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Wang D, Dong X, Zhong MC, Jiang XD, Cui WH, Bendahmane M, Hu JY. Molecular and genetic regulation of petal number variation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3233-3247. [PMID: 38546444 DOI: 10.1093/jxb/erae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/26/2024] [Indexed: 06/11/2024]
Abstract
Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.
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Affiliation(s)
- Dan Wang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, Yunnan, China
| | - Xue Dong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
| | - Mi-Cai Zhong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRAE-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jin-Yong Hu
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Sun P, Yuan H, Pan J, Wu Z, Li W, Wang X, Kuang H, Chen J. A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce. THE NEW PHYTOLOGIST 2024; 242:2857-2871. [PMID: 38584520 DOI: 10.1111/nph.19738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
The loss of spines is one of the most important domestication traits for lettuce (Lactuca sativa). However, the genetics and regulation of spine development in lettuce remain unclear. We examined the genetics of spines in lettuce using a segregating population derived from a cross between cultivated and wild lettuce (Lactuca serriola). A gene encoding WUSCHEL-related homeobox transcription factor, named as WOX-SPINE1 (WS1), was identified as the candidate gene controlling the spine development in lettuce, and its function on spines was verified. A CACTA transposon was found to be inserted into the first exon of the ws1 allele, knocking out its function and leading to the lack of spines in cultivated lettuce. All lettuce cultivars investigated have the nonfunctional ws1 gene, and a selection sweep was found at the WS1 locus, suggesting its important role in lettuce domestication. The expression levels of WS1 were associated with the density of spines among different accessions of wild lettuce. At least two independent loss-of-function mutations in the ws1 gene caused the loss of spines in wild lettuce. These findings provide new insights into the development of spines and facilitate the exploitation of wild genetic resources in future lettuce breeding programs.
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Affiliation(s)
- Peinan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Huanran Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiangpeng Pan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Weibo Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiongjiong Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
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Wu T, Yang Q, Zhou R, Yu T, Shen S, Cao R, Ma X, Song X. Large-scale analysis of trihelix transcription factors reveals their expansion and evolutionary footprint in plants. PHYSIOLOGIA PLANTARUM 2023; 175:e14039. [PMID: 37882297 DOI: 10.1111/ppl.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The trihelix transcription factor (TTF) gene family is an important class of transcription factors that play key roles in regulating developmental processes and responding to various stresses. To date, no comprehensive analysis of the TTF gene family in large-scale species has been performed. A cross-genome exploration of its origin, copy number variation, and expression pattern in plants is also unavailable. Here, we identified and characterized the TTF gene family in 110 species representing typical plant phylogenetic taxa. Interestingly, we found that the number of TTF genes was significantly expanded in Chara braunii compared to other species. Based on the available plant genomic datasets, our comparative analysis suggested that the TTF gene family likely originated from the GT-1-1 group and then expanded to form other groups through duplication or deletion of some domains. We found evidence that whole-genome duplication/triplication contributed most to the expansion of the TTF gene family in dicots, monocots and basal angiosperms. In contrast, dispersed and proximal duplications contributed to the expansion of the TTF gene family in algae and bryophyta. The expression patterns of TTF genes and their upstream and downstream genes in different treatments showed a functional divergence of TTF-related genes. Furthermore, we constructed the interaction network between TTF genes and the corresponding upstream and downstream genes, providing a blueprint for their regulatory pathways. This study provided a cross-genome comparative analysis of TTF genes in 110 species, which contributed to understanding their copy number expansion and evolutionary footprint in plants.
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Affiliation(s)
- Tong Wu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qihang Yang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, Denmark
| | - Tong Yu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shaoqin Shen
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
- College of Horticultural Science & Technology, Hebei Normal University Of Science & Technology, Qinhuangdao, Hebei, China
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
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Smyth DR. How flower development genes were identified using forward genetic screens in Arabidopsis thaliana. Genetics 2023; 224:iyad102. [PMID: 37294732 PMCID: PMC10411571 DOI: 10.1093/genetics/iyad102] [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: 04/04/2023] [Accepted: 05/20/2023] [Indexed: 06/11/2023] Open
Abstract
In the later part of the 1980s, the time was ripe for identifying genes controlling flower development. In that pregenomic era, the easiest way to do this was to induce random mutations in seeds by chemical mutagens (or irradiation) and to screen thousands of plants for those with phenotypes specifically defective in floral morphogenesis. Here, we discuss the results of premolecular screens for flower development mutants in Arabidopsis thaliana, carried out at Caltech and Monash University, emphasizing the usefulness of saturation mutagenesis, multiple alleles to identify full loss-of-function, conclusions based on multiple mutant analyses, and from screens for enhancer and suppressor modifiers of original mutant phenotypes. One outcome was a series of mutants that led to the ABC floral organ identity model (AP1, AP2, AP3, PI, and AG). In addition, genes controlling flower meristem identity (AP1, CAL, and LFY), floral meristem size (CLV1 and CLV3), development of individual floral organ types (CRC, SPT, and PTL), and inflorescence meristem properties (TFL1, PIN1, and PID) were defined. These occurrences formed targets for cloning that eventually helped lead to an understanding of transcriptional control of the identity of floral organs and flower meristems, signaling within meristems, and the role of auxin in initiating floral organogenesis. These findings in Arabidopsis are now being applied to investigate how orthologous and paralogous genes act in other flowering plants, allowing us to wander in the fertile fields of evo-devo.
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Affiliation(s)
- David R Smyth
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
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Li S, Chen H, Hong J, Ye X, Wang J, Chen Y, Zhang L, Su Z, Yang Z. Chlorate-induced molecular floral transition revealed by transcriptomes. Open Life Sci 2023; 18:20220612. [PMID: 37528883 PMCID: PMC10389677 DOI: 10.1515/biol-2022-0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 08/03/2023] Open
Abstract
Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.
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Affiliation(s)
- Songgang Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Jiwang Hong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Jiabao Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Lei Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Zuanxian Su
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Ziqin Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
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Min Y, Ballerini ES, Edwards MB, Hodges SA, Kramer EM. Genetic architecture underlying variation in floral meristem termination in Aquilegia. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6241-6254. [PMID: 35731618 PMCID: PMC9756955 DOI: 10.1093/jxb/erac277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of an FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl number (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We explored potential candidate genes under each QTL and characterized novel expression patterns of select loci of interest using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated, and our results provide insight into how floral morphological diversity can be generated at the meristematic level.
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Affiliation(s)
| | - Evangeline S Ballerini
- Department of Biological Sciences, California State University, Sacramento, Sacramento, CA, USA
| | - Molly B Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Scott A Hodges
- Department of Ecology & Marine Biology, University of California, Santa Barbara, CA, USA
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7
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Valderrama E, Landis JB, Skinner D, Maas PJM, Maas-van de Kramer H, André T, Grunder N, Sass C, Pinilla-Vargas M, Guan CJ, Phillips HR, de Almeida AMR, Specht CD. The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L. FRONTIERS IN PLANT SCIENCE 2022; 13:874322. [PMID: 36161003 PMCID: PMC9493542 DOI: 10.3389/fpls.2022.874322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 06/27/2022] [Indexed: 06/16/2023]
Abstract
Selection together with variation in floral traits can act to mold floral form, often driven by a plant's predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.
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Affiliation(s)
- Eugenio Valderrama
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Dave Skinner
- Le Jardin Ombragé, Tallahassee, FL, United States
| | - Paul J. M. Maas
- Section Botany, Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - Thiago André
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Nikolaus Grunder
- Department of Biological Sciences, California State University, East Bay, Hayward, CA, United States
| | - Chodon Sass
- University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Maria Pinilla-Vargas
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Clarice J. Guan
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Heather R. Phillips
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | | | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
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Takeda S, Hamamura Y, Sakamoto T, Kimura S, Aida M, Higashiyama T. Non-cell-autonomous regulation of petal initiation in Arabidopsis thaliana. Development 2022; 149:276288. [DOI: 10.1242/dev.200684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/04/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
In many flowering plants, petals initiate in alternate positions from first whorl sepals, suggesting possible signaling between sepal boundaries and petal initiation sites. PETAL LOSS (PTL) and RABBIT EARS (RBE) regulate petal initiation in Arabidopsis thaliana and their transcripts are expressed in sepal boundary and petal initiation sites, respectively, suggesting that PTL acts in a non-cell-autonomous manner. Here, we determined that cells expressing PTL and RBE fusion proteins did not overlap but were adjacent, confirming the non-cell-autonomous function of PTL. Genetic ablation of intersepal cells by expressing the diphtheria toxin-A chain gene driven by the PTL promoter resulted in flowers lacking petals, suggesting these cells are required for petal initiation. Transcriptome analysis combined with a PTL induction system revealed 42 genes that were upregulated under PTL activation, including UNUSUAL FLORAL ORGANS (UFO), which likely plays an important role in petal initiation. These findings suggest a molecular mechanism in which PTL indirectly regulates petal initiation and UFO mediates positional signaling between the sepal boundary and petal initiation sites.
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Affiliation(s)
- Seiji Takeda
- Department of Agricultural and Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University 1 , Shimogamo Hangi-cho, Sakyo-ku, Kyoto 606-8522 , Japan
- Kyoto Prefectural Agriculture Forestry and Fisheries Technology Centre 2 Biotechnology Research Department , , Kitaina Yazuma Oji 74, Seika, Kyoto 619-0244 , Japan
| | - Yuki Hamamura
- Graduate School of Science, Nagoya University 3 Division of Biological Science , , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602 , Japan
- University of Hamburg 4 Department of Developmental Biology , , Ohnhorststr. 18, Hamburg 22609 , Germany
| | - Tomoaki Sakamoto
- Center for Plant Sciences, Kyoto Sangyo University 5 , Kyoto 603-8555 , Japan
| | - Seisuke Kimura
- Center for Plant Sciences, Kyoto Sangyo University 5 , Kyoto 603-8555 , Japan
- Faculty of Life Sciences, Kyoto Sangyo University 6 Department of Industrial Life Sciences , , Kyoto 603-8555 , Japan
| | - Mitsuhiro Aida
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University 7 , 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555 , Japan
- International Research Center for Agricultural and Environmental Biology, Kumamoto University 8 , 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555 , Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University 3 Division of Biological Science , , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602 , Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University 9 , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 , Japan
- Graduate School of Science, The University of Tokyo 10 Department of Biological Sciences , , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 , Japan
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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. ANNALS OF BOTANY 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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10
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Bull–Hereñu K, dos Santos P, Toni JFG, El Ottra JHL, Thaowetsuwan P, Jeiter J, Ronse De Craene LP, Iwamoto A. Mechanical Forces in Floral Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:661. [PMID: 35270133 PMCID: PMC8912604 DOI: 10.3390/plants11050661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/19/2022] [Accepted: 02/17/2022] [Indexed: 05/12/2023]
Abstract
Mechanical forces acting within the plant body that can mold flower shape throughout development received little attention. The palette of action of these forces ranges from mechanical pressures on organ primordia at the microscopic level up to the twisting of a peduncle that promotes resupination of a flower at the macroscopic level. Here, we argue that without these forces acting during the ontogenetic process, the actual flower phenotype would not be achieved as it is. In this review, we concentrate on mechanical forces that occur at the microscopic level and determine the fate of the flower shape by the physical constraints on meristems at an early stage of development. We thus highlight the generative role of mechanical forces over the floral phenotype and underline our general view of flower development as the sum of interactions of known physiological and genetic processes, together with physical aspects and mechanical events that are entangled towards the shaping of the mature flower.
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Affiliation(s)
- Kester Bull–Hereñu
- Fundación Flores, Ministro Carvajal 30, Santiago 7500801, Chile;
- Museo Nacional de Historia Natural, Área Botánica, Parque Quinta Normal S/N, Santiago 8350701, Chile
| | - Patricia dos Santos
- Centre for Ecology Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, Piso 5, 1749-016 Lisbon, Portugal;
- Department of Environmental Sciences–Botany, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland
| | | | - Juliana Hanna Leite El Ottra
- Department of Botany, Institute of Biological Sciences, University of São Paulo, São Paulo 05508-090, Brazil;
- Open University of Brazil, Federal University of ABC, Santo André 09210-580, Brazil
| | - Pakkapol Thaowetsuwan
- Department of Biology, Faculty of Science, Sanam Chandra Palace Campus, Silpakorn University, Nakhorn Pathom 73000, Thailand;
| | - Julius Jeiter
- Nees-Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany;
| | | | - Akitoshi Iwamoto
- Department of Biological sciences, Faculty of Science, Kanagawa University, Hiratsuka 259-1293, Japan
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11
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Aslam M, She Z, Jakada BH, Fakher B, Greaves JG, Yan M, Chen Y, Zheng P, Cheng Y, Qin Y. Interspecific complementation-restoration of phenotype in Arabidopsis cuc2cuc3 mutant by sugarcane CUC2 gene. BMC PLANT BIOLOGY 2022; 22:47. [PMID: 35065620 PMCID: PMC8783490 DOI: 10.1186/s12870-022-03440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. RESULTS Here, we have identified the CUP-SHAPED COTYLEDON (CUC) genes in sugarcane and named SsCUC2 (for the orthologous gene of CUC1 and CUC2) and SsCUC3. The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of CUC genes showed that most of the CUC3 genes were accompanied by an intron gain during eudicot divergence. Besides, the study of SsCUCs expression in the RNA-seq obtained during different stages of ovule development revealed that SsCUCs express in developing young tissues, and the expression of SsCUC2 is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the cuc2cuc3 mutant phenotype of Arabidopsis (eudicot). CONCLUSIONS This study further supports that CUC2 has diverged in CUC1 and CUC2 during the evolution of monocots and eudicots from ancestral plants. The functional analysis of CUC expression patterns during sugarcane ovule development and ectopic expression of SsCUC2 in Arabidopsis showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane CUC genes. Our results reveal the crucial functional role of CUC genes in sugarcane.
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Affiliation(s)
- Mohammad Aslam
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Zeyuan She
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Bello Hassan Jakada
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Beenish Fakher
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Joseph G Greaves
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Maokai Yan
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Yingzhi Chen
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Ping Zheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yan Cheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yuan Qin
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China.
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12
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Lin Z, Cao D, Damaris RN, Yang P. Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus ( Nelumbo nucifera). PeerJ 2021; 9:e12322. [PMID: 34754621 PMCID: PMC8552788 DOI: 10.7717/peerj.12322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/25/2021] [Indexed: 11/20/2022] Open
Abstract
Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
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Affiliation(s)
- Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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13
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An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem. PLoS Genet 2020; 16:e1008661. [PMID: 32294082 PMCID: PMC7266345 DOI: 10.1371/journal.pgen.1008661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/02/2020] [Accepted: 02/11/2020] [Indexed: 12/27/2022] Open
Abstract
In the Arabidopsis thaliana shoot apical meristem (SAM) the expression domains of Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) genes are separated by a narrow boundary region from which new organs are initiated. Disruption of this boundary through either loss of function or ectopic expression of HD-ZIPIII and KAN causes ectopic or suppression of organ formation respectively, raising the question of how these transcription factors regulate organogenesis at a molecular level. In this study we develop a multi-channel FACS/RNA-seq approach to characterize global patterns of gene expression across the HD-ZIPIII-KAN1 SAM boundary. We then combine FACS, RNA-seq and perturbations of HD-ZIPIII and KAN expression to identify genes that are both responsive to REV and KAN1 and normally expressed in patterns that correlate with REV and KAN1. Our data reveal that a significant number of genes responsive to REV are regulated in opposite ways depending on time after induction, with genes associated with auxin response and synthesis upregulated initially, but later repressed. We also characterize the cell type specific expression patterns of auxin responsive genes and identify a set of genes involved in organogenesis repressed by both REV and KAN1. The plant hormone auxin promotes the formation of lateral organs such as leaves and flowers in a specific region of the shoot called the peripheral zone. Although the restriction of organogenesis to the peripheral zone is known to depend on the Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI1 (KAN1) genes, the transcriptional pathways downstream of these genes have not been studied in the shoot. In this study we investigate regulatory interactions between REVOLUTA (REV), KAN1 and auxin by developing a cell-type specific transcriptomics approach to analyse gene expression patterns and responses to perturbations. Using this approach, we identify cell-type specific genes that respond to changes in REV and KAN1 expression in the shoot. Our data reveal that while REV promotes auxin-related gene expression over the short term, both REV and KAN1 repress auxin induced genes over the long-term, consistent with their influence on organogenesis. We also identify a common set of genes repressed by REV and KAN1 that promote organogenesis.
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14
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Ding L, Zhao K, Zhang X, Song A, Su J, Hu Y, Zhao W, Jiang J, Chen F. Comprehensive characterization of a floral mutant reveals the mechanism of hooked petal morphogenesis in Chrysanthemum morifolium. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2325-2340. [PMID: 31050173 PMCID: PMC6835125 DOI: 10.1111/pbi.13143] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 05/17/2023]
Abstract
The diversity of form of the chrysanthemum flower makes this species an ideal model for studying petal morphogenesis, but as yet, the molecular mechanisms underlying petal shape development remain largely unexplored. Here, a floral mutant, which arose as a bud sport in a plant of the variety 'Anastasia Dark Green', and formed straight, rather than hooked petals, was subjected to both comparative morphological analysis and transcriptome profiling. The hooked petals only became discernible during a late stage of flower development. At the late stage of 'Anastasia Dark Green', genes related to chloroplast, hormone metabolism, cell wall and microtubules were active, as were cell division-promoting factors. Auxin concentration was significantly reduced, and a positive regulator of cell expansion was down-regulated. Two types of critical candidates, boundary genes and adaxial-abaxial regulators, were identified from 7937 differentially expressed genes in pairwise comparisons, which were up-regulated at the late stage in 'Anastasia Dark Green' and another two hooked varieties. Ectopic expression of a candidate abaxial gene, CmYAB1, in chrysanthemum led to changes in petal curvature and inflorescence morphology. Our findings provide new insights into the regulatory networks underlying chrysanthemum petal morphogenesis.
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Affiliation(s)
- Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yueheng Hu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
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15
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Chen W, Hsu W, Hsu H, Yang C. A tetraspanin gene regulating auxin response and affecting orchid perianth size and various plant developmental processes. PLANT DIRECT 2019; 3:e00157. [PMID: 31406958 PMCID: PMC6680136 DOI: 10.1002/pld3.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 05/25/2023]
Abstract
The competition between L (lip) and SP (sepal/petal) complexes in P-code model determines the identity of complex perianth patterns in orchids. Orchid tetraspanin gene Auxin Activation Factor (AAF) orthologs, whose expression strongly correlated with the expansion and size of the perianth after P code established, were identified. Virus-induced gene silencing (VIGS) of OAGL6-2 in L complex resulted in smaller lips and the down-regulation of Oncidium OnAAF. VIGS of PeMADS9 in L complex resulted in the enlarged lips and up-regulation of Phalaenopsis PaAAF. Furthermore, the larger size of Phalaenopsis variety flowers was associated with higher PaAAF expression, larger and more cells in the perianth. Thus, a rule is established that whenever bigger perianth organs are made in orchids, higher OnAAF/PaAAF expression is observed after their identities are determined by P-code complexes. Ectopic expression Arabidopsis AtAAF significantly increased the size of flower organs by promoting cell expansion in transgenic Arabidopsis due to the enhancement of the efficiency of the auxin response and the subsequent suppression of the jasmonic acid (JA) biosynthesis genes (DAD1/OPR3) and BIGPETAL gene during late flower development. In addition, auxin-controlled phenotypes, such as indehiscent anthers, enhanced drought tolerance, and increased lateral root formation, were also observed in 35S::AtAAF plants. Furthermore, 35S::AtAAF root tips maintained gravitropism during auxin treatment. In contrast, the opposite phenotype was observed in palmitoylation-deficient AtAAF mutants. Our data demonstrate an interaction between the tetraspanin AAF and auxin/JA that regulates the size of flower organs and impacts various developmental processes.
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Affiliation(s)
- Wei‐Hao Chen
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Wei‐Han Hsu
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Hsing‐Fun Hsu
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Chang‐Hsien Yang
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
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16
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Monniaux M, Pieper B, McKim SM, Routier-Kierzkowska AL, Kierzkowski D, Smith RS, Hay A. The role of APETALA1 in petal number robustness. eLife 2018; 7:39399. [PMID: 30334736 PMCID: PMC6205810 DOI: 10.7554/elife.39399] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 10/11/2018] [Indexed: 01/31/2023] Open
Abstract
Invariant floral forms are important for reproductive success and robust to natural perturbations. Petal number, for example, is invariant in Arabidopsis thaliana flowers. However, petal number varies in the closely related species Cardamine hirsuta, and the genetic basis for this difference between species is unknown. Here we show that divergence in the pleiotropic floral regulator APETALA1 (AP1) can account for the species-specific difference in petal number robustness. This large effect of AP1 is explained by epistatic interactions: A. thaliana AP1 confers robustness by masking the phenotypic expression of quantitative trait loci controlling petal number in C. hirsuta. We show that C. hirsuta AP1 fails to complement this function of A. thaliana AP1, conferring variable petal number, and that upstream regulatory regions of AP1 contribute to this divergence. Moreover, variable petal number is maintained in C. hirsuta despite sufficient standing genetic variation in natural accessions to produce plants with four-petalled flowers.
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Affiliation(s)
- Marie Monniaux
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sarah M McKim
- Plant Sciences Department, University of Oxford, Oxford, United Kingdom
| | | | | | - Richard S Smith
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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17
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Smyth DR. Evolution and genetic control of the floral ground plan. THE NEW PHYTOLOGIST 2018; 220:70-86. [PMID: 29959892 DOI: 10.1111/nph.15282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 70 I. Introduction 70 II. What is the floral ground plan? 71 III. Diversity and evolution of the floral ground plan 72 IV. Genetic mechanisms 77 V. What's next? 82 Acknowledgements 83 References 83 SUMMARY: The floral ground plan is a map of where and when floral organ primordia arise. New results combining the defined phylogeny of flowering plants with extensive character mapping have predicted that the angiosperm ancestor had whorls rather than spirals of floral organs in large numbers, and was bisexual. More confidently, the monocot ancestor likely had three organs in each whorl, whereas the rosid and asterid ancestor (Pentapetalae) had five, with the perianth now divided into sepals and petals. Genetic mechanisms underlying the establishment of the floral ground plan are being deduced using model species, the rosid Arabidopsis, the asterid Antirrhinum, and in grasses such as rice. In this review, evolutionary and genetic conclusions are drawn together, especially considering how known genes may control individual processes in the development and evolution of ground plans. These components include organ phyllotaxis, boundary formation, organ identity, merism (the number or organs per whorl), variation in the form of primordia, organ fusion, intercalary growth, floral symmetry, determinacy and, finally, cases where the distinction between flowers and inflorescences is blurred. It seems likely that new pathways of ground plan evolution, and new signalling mechanisms, will soon be uncovered by integrating morphological and genetic approaches.
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Affiliation(s)
- David R Smyth
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
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18
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Wang Z, Zhao K, Pan Y, Wang J, Song X, Ge W, Yuan M, Lei T, Wang L, Zhang L, Li Y, Liu T, Chen W, Meng W, Sun C, Cui X, Bai Y, Wang X. Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory. BMC Genomics 2018; 19:665. [PMID: 30208846 PMCID: PMC6134603 DOI: 10.1186/s12864-018-5051-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains. Results As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What’s more interesting is that it may have bridge the interaction with different proteins. Conclusions By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory. Electronic supplementary material The online version of this article (10.1186/s12864-018-5051-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
| | - Kanglu Zhao
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxin Pan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Jinpeng Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Min Yuan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tianyu Lei
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Li Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Lan Zhang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxian Li
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wei Chen
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wenjing Meng
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Changkai Sun
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaobo Cui
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yun Bai
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiyin Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
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19
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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20
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Woźniak NJ, Sicard A. Evolvability of flower geometry: Convergence in pollinator-driven morphological evolution of flowers. Semin Cell Dev Biol 2018; 79:3-15. [DOI: 10.1016/j.semcdb.2017.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
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21
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González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One 2017; 12:e0185106. [PMID: 28934292 PMCID: PMC5608315 DOI: 10.1371/journal.pone.0185106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/06/2017] [Indexed: 12/02/2022] Open
Abstract
The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene.
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Affiliation(s)
- Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Veronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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Global gene expression defines faded whorl specification of double flower domestication in Camellia. Sci Rep 2017; 7:3197. [PMID: 28600507 PMCID: PMC5466612 DOI: 10.1038/s41598-017-03575-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 12/03/2022] Open
Abstract
Double flowers in cultivated camellias are divergent in floral patterns which present a rich resource for demonstrating molecular modifications influenced by the human demands. Despite the key principle of ABCE model in whorl specification, the underlying mechanism of fine-tuning double flower formation remains largely unclear. Here a comprehensive comparative transcriptomics interrogation of gene expression among floral organs of wild type and “formal double” and “anemone double” is presented. Through a combination of transcriptome, small RNA and “degradome” sequencing, we studied the regulatory gene expression network underlying the double flower formation. We obtained the differentially expressed genes between whorls in wild and cultivated Camellia. We showed that the formation of double flowers tends to demolish gene expression canalization of key functions; the faded whorl specification mechanism was fundamental under the diverse patterns of double flowers. Furthermore, we identified conserved miRNA-targets regulations in the control of double flowers, and we found that miR172-AP2, miR156-SPLs were critical regulatory nodes contributing to the diversity of double flower forms. This work highlights the hierarchical patterning of global gene expression in floral development, and supports the roles of “faded ABC model” mechanism and miRNA-targets regulations underlying the double flower domestication.
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Quon T, Lampugnani ER, Smyth DR. PETAL LOSS and ROXY1 Interact to Limit Growth Within and between Sepals But to Promote Petal Initiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:152. [PMID: 28228771 PMCID: PMC5296375 DOI: 10.3389/fpls.2017.00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/25/2017] [Indexed: 05/28/2023]
Abstract
The activity of genes controlling organ development may be associated with the redox state of subregions within the meristem. Glutaredoxins react to the level of oxidative potential and can reduce cysteine dithiols, in some cases to activate specific transcription factors. In Arabidopsis, loss of function of the glutaredoxin ROXY1 or the trihelix transcription factor PETAL LOSS (PTL) each results in reduced numbers of petals. Here, genetic studies have revealed that loss of petals in ptl mutant plants depends on ROXY1 function. The two genes also act together to restrain stamen-identifying C function from entering the outer whorls. On the other hand, they suppress growth between sepals and in sepal margins, with ROXY1 action partially redundant to that of PTL. Genetic interactions with aux1 mutations indicate that auxin activity is reduced in the petal whorl of roxy1 mutants as in ptl mutants. However, it is apparently increased in the sepal whorl of triple mutants associated with the ectopic outgrowth of sepal margins, and of finger-like extensions of inter-sepal zones that in 20% of cases are topped with bunches of ectopic sepals. These interactions may be indirect, although PTL and ROXY1 proteins can interact directly when co-expressed in a transient assay. Changes of conserved cysteines within PTL to similar amino acids that cannot be oxidized did not block its function. It may be in some cases that under reducing conditions ROXY1 binds PTL and activates it by reducing specific conserved cysteines, thus resulting in growth suppression.
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Zheng X, Liu H, Ji H, Wang Y, Dong B, Qiao Y, Liu M, Li X. The Wheat GT Factor TaGT2L1D Negatively Regulates Drought Tolerance and Plant Development. Sci Rep 2016; 6:27042. [PMID: 27245096 PMCID: PMC4887992 DOI: 10.1038/srep27042] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/13/2016] [Indexed: 01/18/2023] Open
Abstract
GT factors are trihelix transcription factors that specifically regulate plant development and stress responses. Recently, several GT factors have been characterized in different plant species; however, little is known about the role of GT factors in wheat. Here, we show that TaGT2L1A, TaGT2L1B, and TaGT2L1D are highly homologous in hexaploid wheat, and are localized to wheat chromosomes 2A, 2B, and 2D, respectively. These TaGT2L1 genes encode proteins containing two SANT domains and one central helix. All three homologs were ubiquitously expressed during wheat development and were responsive to osmotic stress. Functional analyses demonstrated that TaGT2L1D acts as a transcriptional repressor; it was able to suppress the expression of AtSDD1 in Arabidopsis by binding directly to the GT3 box in its promoter that negatively regulates drought tolerance. TaGT2L1D overexpression markedly increased the number of stomata and reduced drought tolerance in gtl1-3 plants. Notably, ectopic expression of TaGT2L1D also affected floral organ development and overall plant growth. These results demonstrate that TaGT2L1 is an ortholog of AtGTL1, and that it plays an evolutionarily conserved role in drought resistance by fine tuning stomatal density in wheat. Our data also highlight the role of TaGT2L1 in plant growth and development.
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Affiliation(s)
- Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Haipei Liu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
| | - Hongtao Ji
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Youning Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Baodi Dong
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P. R. China
| | - Yunzhou Qiao
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P. R. China
| | - Mengyu Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P. R. China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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Akagi T, Hanada T, Yaegaki H, Gradziel TM, Tao R. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Res 2016; 23:271-82. [PMID: 27085183 PMCID: PMC4909313 DOI: 10.1093/dnares/dsw014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/02/2016] [Indexed: 01/19/2023] Open
Abstract
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
| | - Toshio Hanada
- Apple Research Division, NARO Institute of Fruit Tree Science, Morioka 020-0123, Japan
| | - Hideaki Yaegaki
- Breeding and Pest Management Division, NARO Institute, Tsukuba, Ibaragi 305-8605, Japan
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California Davis, CA 95616, USA
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
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Endress PK. Development and evolution of extreme synorganization in angiosperm flowers and diversity: a comparison of Apocynaceae and Orchidaceae. ANNALS OF BOTANY 2016; 117:749-67. [PMID: 26292994 PMCID: PMC4845794 DOI: 10.1093/aob/mcv119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/22/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Apocynaceae and Orchidaceae are two angiosperm families with extreme flower synorganization. They are unrelated, the former in eudicots, the latter in monocots, but they converge in the formation of pollinia and pollinaria, which do not occur in any other angiosperm family, and for which extreme synorganization of floral organs is a precondition. In each family extensive studies on flower development and evolution have been performed; however, newer comparative studies focusing on flower synorganization and involving both families together are lacking. SCOPE For this study an extensive search through the morphological literature has been conducted. Based on this and my own studies on flowers in various Apocynaceae and Orchidaceae and complex flowers in other angiosperms with scanning electron microscopy and with microtome section series, a review on convergent floral traits in flower development and architecture in the two families is presented. KEY FINDINGS There is a tendency of protracted development of synorganized parts in Apocynaceae and Orchidaceae (development of synorganization of two or more organs begins earlier the more accentuated it is at anthesis). Synorganization (or complexity) also paves the way for novel structures. One of the most conspicuous such novel structures in Apocynaceae is the corona, which is not the product of synorganization of existing organs; however, it is probably enhanced by synorganization of other, existing, floral parts. In contrast to synorganized parts, the corona appears developmentally late. CONCLUSIONS Synorganization of floral organs may lead to a large number of convergences in clades that are only very distantly related. The convergences that have been highlighted in this comparative study should be developmentally investigated directly in parallel in future studies.
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Affiliation(s)
- Peter K Endress
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Monniaux M, Pieper B, Hay A. Stochastic variation in Cardamine hirsuta petal number. ANNALS OF BOTANY 2016; 117:881-7. [PMID: 26346720 PMCID: PMC4845797 DOI: 10.1093/aob/mcv131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Floral development is remarkably robust in terms of the identity and number of floral organs in each whorl, whereas vegetative development can be quite plastic. This canalization of flower development prevents the phenotypic expression of cryptic genetic variation, even in fluctuating environments. A cruciform perianth with four petals is a hallmark of the Brassicaceae family, typified in the model species Arabidopsis thaliana However, variable petal loss is found in Cardamine hirsuta, a genetically tractable relative of A. thaliana Cardamine hirsuta petal number varies in response to stochastic, genetic and environmental perturbations, which makes it an interesting model to study mechanisms of decanalization and the expression of cryptic variation. METHODS Multitrait quantitative trait locus (QTL) analysis in recombinant inbred lines (RILs) was used to identify whether the stochastic variation found in C. hirsuta petal number had a genetic basis. KEY RESULTS Stochastic variation (standard error of the average petal number) was found to be a heritable phenotype, and four QTL that influenced this trait were identified. The sensitivity to detect these QTL effects was increased by accounting for the effect of ageing on petal number variation. All QTL had significant effects on both average petal number and its standard error, indicating that these two traits share a common genetic basis. However, for some QTL, a degree of independence was found between the age of the flowers where allelic effects were significant for each trait. CONCLUSIONS Stochastic variation in C. hirsuta petal number has a genetic basis, and common QTL influence both average petal number and its standard error. Allelic variation at these QTL can, therefore, modify petal number in an age-specific manner via effects on the phenotypic mean and stochastic variation. These results are discussed in the context of trait evolution via a loss of robustness.
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Affiliation(s)
- Marie Monniaux
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
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28
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Yu H, Huang T. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int J Mol Sci 2016; 17:317. [PMID: 26950117 PMCID: PMC4813180 DOI: 10.3390/ijms17030317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 01/03/2023] Open
Abstract
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M-O) boundaries and floral organ development depends on the establishment of organ-to-organ (O-O) boundaries. Studies in this field have revealed a suite of genes and regulatory pathways controlling floral boundary formation. Many of these genes are transcription factors that interact with phytohormone pathways. This review will focus on the functions and interactions of the genes that play important roles in the floral boundaries and discuss the molecular mechanisms that integrate these regulatory pathways to control the floral boundary formation.
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Affiliation(s)
- Hongyang Yu
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
- College of Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
| | - Tengbo Huang
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
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29
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Pieper B, Monniaux M, Hay A. The genetic architecture of petal number in Cardamine hirsuta. THE NEW PHYTOLOGIST 2016; 209:395-406. [PMID: 26268614 DOI: 10.1111/nph.13586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/04/2015] [Indexed: 05/22/2023]
Abstract
Invariant petal number is a characteristic of most flowers and is generally robust to genetic and environmental variation. We took advantage of the natural variation found in Cardamine hirsuta petal number to investigate the genetic basis of this trait in a case where robustness was lost during evolution. We used quantitative trait locus (QTL) analysis to characterize the genetic architecture of petal number. Αverage petal number showed transgressive variation from zero to four petals in five C. hirsuta mapping populations, and this variation was highly heritable. We detected 15 QTL at which allelic variation affected petal number. The effects of these QTL were relatively small in comparison with alleles induced by mutagenesis, suggesting that natural selection may act to maintain petal number within its variable range below four. Petal number showed a temporal trend during plant ageing, as did sepal trichome number, and multi-trait QTL analysis revealed that these age-dependent traits share a common genetic basis. Our results demonstrate that petal number is determined by many genes of small effect, some of which are age-dependent, and suggests a mechanism of trait evolution via the release of cryptic variation.
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Affiliation(s)
- Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Marie Monniaux
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
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30
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Zhong J, Preston JC. Bridging the gaps: evolution and development of perianth fusion. THE NEW PHYTOLOGIST 2015; 208:330-335. [PMID: 26094556 DOI: 10.1111/nph.13517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
Abstract
One of the most striking innovations in flower development is the congenital or postgenital union of petals (sympetaly) which has enabled dramatic specialization in flower structure and possibly accelerated speciation rates. Sympetalous flowers exhibit extraordinary variation in development, including the degree and timing of fusion, and fusion with other floral organs. Different axes of corolla tube complexity can be disentangled at the developmental level, with most variation being explained by differences in coordinated growth between interconnected and lobed regions of neighboring petal primordia, and between lower and upper portions of the corolla tube, defined by the stamen insertion boundary. Genetically, inter- and intra-specific variation in the degree of petal fusion is controlled by various inputs from genes that affect organ boundary and lateral growth, signaling between different cell types, and production of the cuticle. It is thus hypothesized that the evolution and diversification of fused petals, at least within the megadiverse Asteridae clade of core eudicots, have occurred through the modification of a conserved genetic pathway previously involved in free petal development.
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Affiliation(s)
- Jinshun Zhong
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Jill C Preston
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
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Ding L, Yan S, Jiang L, Zhao W, Ning K, Zhao J, Liu X, Zhang J, Wang Q, Zhang X. HANABA TARANU (HAN) Bridges Meristem and Organ Primordia Boundaries through PINHEAD, JAGGED, BLADE-ON-PETIOLE2 and CYTOKININ OXIDASE 3 during Flower Development in Arabidopsis. PLoS Genet 2015; 11:e1005479. [PMID: 26390296 PMCID: PMC4577084 DOI: 10.1371/journal.pgen.1005479] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/31/2015] [Indexed: 01/02/2023] Open
Abstract
Shoot organ primordia are initiated from the shoot apical meristem and develop into leaves during the vegetative stage, and into flowers during the reproductive phase. Between the meristem and the newly formed organ primordia, a boundary with specialized cells is formed that separates meristematic activity from determinate organ growth. Despite interactions that have been found between boundary regulators with genes controlling meristem maintenance or primordial development, most boundary studies were performed during embryogenesis or vegetative growth, hence little is known about whether and how boundaries communicate with meristem and organ primordia during the reproductive stage. We combined genetic, molecular and biochemical tools to explore interactions between the boundary gene HANABA TARANU (HAN) and two meristem regulators BREVIPEDICELLUS (BP) and PINHEAD (PNH), and three primordia-specific genes PETAL LOSS (PTL), JAGGED (JAG) and BLADE-ON-PETIOLE (BOP) during flower development. We demonstrated the key role of HAN in determining petal number, as part of a set of complex genetic interactions. HAN and PNH transcriptionally promote each other, and biochemically interact to regulate meristem organization. HAN physically interacts with JAG, and directly stimulates the expression of JAG and BOP2 to regulate floral organ development. Further, HAN directly binds to the promoter and intron of CYTOKININ OXIDASE 3 (CKX3) to modulate cytokinin homeostasis in the boundary. Our data suggest that boundary-expressing HAN communicates with the meristem through the PNH, regulates floral organ development via JAG and BOP2, and maintains boundary morphology through CKX3 during flower development in Arabidopsis.
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Affiliation(s)
- Lian Ding
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Shuangshuang Yan
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Li Jiang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wensheng Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Kang Ning
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Jianyu Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaofeng Liu
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Juan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
- * E-mail:
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32
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O'Brien M, Kaplan-Levy RN, Quon T, Sappl PG, Smyth DR. PETAL LOSS, a trihelix transcription factor that represses growth in Arabidopsis thaliana, binds the energy-sensing SnRK1 kinase AKIN10. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2475-85. [PMID: 25697797 PMCID: PMC4986862 DOI: 10.1093/jxb/erv032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Organogenesis in plants involves differential growth. Rapidly growing primordia are distinguished from the meristem and each other by slower growing boundaries. PETAL LOSS (PTL) is a trihelix transcription factor of Arabidopsis that represses growth in boundaries between newly arising sepals. To identify partners involved in this growth limitation, a young inflorescence cDNA library was screened by yeast two-hybrid technology with PTL as bait. The most frequent prey identified was AKIN10, the catalytic α-subunit of the Snf1-related kinase1 (SnRK1). Interaction was mapped to the C-terminal (non-kinase) half of AKIN10 and the N-terminal portion of PTL. Binding of PTL was specific to AKIN10 as there was little binding to the related AKIN11. The interaction was confirmed by co-immunoprecipitation in vitro. Fluorescently tagged products of 35S:YFP-AKIN10 and 35S:CFP-PTL also interacted when transiently expressed together in leaf cells of Nicotiana benthamiana. In this case, most of the cytoplasmic AKIN10 was preferentially moved to the nucleus where PTL accumulated, possibly because a nuclear export sequence in AKIN10 was now masked. During these experiments, we observed that AKIN10 could variably accumulate in the Golgi, shown by its co-localization with a tagged Golgi marker and through its dispersal by brefeldin A. Tests of phosphorylation of PTL by AKIN10 gave negative results. The functional significance of the PTL-AKIN10 interaction remains open, although a testable hypothesis is that AKIN10 senses lower energy levels in inter-sepal zones and, in association with PTL, promotes reduced cell division.
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Affiliation(s)
- Martin O'Brien
- School of Biological Sciences, Monash University, Melbourne, Vic. 3800, Australia
| | - Ruth N Kaplan-Levy
- School of Biological Sciences, Monash University, Melbourne, Vic. 3800, Australia
| | - Tezz Quon
- School of Biological Sciences, Monash University, Melbourne, Vic. 3800, Australia
| | - Pia G Sappl
- School of Biological Sciences, Monash University, Melbourne, Vic. 3800, Australia
| | - David R Smyth
- School of Biological Sciences, Monash University, Melbourne, Vic. 3800, Australia
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33
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Specht CD, Howarth DG. Adaptation in flower form: a comparative evodevo approach. THE NEW PHYTOLOGIST 2015; 206:74-90. [PMID: 25470511 DOI: 10.1111/nph.13198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/15/2014] [Indexed: 05/10/2023]
Abstract
Evolutionary developmental biology (evodevo) attempts to explain how the process of organismal development evolves, utilizing a comparative approach to investigate changes in developmental pathways and processes that occur during the evolution of a given lineage. Evolutionary genetics uses a population approach to understand how organismal changes in form or function are linked to underlying genetics, focusing on changes in gene and genotype frequencies within populations and the fixation of genotypic variation into traits that define species or evoke speciation events. Microevolutionary processes, including mutation, genetic drift, natural selection and gene flow, can provide the foundation for macroevolutionary patterns observed as morphological evolution and adaptation. The temporal element linking microevolutionary processes to macroevolutionary patterns is development: an organism's genotype is converted to phenotype by ontogenetic processes. Because selection acts upon the phenotype, the connection between evolutionary genetics and developmental evolution becomes essential to understanding adaptive evolution in organismal form and function. Here, we discuss how developmental genetic studies focused on key developmental processes could be linked within a comparative framework to study the developmental genetics of adaptive evolution, providing examples from research on two key processes of plant evodevo - floral symmetry and organ fusion - and their role in the adaptation of floral form.
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Affiliation(s)
- Chelsea D Specht
- Departments of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Dianella G Howarth
- Department of Biological Sciences, St John's University, 8000 Utopia Pkwy, Jamaica, NY, 11439, USA
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Rossmann S, Kohlen W, Hasson A, Theres K. Lateral suppressor and Goblet act in hierarchical order to regulate ectopic meristem formation at the base of tomato leaflets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:837-848. [PMID: 25641652 DOI: 10.1111/tpj.12782] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
In seed plants, new axes of growth are established by the formation of meristems, groups of pluripotent cells that maintain themselves and initiate the formation of lateral organs. After embryonic development, secondary shoot meristems form in the boundary zones between the shoot apical meristem and leaf primordia, the leaf axils. In addition, many plant species develop ectopic meristems at different positions of the plant body. In the compound tomato leaf, ectopic meristems can initiate at the base of leaflets, which are delimited by two distinct boundary zones, referred to as the proximal (PLB) and distal (DLB) leaflet boundaries. We demonstrate that the two leaflet boundaries differ from each other and that ectopic meristem formation is strictly limited to the DLB. Our data suggest that the DLB harbours a group of pluripotent cells that seems to be the launching pad for meristem formation. Initiation of these meristems is dependent on the activities of the transcriptional regulators Goblet (Gob) and Lateral suppressor (Ls), specifically expressed in the DLB. Gob and Ls act in hierarchical order, because Ls transcript accumulation is dependent on Gob activity, but not vice versa. Ectopic meristem formation at the DLB is also observed in other seed plants, like Cardamine pratensis, indicating that it is part of a widespread developmental program. Ectopic meristem formation leads to an increase in the number of buds, enhances the capacity for survival and opens the route to vegetative propagation.
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Affiliation(s)
- Susanne Rossmann
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Cologne, Germany
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Wilson SM, Ho YY, Lampugnani ER, Van de Meene AML, Bain MP, Bacic A, Doblin MS. Determining the subcellular location of synthesis and assembly of the cell wall polysaccharide (1,3; 1,4)-β-D-glucan in grasses. THE PLANT CELL 2015; 27:754-71. [PMID: 25770111 PMCID: PMC4558670 DOI: 10.1105/tpc.114.135970] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/17/2015] [Accepted: 02/20/2015] [Indexed: 05/05/2023]
Abstract
The current dogma for cell wall polysaccharide biosynthesis is that cellulose (and callose) is synthesized at the plasma membrane (PM), whereas matrix phase polysaccharides are assembled in the Golgi apparatus. We provide evidence that (1,3;1,4)-β-D-glucan (mixed-linkage glucan [MLG]) does not conform to this paradigm. We show in various grass (Poaceae) species that MLG-specific antibody labeling is present in the wall but absent over Golgi, suggesting it is assembled at the PM. Antibodies to the MLG synthases, cellulose synthase-like F6 (CSLF6) and CSLH1, located CSLF6 to the endoplasmic reticulum, Golgi, secretory vesicles, and the PM and CSLH1 to the same locations apart from the PM. This pattern was recreated upon expression of VENUS-tagged barley (Hordeum vulgare) CSLF6 and CSLH1 in Nicotiana benthamiana leaves and, consistent with our biochemical analyses of native grass tissues, shown to be catalytically active with CSLF6 and CSLH1 in PM-enriched and PM-depleted membrane fractions, respectively. These data support a PM location for the synthesis of MLG by CSLF6, the predominant enzymatically active isoform. A model is proposed to guide future experimental approaches to dissect the molecular mechanism(s) of MLG assembly.
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Affiliation(s)
- Sarah M Wilson
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Yin Ying Ho
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Edwin R Lampugnani
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Allison M L Van de Meene
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Melissa P Bain
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Victoria 3010, Australia
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Thoma R, Chandler JW. Polarity in the early floral meristem of Arabidopsis. PLANT SIGNALING & BEHAVIOR 2015; 10:e992733. [PMID: 25806573 PMCID: PMC4622712 DOI: 10.4161/15592324.2014.992733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 05/30/2023]
Abstract
The diversity of angiosperm flowers depends on organ meristy and position. However, the signaling pathways that establish polarity and positional information remain largely unelucidated. Use of the founder-cell marker DORNRÖSCHEN-LIKE (DRNL) in Arabidopsis has recently highlighted the importance of the abaxial-adaxial axis for early floral development. We have extended the use of DRNL::GFP to further characterize floral organogenesis in genotypes that are altered in floral organ meristy or position, including ettin (ett-3) and blade-on-petiole (bop)1-11 bop2-4 double mutants. The creation of supernumery sepals by the splitting of sepal founder-cell populations along an ab-/adaxial axis strengthens the importance of the ab-/adaxial developmental axis in early floral meristem development. Furthermore, we confirm the dependency of the wildtype sequence of sepal initiation on bract suppression and demonstrate that supernumery stamens derive from the imprecise resolution of a ring of DRNL expression. Expression of DRNL in apetala1 (ap1-1) and ap2-8 mutants reflect the altered whorl structure and show that these homeotic genes function upstream of DRNL. Analyzing the dynamism of early floral meristem ontogeny at a fine temporal and spatial resolution in Arabidopsis can reveal mechanisms of organogenesis and is applicable to other species with differing floral body plans in a comparative evolutionary context.
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Affiliation(s)
- Rahere Thoma
- Institute of Developmental Biology; Cologne Biocenter; University of Cologne; Cologne, Germany
| | - John William Chandler
- Institute of Developmental Biology; Cologne Biocenter; University of Cologne; Cologne, Germany
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Hepworth SR, Pautot VA. Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1052. [PMID: 26697027 PMCID: PMC4673312 DOI: 10.3389/fpls.2015.01052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/12/2015] [Indexed: 05/04/2023]
Abstract
The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.
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Affiliation(s)
- Shelley R. Hepworth
- Department of Biology, Institute of Biochemistry, Carleton University, OttawaON, Canada
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
| | - Véronique A. Pautot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
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Wang XH, Li QT, Chen HW, Zhang WK, Ma B, Chen SY, Zhang JS. Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:339. [PMID: 25465615 PMCID: PMC4267404 DOI: 10.1186/s12870-014-0339-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/18/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Trihelix transcription factor family is plant-specific and plays important roles in developmental processes. However, their function in abiotic stress response is largely unclear. RESULTS We studied one member GT-4 from Arabidopsis in relation to salt stress response. GT-4 expression is induced by salt stress and GT-4 protein is localized in nucleus and cytoplasm. GT-4 acts as a transcriptional activator and its C-terminal end is the activation domain. The protein can bind to the cis-elements GT-3 box, GT-3b box and MRE4. GT-4 confers enhanced salt tolerance in Arabidopsis likely through direct binding to the promoter and activation of Cor15A, in addition to possible regulation of other relevant genes. The gt-4 mutant shows salt sensitivity. TEM2, a member of AP2/ERF family was identified to interact with GT-4 in yeast two-hybrid, BiFC and Co-IP assays. Loss-of-function of TEM2 exerts no significant difference on salt tolerance or Cor15A expression in Arabidopsis. However, double mutant gt-4/tem2 shows greater sensitivity to salt stress and lower transcript level of Cor15A than gt-4 single mutant. GT-4 plus TEM2 can synergistically increase the promoter activity of Cor15A. CONCLUSIONS GT-4 interacts with TEM2 and then co-regulates the salt responsive gene Cor15A to improve salt stress tolerance.
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Affiliation(s)
- Xiao-Hong Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hao-Wei Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Biao Ma
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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Busch A, Horn S, Zachgo S. Differential transcriptome analysis reveals insight into monosymmetric corolla development of the crucifer Iberis amara. BMC PLANT BIOLOGY 2014; 14:285. [PMID: 25407089 PMCID: PMC4245847 DOI: 10.1186/s12870-014-0285-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/14/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND In the co-evolution between insects and plants, the establishment of floral monosymmetry was an important step in angiosperm development as it facilitated the interaction with insect pollinators and, by that, likely enhanced angiosperm diversification. In Antirrhinum majus, the TCP transcription factor CYCLOIDEA is the molecular key regulator driving the formation of floral monosymmetry. Although most Brassicaceae form a polysymmetric corolla, six genera develop monosymmetric flowers with two petal pairs of unequal size. In the monosymmetric crucifer Iberis amara, formation of the different petal pairs coincides with a stronger expression of the CYC-homolog IaTCP1 in the small, adaxial petals. RESULTS In this study, RNA-Seq was employed to reconstruct the petal transcriptome of the non-model species Iberis amara. About 9 Gb of sequence data was generated, processed and re-assembled into 18,139 likely Iberis unigenes, from which 15,983 showed high sequence homology to Arabidopsis proteins. The transcriptome gives detailed insight into the molecular mechanisms governing late petal development. In addition, it was used as a scaffold to detect genes differentially expressed between the small, adaxial and the large, abaxial petals in order to understand the molecular mechanisms driving unequal petal growth. Far more genes are expressed in adaxial compared to abaxial petals implying that IaTCP1 activates more genes than it represses. Amongst all genes upregulated in adaxial petals, a significantly enhanced proportion is associated with cell wall modification and cell-cell signalling processes. Furthermore, microarrays were used to detect and compare quantitative differences in TCP target genes in transgenic Arabidopsis plants ectopically expressing different TCP transcription factors. CONCLUSIONS The increased occurrences of genes implicated in cell wall modification and signalling implies that unequal petal growth is achieved through an earlier stop of the cell proliferation phase in the small, adaxial petals, followed by the onset of cell expansion. This process, which forms the monosymmetric corolla of Iberis amara, is likely driven by the enhanced activity of IaTCP1 in adaxial petals.
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Affiliation(s)
- Andrea Busch
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
| | - Stefanie Horn
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
| | - Sabine Zachgo
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
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Tian C, Zhang X, He J, Yu H, Wang Y, Shi B, Han Y, Wang G, Feng X, Zhang C, Wang J, Qi J, Yu R, Jiao Y. An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation. Mol Syst Biol 2014; 10:755. [PMID: 25358340 PMCID: PMC4299377 DOI: 10.15252/msb.20145470] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/14/2014] [Accepted: 09/24/2014] [Indexed: 12/11/2022] Open
Abstract
Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellular-resolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein-DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process.
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Affiliation(s)
- Caihuan Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
| | - Xiaoni Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China College of Life Sciences, Capital Normal University, Beijing, China
| | - Jun He
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
| | - Haopeng Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
| | - Bihai Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Guoxun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
| | - Cui Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
| | - Jin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Jiyan Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Rong Yu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
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Kaplan-Levy RN, Quon T, O'Brien M, Sappl PG, Smyth DR. Functional domains of the PETAL LOSS protein, a trihelix transcription factor that represses regional growth in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:477-91. [PMID: 24889508 DOI: 10.1111/tpj.12574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/25/2014] [Accepted: 05/27/2014] [Indexed: 05/11/2023]
Abstract
PETAL LOSS (PTL) is a trihelix transcription factor that represses growth, especially between sepal primordia. As one of 30 trihelix proteins in Arabidopsis, it falls in the GT2 clade with duplicated trihelix DNA-binding domains and a long α-helical central domain. PTL orthologs occur in all angiosperm genomes examined except grasses, and sequence comparisons reveal that there are two further short conserved domains at each end. GT2 itself carries two nuclear localization sequences, but PTL has an additional nuclear localization sequence (NLS). We show that PTL can act as a transcriptional activator in yeast and in planta, with the latter tested by two different functional assays. Specific deletions revealed that the activation region is C-terminal. Site-directed mutagenesis of the DNA-binding domains has shown that a conserved tryptophan and two downstream acidic amino acids in the second trihelix, predicted to promote folding, are each required for PTL function. Also, three basic residues in the third helix, near the DNA interaction sites, support its function. PTL was found to dimerize in yeast. This was confirmed and extended by jointly expressing differentially tagged forms of PTL in a transient expression system in Nicotiana benthamiana leaves. Cytoplasmic PTL (with mutant NLS sequences) was carried into the nucleus upon binding with nuclear-localized PTL, providing each partner carried intact central domains. As this 90-amino acid domain is conserved in most trihelix family members, it seems likely that they all function in dimeric form.
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Affiliation(s)
- Ruth N Kaplan-Levy
- School of Biological Sciences, Monash University, Melbourne, 3800, Vic., Australia
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Yamaguchi N, Wu MF, Winter CM, Wagner D. LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. PLANTS 2014; 3:251-65. [PMID: 27135503 PMCID: PMC4844297 DOI: 10.3390/plants3020251] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/06/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022]
Abstract
The plant specific transcription factor LEAFY (LFY) plays a pivotal role in the developmental switch to floral meristem identity in Arabidopsis. Our recent study revealed that LFY additionally acts downstream of AUXIN RESPONSE FACTOR5/MONOPTEROS to promote flower primordium initiation. LFY also promotes initiation of the floral organ and floral organ identity. To further investigate the interplay between LFY and auxin during flower development, we examined the phenotypic consequence of disrupting polar auxin transport in lfy mutants by genetic means. Plants with compromised LFY activity exhibit increased sensitivity to disruption of polar auxin transport. Compromised polar auxin transport activity in the lfy mutant background resulted in formation of fewer floral organs, abnormal gynoecium development, and fused sepals. In agreement with these observations, expression of the auxin response reporter DR5rev::GFP as well as of the direct LFY target CUP-SHAPED COTYLEDON2 were altered in lfy mutant flowers. We also uncovered reduced expression of ETTIN, a regulator of gynoecium development and a direct LFY target. Our results suggest that LFY and polar auxin transport coordinately modulate flower development by regulating genes required for elaboration of the floral organs.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Cara M Winter
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Takeda S, Noguchi M, Hamamura Y, Higashiyama T. Spatial distribution of the RABBIT EARS protein and effects of its ectopic expression in Arabidopsis thaliana flowers. PLANTA 2014; 239:707-715. [PMID: 24366683 DOI: 10.1007/s00425-013-2010-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
In many flowering plants, flowers consist of two peripheral organs, sepals and petals, occurring in outer two whorls, and two inner reproductive organs, stamens and carpels. These organs are arranged in a concentric pattern in a floral meristem, and the organ identity is established by the combined action of floral homeotic genes expressed along the whorls. Floral organ primordia arise at fixed positions in the floral meristem within each whorl. The RABBIT EARS (RBE) gene is transcribed in the petal precursor cells and primordia, and regulates petal initiation and early growth in Arabidopsis thaliana. We investigated the spatial and temporal expression pattern of a RBE protein fused to the green fluorescent protein (GFP). Expression of the GFP:RBE fusion gene under the RBE cis-regulatory genomic fragment rescues the rbe petal defects, indicating that the fusion protein is functional. The GFP signal is located to the cells where RBE is transcribed, suggesting that RBE function is cell-autonomous. Ectopic expression of GFP:RBE under the APETALA1 promoter causes the homeotic conversion of floral organs, resulting in sterile flowers. In these plants, the class B homeotic genes APETALA3 and PISTILLATA are down-regulated, suggesting that the restriction of the RBE expression to the petal precursor cells is crucial for flower development.
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Affiliation(s)
- Seiji Takeda
- Cell and Genome Biology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kitaina-Yazuma Oji 74, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan,
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Žádníková P, Simon R. How boundaries control plant development. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:116-25. [PMID: 24507503 DOI: 10.1016/j.pbi.2013.11.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/19/2013] [Accepted: 11/19/2013] [Indexed: 05/05/2023]
Abstract
Continuous growth and organ development from the shoot apical meristem (SAM) requires a precise coordination of stem cell proliferation, commitment of stem cell descendants to diverse differentiation pathways and establishment of morphological meristem-to-organ boundaries. These complex biological processes require extensive integration of several components of cell-to-cell signaling and gene regulatory networks whose coordinated actions have an impact on cell division and growth. Here we review the current knowledge of gene networks involved in organogenesis from the SAM in higher plants. We focus on recent advances to show how the interaction between transcriptional regulators, hormonal crosstalk and physical stress regulates the establishment and maintenance of meristem-to-organ boundaries. Continuous growth and organ development from the shoot apical meristem (SAM) requires a precise coordination of stem cell proliferation, commitment of stem cell descendants to diverse differentiation pathways and establishment of morphological meristem-to-organ boundaries. These complex biological processes require extensive integration of several components of cell-to-cell signaling and gene regulatory networks whose coordinated actions have an impact on cell division and growth. Here we review the current knowledge of gene networks involved in organogenesis from the SAM in higher plants. We focus on recent advances to show how the interaction between transcriptional regulators, hormonal crosstalk and physical stress regulates the establishment and maintenance of meristem-to-organ boundaries.
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Affiliation(s)
- Petra Žádníková
- Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Rüdiger Simon
- Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
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45
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Wellmer F, Bowman JL, Davies B, Ferrándiz C, Fletcher JC, Franks RG, Graciet E, Gregis V, Ito T, Jack TP, Jiao Y, Kater MM, Ma H, Meyerowitz EM, Prunet N, Riechmann JL. Flower development: open questions and future directions. Methods Mol Biol 2014; 1110:103-24. [PMID: 24395254 DOI: 10.1007/978-1-4614-9408-9_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Almost three decades of genetic and molecular analyses have resulted in detailed insights into many of the processes that take place during flower development and in the identification of a large number of key regulatory genes that control these processes. Despite this impressive progress, many questions about how flower development is controlled in different angiosperm species remain unanswered. In this chapter, we discuss some of these open questions and the experimental strategies with which they could be addressed. Specifically, we focus on the areas of floral meristem development and patterning, floral organ specification and differentiation, as well as on the molecular mechanisms underlying the evolutionary changes that have led to the astounding variations in flower size and architecture among extant and extinct angiosperms.
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Affiliation(s)
- Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland,
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Prunet N, Jack TP. Flower development in Arabidopsis: there is more to it than learning your ABCs. Methods Mol Biol 2014; 1110:3-33. [PMID: 24395250 DOI: 10.1007/978-1-4614-9408-9_1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of Arabidopsis flower development began in the early 1980s with the initial description of several mutants including apetala1, apetala2, and agamous that altered floral organ identity (Koornneef and van der Veen, Theor Appl Genet 58:257-263, 1980; Koornneef et al., J Hered 74:265-272, 1983). By the end of the 1980s, these mutants were receiving more focused attention to determine precisely how they affected flower development (Komaki et al., Development 104:195-203, 1988; Bowman et al., Plant Cell 1:37-52, 1989). In the last quarter century, impressive progress has been made in characterizing the gene products and molecular mechanisms that control the key events in flower development. In this review, we briefly summarize the highlights of work from the past 25 years but focus on advances in the field in the last several years.
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Affiliation(s)
- Nathanaël Prunet
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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Sauret-Güeto S, Schiessl K, Bangham A, Sablowski R, Coen E. JAGGED controls Arabidopsis petal growth and shape by interacting with a divergent polarity field. PLoS Biol 2013; 11:e1001550. [PMID: 23653565 PMCID: PMC3641185 DOI: 10.1371/journal.pbio.1001550] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/19/2013] [Indexed: 11/19/2022] Open
Abstract
A flowering plant generates many different organs such as leaves, petals, and stamens, each with a particular function and shape. These types of organ are thought to represent variations on a common underlying developmental program. However, it is unclear how this program is modulated under different selective constraints to generate the diversity of forms observed. Here we address this problem by analysing the development of Arabidopsis petals and comparing the results to models of leaf development. We show that petal development involves a divergent polarity field with growth rates perpendicular to local polarity increasing towards the distal end of the petal. The hypothesis is supported by the observed pattern of clones induced at various stages of development and by analysis of polarity markers, which show a divergent pattern. We also show that JAGGED (JAG) has a key role in promoting distal enhancement of growth rates and influences the extent of the divergent polarity field. Furthermore, we reveal links between the polarity field and auxin function: auxin-responsive markers such as DR5 have a broader distribution along the distal petal margin, consistent with the broad distal organiser of polarity, and PETAL LOSS (PTL), which has been implicated in the control of auxin dynamics during petal initiation, is directly repressed by JAG. By comparing these results with those from studies on leaf development, we show how simple modifications of an underlying developmental system may generate distinct forms, providing flexibility for the evolution of different organ functions.
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Affiliation(s)
- Susanna Sauret-Güeto
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Katharina Schiessl
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Andrew Bangham
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Robert Sablowski
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Van Landeghem S, De Bodt S, Drebert ZJ, Inzé D, Van de Peer Y. The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. THE PLANT CELL 2013; 25:794-807. [PMID: 23532071 PMCID: PMC3634689 DOI: 10.1105/tpc.112.108753] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/27/2013] [Accepted: 03/08/2013] [Indexed: 05/21/2023]
Abstract
Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.
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Affiliation(s)
- Sofie Van Landeghem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Zuzanna J. Drebert
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Lampugnani ER, Kilinc A, Smyth DR. Auxin controls petal initiation in Arabidopsis. Development 2013; 140:185-94. [DOI: 10.1242/dev.084582] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Floral organs are usually arranged in concentric whorls of sepals, petals, stamens and carpels. How founder cells of these organs are specified is unknown. In Arabidopsis, the PETAL LOSS (PTL) transcription factor functions in the sepal whorl, where it restricts the size of the inter-sepal zone. Genetic evidence suggests that PTL acts to support a petal initiation signal active in the adjacent whorl. Here we aimed to characterise the signal by identifying enhancers that disrupt initiation of the remaining petals in ptl mutants. One such enhancer encodes the auxin influx protein AUX1. We have established that auxin is a direct and mobile petal initiation signal by promoting its biosynthesis in the inter-sepal zone in ptl mutant plants and restoring nearby petal initiation. Consistent with this, loss of PTL function disrupts DR5 expression, an auxin-inducible indicator of petal-initiation sites. The signalling network was extended by demonstrating that: (1) loss of RABBIT EARS (RBE) function apparently disrupts the same auxin influx process as PTL; (2) the action of AUX1 is supported by AXR4, its upstream partner in auxin influx; (3) polar auxin transport, which is controlled by PINOID (PID) and PIN-FORMED1 (PIN1), functions downstream of PTL; and (4) the action of pmd-1d, a dominant modifier of the ptl mutant phenotype, is dependent on auxin transport. Thus, loss of PTL function disrupts auxin dynamics, allowing the role of auxin in promoting petal initiation to be revealed.
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Affiliation(s)
- Edwin R. Lampugnani
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Aydin Kilinc
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - David R. Smyth
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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Luo JL, Zhao N, Lu CM. [Plant Trihelix transcription factors family]. YI CHUAN = HEREDITAS 2012; 34:1551-60. [PMID: 23262102 DOI: 10.3724/sp.j.1005.2012.01551] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Trihelix transcription factor family has raised great concerns only in recent years. It was named after its conserved DNA binding domain containing three tandem helix (helix-loop-helix-loop-helix), which could bind specifically with GT element, a light-responsive DNA element. So, this family is also known as GT factors. At the early stage of study, the knowledge of this family was only confined to their functions in regulation of light-responsive genes. However, recent researches indicated that Trihelix family also plays important roles in different growth and development processes involving flowers, stomata, trichomes, embryos, and seeds, as well as roles in response to abiotic and biotic stresses. This review mainly focused on the structural characteristics, classification, and the latest functional research progresses on the Trihelix family.
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Affiliation(s)
- Jun-Ling Luo
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
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