IV gene family encoding plant-specific transcription factors that are mainly involved in epidermis differentiation and specialization. The biogenesis of small1 depends on DICER-like 3 (DCL3), RNA-dependent RNA polymerase 2 (RDR2) and RNA polymerase IV, components that are usually required for RNA-dependent DNA-methylation. Unexpectedly, GFP sensor experiments in transient and stable transformation systems revealed that small1 may regulate its target at the post-transcriptional level, mainly through translational repression. This translational repression is attenuated in an rdr2 mutant background in which small1 does not accumulate. Our experiments further showed the possible involvement of a secondary stem-loop structure present in the 3' UTR of OCL1 for efficient target repression, suggesting the existence of several regulatory mechanisms affecting OCL1 mRNA stability and translation.
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Affiliation(s)
- Catherine Klein-Cosson
- Unité Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, F-69364, Lyon, France; Institut National de la Recherche Agronomique, UMR879 Reproduction et Développement des Plantes, F-69364, Lyon, France; Centre National de la Recherche Scientifique, UMR5667 Reproduction et Développement des Plantes, F-69364, Lyon, France
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Identification of microRNAs differentially expressed involved in male flower development. Funct Integr Genomics 2015; 15:225-32. [PMID: 25576251 DOI: 10.1007/s10142-014-0409-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.
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Ectopic expression of miR156 represses nodulation and causes morphological and developmental changes in Lotus japonicus. Mol Genet Genomics 2014; 290:471-84. [PMID: 25293935 PMCID: PMC4361721 DOI: 10.1007/s00438-014-0931-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/20/2014] [Indexed: 11/03/2022]
Abstract
The effects of microRNA156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, Lotus japonicus. We cloned an miR156 homolog, LjmiR156a, from L. japonicus, and investigated its SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. Thirteen potential targets for LjmiR156 were identified in vitro and their expression profiles were determined in aerial and underground parts of mature plants, including genes coding for eight SPLs, one WD-40, one RNA-directed DNA polymerase, two transport proteins, and one histidine-phosphotransfer protein. Two SPL and one WD-40 cleavage targets for LjmiR156-TC70253, AU089191, and TC57859-were identified. Transgenic plants with ectopic expression of LjmiR156a showed enhanced branching, dramatically delayed flowering, underdeveloped roots, and reduced nodulation. We also examined the transcript levels of key genes involved in nodule organogenesis and infection thread formation to determine the role of miR156 in regulating symbiosis. Overexpression of LjmiR156a led to repression of several nodulation genes during the early stages of root development such as three ENOD genes, SymPK, POLLUX, CYCLOPS, Cerberus, and Nsp1, and the stimulation of NFR1. Our results show that miR156 regulates vegetative biomass yield, flowering time and nodulation by silencing downstream target SPLs and other genes, suggesting that the miR156 regulatory network could be modified in forage legumes (such as alfalfa and trefoils) and in leafy vegetables (like lettuce and spinach) to positively impact economically valuable crop species.
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Formey D, Sallet E, Lelandais-Brière C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier JP, Debellé F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J, Crespi M. The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. Genome Biol 2014; 15:457. [PMID: 25248950 PMCID: PMC4212123 DOI: 10.1186/s13059-014-0457-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. RESULTS In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. CONCLUSIONS We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
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Li C, Lu S. Molecular characterization of the SPL gene family in Populus trichocarpa. BMC PLANT BIOLOGY 2014; 14:131. [PMID: 24884654 PMCID: PMC4035897 DOI: 10.1186/1471-2229-14-131] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/06/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND SPLs, a family of transcription factors specific to plants, play vital roles in plant growth and development through regulation of various physiological and biochemical processes. Although Populus trichocarpa is a model forest tree, the PtSPL gene family has not been systematically studied. RESULTS Here we report the identification of 28 full-length PtSPLs, which distribute on 14 P. trichocarpa chromosomes. Based on the phylogenetic relationships of SPLs in P. trichocarpa and Arabidopsis, plant SPLs can be classified into 6 groups. Each group contains at least a PtSPL and an AtSPL. The N-terminal zinc finger 1 (Zn1) of SBP domain in group 6 SPLs has four cysteine residues (CCCC-type), while Zn1 of SPLs in the other groups mainly contains three cysteine and one histidine residues (C2HC-type). Comparative analyses of gene structures, conserved motifs and expression patterns of PtSPLs and AtSPLs revealed the conservation of plant SPLs within a group, whereas among groups, the P. trichocarpa and Arabidopsis SPLs were significantly different. Various conserved motifs were identified in PtSPLs but not found in AtSPLs, suggesting the diversity of plant SPLs. A total of 11 pairs of intrachromosome-duplicated PtSPLs were identified, suggesting the importance of gene duplication in SPL gene expansion in P. trichocarpa. In addition, 18 of the 28 PtSPLs, belonging to G1, G2 and G5, were found to be targets of miR156. Consistently, all of the AtSPLs in these groups are regulated by miR156. It suggests the conservation of miR156-mediated posttranscriptional regulation in plants. CONCLUSIONS A total of 28 full-length SPLs were identified from the whole genome sequence of P. trichocarpa. Through comprehensive analyses of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156-mediated posttranscriptional regulation, the PtSPL gene family was characterized. Our results provide useful information for evolution and biological function of plant SPLs.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, China
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Madzima TF, Huang J, McGinnis KM. Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays. Epigenetics 2014; 9:1047-59. [PMID: 24786611 PMCID: PMC4143406 DOI: 10.4161/epi.29022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Though the mechanisms governing nuclear organization are not well understood, it is apparent that epigenetic modifications coordinately modulate chromatin organization as well as transcription. In maize, MEDIATOR OF PARAMUTATION1 (MOP1) is required for 24 nt siRNA-mediated epigenetic regulation and transcriptional gene silencing via a putative Pol IV- RdDM pathway. To elucidate the mechanisms of nuclear chromatin organization, we investigated the relationship between chromatin structure and transcription in response to loss of MOP1 function. We used a microarray based micrococcal nuclease sensitivity assay to identify genome-wide changes in chromatin structure in mop1-1 immature ears and observed an increase in chromatin accessibility at chromosome arms associated with loss of MOP1 function. Within the many genes misregulated in mop1 mutants, we identified one subset likely to be direct targets of epigenetic transcriptional silencing via Pol-IV RdDM. We found that target specificity for MOP1-mediated RdDM activity is governed by multiple signals that include accumulation of 24 nt siRNAs and the presence of specific classes of gene-proximal transposons, but neither of these attributes alone is sufficient to predict transcriptional misregulation in mop1-1 homozygous mutants. Our results suggest a role for MOP1 in regulation of higher-order chromatin organization where loss of MOP1 activity at a subset of loci triggers a broader cascade of transcriptional consequences and genome-wide changes in chromatin structure.
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Affiliation(s)
- Thelma F Madzima
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Ji Huang
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Karen M McGinnis
- Department of Biological Science; Florida State University; Tallahassee, FL USA
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Aryal R, Ming R. Sex determination in flowering plants: papaya as a model system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 217-218:56-62. [PMID: 24467896 DOI: 10.1016/j.plantsci.2013.10.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 05/23/2023]
Abstract
Unisexuality in flowering plants evolved from a hermaphrodite ancestor. Transition from hermaphrodite to unisexual flowers has occurred multiple times across the different lineages of the angiosperms. Sexuality in plants is regulated by genetic, epigenetic and physiological mechanisms. The most specialized mechanism of sex determination is sex chromosomes. The sex chromosomes ensure the stable segregation of sexual phenotypes by preventing the recombination of sex determining genes. Despite continuous efforts, sex determining genes of dioecious plants have not yet been cloned. Concerted efforts with various model systems are necessary to understand the complex mechanism of sex determination in plants. Papaya (Carica papaya L.) is a tropical fruit tree with three sex forms, male, hermaphrodite, and female. Sexuality in papaya is determined by an XY chromosome system that is in an early evolutionary stage. The male and hermaphrodite of papaya are controlled by two different types of Y chromosomes: Y and Y(h). Large amounts of information in the area of genetics, genomics, and epigenetics of papaya have been accumulated over the last few decades. Relatively short lifecycle, small genome size, and readily available genetic and genomic resources render papaya an excellent model system to study sex determination and sex chromosomes in flowering plants.
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Affiliation(s)
- Rishi Aryal
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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41
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Evolutionary conservation of microRNA regulatory programs in plant flower development. Dev Biol 2013; 380:133-44. [PMID: 23707900 DOI: 10.1016/j.ydbio.2013.05.009] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/05/2013] [Accepted: 05/09/2013] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. Flowering is critical for the reproduction of angiosperms. Flower development entails the transition from vegetative growth to reproductive growth, floral organ initiation, and the development of floral organs. These developmental processes are genetically regulated by miRNAs, which participate in complex genetic networks of flower development. A survey of the literature shows that miRNAs, their specific targets, and the regulatory programs in which they participate are conserved throughout the plant kingdom. This review summarizes the role of miRNAs and their targets in the regulation of gene expression during the floral developmental phase, which includes the floral transition stage, followed by floral patterning, and then the development of floral organs. The conservation patterns observed in each component of the miRNA regulatory system suggest that these miRNAs play important roles in the evolution of flower development.
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Preston JC, Hileman LC. Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family. FRONTIERS IN PLANT SCIENCE 2013; 4:80. [PMID: 23577017 PMCID: PMC3617394 DOI: 10.3389/fpls.2013.00080] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/19/2013] [Indexed: 05/18/2023]
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors is functionally diverse, controlling a number of fundamental aspects of plant growth and development, including vegetative phase change, flowering time, branching, and leaf initiation rate. In natural plant populations, variation in flowering time and shoot architecture have major consequences for fitness. Likewise, in crop species, variation in branching and developmental rate impact biomass and yield. Thus, studies aimed at dissecting how the various functions are partitioned among different SPL genes in diverse plant lineages are key to providing insight into the genetic basis of local adaptation and have already garnered attention by crop breeders. Here we use phylogenetic reconstruction to reveal nine major SPL gene lineages, each of which is described in terms of function and diversification. To assess evidence for ancestral and derived functions within each SPL gene lineage, we use ancestral character state reconstructions. Our analyses suggest an emerging pattern of sub-functionalization, neo-functionalization, and possible convergent evolution following both ancient and recent gene duplication. Based on these analyses we suggest future avenues of research that may prove fruitful for elucidating the importance of SPL gene evolution in plant growth and development.
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Affiliation(s)
| | - Lena C. Hileman
- Ecology and Evolutionary Biology, The University of KansasLawrence, KS, USA
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Salinas M, Xing S, Höhmann S, Berndtgen R, Huijser P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. PLANTA 2012; 235:1171-84. [PMID: 22160465 DOI: 10.1007/s00425-011-1565-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/25/2011] [Indexed: 05/07/2023]
Abstract
SBP-box genes represent transcription factors ubiquitously found in the plant kingdom and recognized as important regulators of many different aspects of plant development. In this study, 15 SBP-box gene family members were identified in tomato and analyzed with respect to their genomic organization and other structural features. Phylogenetic reconstruction based on the DNA-binding SBP-domain, allowed the classification of the SlySBP proteins into eight groups representing clear orthologous relationships to family members of other flowering plants and the moss Physcomitrella. In order to have a better understanding of their possible function in the development of a fleshy-fruit species like tomato, the mRNA expression levels of all SlySBP genes were quantified in vegetative and reproductive organs of plants, at different stages of growth. As transcripts of ten SlySBP genes were found to carry putative miR156- and miR157-response elements, the expression levels of the corresponding microRNAs were determined as well, revealing different patterns of expression. In addition, eight putative miR156 and four miR157 encoding loci could be identified in the tomato genome, four of them forming a polycistronic cluster. Whereas miR156 and miR157 levels were highest in seedlings, leaves and anthers of young flowers, most miR156-targeted SlySBP genes were found to be expressed in young inflorescences and during fruit development and ripening, suggesting a particularly important role during tomato reproductive growth. The data presented provide a basis for future clarification of the various functions that SBP-box gene family members play in tomato growth and development.
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Affiliation(s)
- María Salinas
- Department of Molecular Plant Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Schwab R. The Roles of miR156 and miR172 in Phase Change Regulation. MICRORNAS IN PLANT DEVELOPMENT AND STRESS RESPONSES 2012. [DOI: 10.1007/978-3-642-27384-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Townsley BT, Sinha NR. A new development: evolving concepts in leaf ontogeny. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:535-62. [PMID: 22404465 DOI: 10.1146/annurev-arplant-042811-105524] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Elucidation of gene regulatory networks (GRNs) underlying aspects of leaf development in multiple model species has uncovered surprisingly plastic regulatory architecture. The meticulously mapped network interactions in one model species cannot now be assumed to map directly onto a different species. Despite these overall differences, however, many modules do appear to be almost universal. Extrapolating findings across different model systems will demand great care but promises to reveal a rich tapestry of themes in GRN architecture and regulation. The purpose of this review is to approach the field of leaf development from the perspectives of the evolution of developmental systems that orchestrate leaf development.
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Affiliation(s)
- Brad T Townsley
- Department of Plant Biology, University of California-Davis, CA 95616, USA
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Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. ANNALS OF BOTANY 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
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Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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Adam H, Collin M, Richaud F, Beulé T, Cros D, Omoré A, Nodichao L, Nouy B, Tregear JW. Environmental regulation of sex determination in oil palm: current knowledge and insights from other species. ANNALS OF BOTANY 2011; 108:1529-37. [PMID: 21712294 PMCID: PMC3219494 DOI: 10.1093/aob/mcr151] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 04/07/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND The African oil palm (Elaeis guineensis) is a monoecious species of the palm subfamily Arecoideae. It may be qualified as 'temporally dioecious' in that it produces functionally unisexual male and female inflorescences in an alternating cycle on the same plant, resulting in an allogamous mode of reproduction. The 'sex ratio' of an oil palm stand is influenced by both genetic and environmental factors. In particular, the enhancement of male inflorescence production in response to water stress has been well documented. SCOPE This paper presents a review of our current understanding of the sex determination process in oil palm and discusses possible insights that can be gained from other species. Although some informative phenological studies have been carried out, nothing is as yet known about the genetic basis of sex determination in oil palm, nor the mechanisms by which this process is regulated. Nevertheless new genomics-based techniques, when combined with field studies and biochemical and molecular cytological-based approaches, should provide a new understanding of the complex processes governing oil palm sex determination in the foreseeable future. Current hypotheses and strategies for future research are discussed.
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Affiliation(s)
| | | | - Frédérique Richaud
- CIRAD, IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394 Montpellier, France
| | - Thierry Beulé
- CIRAD, IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394 Montpellier, France
| | | | | | | | - Bruno Nouy
- PalmElit SAS, Parc Agropolis Bt. 14, 2214 Boulevard de la Lironde, 34980 Montferrier sur Lez, France
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Abstract
Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs - miR156 and miR172 - and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.
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Affiliation(s)
- Peter Huijser
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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Xing S, Salinas M, Huijser P. New players unveiled in early anther development. PLANT SIGNALING & BEHAVIOR 2011; 6:934-8. [PMID: 21633200 PMCID: PMC3257765 DOI: 10.4161/psb.6.7.15668] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 05/08/2023]
Abstract
Anther development is an important process for the successful sexual reproduction in plants. Whereas the regulation of the late stages of anther development is quite well described in A. thaliana, little is known about the regulation of the early stages of this process. Two novel groups of factors involved in these early stages have recently been described, namely ROXYs, members of the Glutaredoxin (GRX) family of small and ubiquitous oxidoreductases involved in various cellular and stress-related responses, and SBP-box Genes. ROXYs belong to the CC-type of GRXs with a CCXC active motif and are specific for higher plants. SBP-box genes encode for SQUAMOSA PROMOTER BINDING PROTEIN transcription factors, many of which are targeted by miR156 and miR157. Strikingly, both the enzymes and the transcription factors represent evolutionary conserved gene families and loss-of-function of these genes exhibits similar anther phenotypes, e.g. arresting sporogenous cell formation and missing pollen sacs. This mini-review gives an overview of how these factors affect early anther development and discusses a possible relationship between these factors and other known early anther genes.
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Affiliation(s)
- Shuping Xing
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
| | - María Salinas
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
- Área de Genética; Departamento de Biología Aplicada; Universidad de Almería; Almería, Spain
| | - Peter Huijser
- Department of Molecular Plant Genetics; Max Planck Institute for Plant Breeding Research; Cologne, Germany
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Xing S, Salinas M, Höhmann S, Berndtgen R, Huijser P. miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. THE PLANT CELL 2010; 22:3935-50. [PMID: 21177480 PMCID: PMC3027167 DOI: 10.1105/tpc.110.079343] [Citation(s) in RCA: 248] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/19/2010] [Accepted: 12/03/2010] [Indexed: 05/18/2023]
Abstract
The SBP-box transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE8 (SPL8) is required for proper development of sporogenic tissues in Arabidopsis thaliana. Here, we show that the semisterile phenotype of SPL8 loss-of-function mutants is due to partial functional redundancy with several other members of the Arabidopsis SPL gene family. In contrast with SPL8, the transcripts of these latter SPL genes are all targeted by miR156/7. Whereas the introduction of single miR156/7-resistant SPL transgenes could only partially restore spl8 mutant fertility, constitutive overexpression of miR156 in an spl8 mutant background resulted in fully sterile plants. Histological analysis of the anthers of such sterile plants revealed an almost complete absence of sporogenous and anther wall tissue differentiation, a phenotype similar to that reported for sporocyteless/nozzle (spl/nzz) mutant anthers. Expression studies indicated a functional requirement for miR156/7-targeted SPL genes limited to early anther development. Accordingly, several miR156/7-encoding loci were found expressed in anther tissues at later stages of development. We conclude that fully fertile Arabidopsis flowers require the action of multiple miR156/7-targeted SPL genes in concert with SPL8. Either together with SPL/NZZ or independently, these SPL genes act to regulate genes mediating cell division, differentiation, and specification early in anther development. Furthermore, SPL8 in particular may be required to secure fertility of the very first flowers when floral transition-related miR156/7 levels might not have sufficiently declined.
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Affiliation(s)
- Shuping Xing
- Department of Molecular Plant Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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