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Bertran Garcia de Olalla E, Cerise M, Rodríguez-Maroto G, Casanova-Ferrer P, Vayssières A, Severing E, López Sampere Y, Wang K, Schäfer S, Formosa-Jordan P, Coupland G. Coordination of shoot apical meristem shape and identity by APETALA2 during floral transition in Arabidopsis. Nat Commun 2024; 15:6930. [PMID: 39138172 PMCID: PMC11322546 DOI: 10.1038/s41467-024-51341-6] [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: 09/03/2023] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Plants flower in response to environmental signals. These signals change the shape and developmental identity of the shoot apical meristem (SAM), causing it to form flowers and inflorescences. We show that the increases in SAM width and height during floral transition correlate with changes in size of the central zone (CZ), defined by CLAVATA3 expression, and involve a transient increase in the height of the organizing center (OC), defined by WUSCHEL expression. The APETALA2 (AP2) transcription factor is required for the rapid increases in SAM height and width, by maintaining the width of the OC and increasing the height and width of the CZ. AP2 expression is repressed in the SAM at the end of floral transition, and extending the duration of its expression increases SAM width. Transcriptional repression by SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) represents one of the mechanisms reducing AP2 expression during floral transition. Moreover, AP2 represses SOC1 transcription, and we find that reciprocal repression of SOC1 and AP2 contributes to synchronizing precise changes in meristem shape with floral transition.
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Affiliation(s)
- Enric Bertran Garcia de Olalla
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, Lyon, France
| | - Martina Cerise
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gabriel Rodríguez-Maroto
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pau Casanova-Ferrer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alice Vayssières
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Edouard Severing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 4, PB, Wageningen, The Netherlands
| | - Yaiza López Sampere
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kang Wang
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sabine Schäfer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pau Formosa-Jordan
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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Long Y, Zeng J, Liu X, Wang Z, Tong Q, Zhou R, Liu X. Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties. 3 Biotech 2024; 14:174. [PMID: 38855147 PMCID: PMC11153451 DOI: 10.1007/s13205-024-04019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024] Open
Abstract
Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04019-1.
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Affiliation(s)
- YuQing Long
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - Juan Zeng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - XiaoRong Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - ZhiHui Wang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - QiaoZhen Tong
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - RiBao Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - XiangDan Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
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3
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Wu J, Li P, Zhu D, Ma H, Li M, Lai Y, Peng Y, Li H, Li S, Wei J, Bian X, Rahman A, Wu S. SlCRCa is a key D-class gene controlling ovule fate determination in tomato. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1966-1980. [PMID: 38561972 PMCID: PMC11182579 DOI: 10.1111/pbi.14317] [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: 08/25/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 04/04/2024]
Abstract
Cell fate determination and primordium initiation on the placental surface are two key events for ovule formation in seed plants, which directly affect ovule density and seed yield. Despite ovules form in the marginal meristematic tissues of the carpels, angiosperm carpels evolved after the ovules. It is not clear how the development of the ovules and carpels is coordinated in angiosperms. In this study, we identify the S. lycopersicum CRABS CLAW (CRC) homologue SlCRCa as an essential determinant of ovule fate. We find that SlCRCa is not only expressed in the placental surface and ovule primordia but also functions as a D-class gene to block carpel fate and promote ovule fate in the placental surface. Loss of function of SlCRCa causes homeotic transformation of the ovules to carpels. In addition, we find low levels of the S. lycopersicum AINTEGUMENTA (ANT) homologue (SlANT2) favour the ovule initiation, whereas high levels of SlANT2 promote placental carpelization. SlCRCa forms heterodimer with tomato INNER NO OUTER (INO) and AGAMOUS (AG) orthologues, SlINO and TOMATO AGAMOUS1 (TAG1), to repress SlANT2 expression during the ovule initiation. Our study confirms that angiosperm basal ovule cells indeed retain certain carpel properties and provides mechanistic insights into the ovule initiation.
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Affiliation(s)
- Junqing Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Pengxue Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Danyang Zhu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Haochuan Ma
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Meng Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yixuan Lai
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yuxin Peng
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Haixiao Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Shuang Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Jinbo Wei
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Xinxin Bian
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Abidur Rahman
- Department of Plant Bio‐Sciences, Faculty of AgricultureIwate UniversityMoriokaJapan
- United Graduate School of Agricultural SciencesIwate UniversityMoriokaJapan
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhouChina
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Yang Q, Luo L, Jiao X, Chen X, Liu Y, Liu Z. APETALA2-like Floral Homeotic Protein Up-Regulating FaesAP1_2 Gene Involved in Floral Development in Long-Homostyle Common Buckwheat. Int J Mol Sci 2024; 25:7193. [PMID: 39000299 PMCID: PMC11241573 DOI: 10.3390/ijms25137193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
In the rosid species Arabidopsis thaliana, the AP2-type AP2 transcription factor (TF) is required for specifying the sepals and petals identities and confers a major A-function to antagonize the C-function in the outer floral whorls. In the asterid species Petunia, the AP2-type ROB TFs are required for perianth and pistil development, as well as repressing the B-function together with TOE-type TF BEN. In Long-homostyle (LH) Fagopyrum esculentum, VIGS-silencing showed that FaesAP2 is mainly involved in controlling filament and style length, but FaesTOE is mainly involved in regulating filament length and pollen grain development. Both FaesAP2 (AP2-type) and FaesTOE (TOE-type) are redundantly involved in style and/or filament length determination instead of perianth development. However, neither FaesAP2 nor FaesTOE could directly repress the B and/or C class genes in common buckwheat. Moreover, the FaesAP1_2 silenced flower showed tepal numbers, and filament length decreased obviously. Interestingly, yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) further suggested that FaesTOE directly up-regulates FaesAP1_2 to be involved in filament length determination in LH common buckwheat. Moreover, the knockdown of FaesTOE expression could result in expression down-regulation of the directly target FaesAP1_2 in the FaesTOE-silenced LH plants. Our findings uncover a stamen development pathway in common buckwheat and offer deeper insight into the functional evolution of AP2 orthologs in the early-diverging core eudicots.
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Affiliation(s)
| | | | | | | | | | - Zhixiong Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China; (Q.Y.); (L.L.); (X.J.); (X.C.); (Y.L.)
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5
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Yang T, Wang Y, Li Y, Liang S, Yang Y, Huang Z, Li Y, Gao J, Ma N, Zhou X. The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2965-2981. [PMID: 38452221 PMCID: PMC11103112 DOI: 10.1093/jxb/erae099] [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: 07/13/2023] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.
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Affiliation(s)
- Tuo Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yuqi Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Shangyi Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yunyao Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Ziwei Huang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yonghong Li
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xiaofeng Zhou
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
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Jiang W, Yin Q, Liu J, Su X, Han X, Li Q, Zhang J, Pang Y. The APETALA2-MYBL2 module represses proanthocyanidin biosynthesis by affecting formation of the MBW complex in seeds of Arabidopsis thaliana. PLANT COMMUNICATIONS 2024; 5:100777. [PMID: 38053331 PMCID: PMC10943577 DOI: 10.1016/j.xplc.2023.100777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/02/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023]
Abstract
Proanthocyanidins (PAs) are the second most abundant plant phenolic natural products. PA biosynthesis is regulated by the well-documented MYB/bHLH/WD40 (MBW) complex, but how this complex itself is regulated remains ill defined. Here, in situ hybridization and β-glucuronidase staining show that APETALA2 (AP2), a well-defined regulator of flower and seed development, is strongly expressed in the seed coat endothelium, where PAs accumulate. AP2 negatively regulates PA content and expression levels of key PA pathway genes. AP2 activates MYBL2 transcription and interacts with MYBL2, a key suppressor of the PA pathway. AP2 exerts its function by directly binding to the AT-rich motifs near the promoter region of MYBL2. Molecular and biochemical analyses revealed that AP2 forms AP2-MYBL2-TT8/EGL3 complexes, disrupting the MBW complex and thereby repressing expression of ANR, TT12, TT19, and AHA10. Genetic analyses revealed that AP2 functions upstream of MYBL2, TT2, and TT8 in PA regulation. Our work reveals a new role of AP2 as a key regulator of PA biosynthesis in Arabidopsis. Overall, this study sheds new light on the comprehensive regulation network of PA biosynthesis as well as the dual regulatory roles of AP2 in seed development and accumulation of major secondary metabolites in Arabidopsis.
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Affiliation(s)
- Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qinggang Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinyue Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaojia Su
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoyan Han
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qian Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jin Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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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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Wang X, Liu Z, Bai J, Sun S, Song J, Li R, Cui X. Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching. THE PLANT CELL 2023; 35:2062-2078. [PMID: 36881857 PMCID: PMC10226558 DOI: 10.1093/plcell/koad065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/30/2023]
Abstract
Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.
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Affiliation(s)
- Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
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Sun S, Wang X, Liu Z, Bai J, Song J, Li R, Cui X. Tomato APETALA2 family member SlTOE1 regulates inflorescence branching by repressing SISTER OF TM3. PLANT PHYSIOLOGY 2023; 192:293-306. [PMID: 36747310 PMCID: PMC10152655 DOI: 10.1093/plphys/kiad075] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 05/03/2023]
Abstract
Inflorescence architecture directly impacts yield potential in most crops. As a model of sympodial plants, tomato (Solanum lycopersicum) inflorescence exhibits highly structural plasticity. However, the genetic regulatory network of inflorescence architecture in tomato remains unclear. Here, we investigated a modulator of inflorescence branching in tomato, TARGET OF EAT1 (SlTOE1), an APETALA2 (AP2) family member found to be predominantly expressed in the floral meristem (FM) of tomato. sltoe1 knockout mutants displayed highly branched inflorescences and defective floral organs. Transcriptome analysis revealed that SISTER OF TM3 (STM3) and certain floral development-related genes were upregulated in the flower meristem of sltoe1. SlTOE1 could directly bind the promoters of STM3 and Tomato MADS-box gene 3 (TM3) to repress their transcription. Simultaneous mutation of STM3 and TM3 partially restored the inflorescence branching of the sltoe1cr mutants, suggesting that SlTOE1 regulates inflorescence development, at least in part through an SlTOE1STM3/TM3 module. Genetic analysis showed that SlTOE1 and ENHANCER OF JOINTLESS 2 (EJ2) additively regulate tomato inflorescence branching; their double mutants showed more extensive inflorescence branching. Our findings uncover a pathway controlling tomato inflorescence branching and offer deeper insight into the functions of AP2 subfamily members.
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Affiliation(s)
- Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, China Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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10
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Meng H, Chen Y, Li T, Shi H, Yu S, Gao Y, Wang Z, Wang X, Zhu JK, Hong Y, Wang Z. APETALA2 is involved in ABA signaling during seed germination. PLANT MOLECULAR BIOLOGY 2023; 112:99-103. [PMID: 37076747 DOI: 10.1007/s11103-023-01349-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
APETALA2 (AP2) is well known for regulating the development of floral organs, ovules, seed coats, and the mass of seeds, but the role of AP2 in seed germination remains unclear. Here, we report that AP2 interacts with ABI5 in nuclear speckles and functions in controlling seed germination. Genetic study showed that the abi5 mutation could restore the ABA-sensitive phenotype of ap2 mutants, supporting that AP2 antagonizes ABI5 in ABA signaling and ABA-mediated inhibition of seed germination. In addition, we observed the interactions of AP2 with SnRK2.2, SnRK2.3, and SnRK2.6 in nuclear speckles, suggesting that AP2 plays a multifaceted role in the ABA signaling pathway. Our findings revealed that the interactions of AP2 with SnRK2s and ABI5 are critical for ABA signaling in control of seed germination.
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Affiliation(s)
- Huiying Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yunjuan Chen
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tingting Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Shuojun Yu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yang Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhiqiang Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xu Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yechun Hong
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhen Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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11
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Wang H, Lu Y, Zhang T, Liu Z, Cao L, Chang Q, Liu Y, Lu X, Yu S, Li H, Jiang J, Liu G, Sederoff HW, Sederoff RR, Zhang Q, Zheng Z. The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion. PLANT PHYSIOLOGY 2023; 191:1122-1137. [PMID: 36494195 PMCID: PMC9922402 DOI: 10.1093/plphys/kiac571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
As essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through bovine serum albumin sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.
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12
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Huang Z, Dinh TT, Luscher E, Li S, Liu X, Won SY, Chen X. Genetic Screens for Floral Mutants in Arabidopsis thaliana: Enhancers and Suppressors. Methods Mol Biol 2023; 2686:131-162. [PMID: 37540357 DOI: 10.1007/978-1-0716-3299-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and morphogenesis. Since the initial studies to identify genes governing processes such as floral organ specification, mutagenesis in sensitized backgrounds has been used to isolate enhancers and suppressors to further probe the molecular basis of floral development. Here, we first describe two commonly employed methods for mutagenesis (using ethyl methanesulfonate (EMS) or T-DNAs as mutagens), and then describe three methods for identifying a mutation that leads to phenotypic alterations: traditional map-based cloning, modified high-efficiency thermal asymmetric interlaced PCR (mhiTAIL-PCR), and deep sequencing in the plant model Arabidopsis thaliana.
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Affiliation(s)
- Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Elizabeth Luscher
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xigang Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - So Youn Won
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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13
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Chahtane H, Lai X, Tichtinsky G, Rieu P, Arnoux-Courseaux M, Cancé C, Marondedze C, Parcy F. Flower Development in Arabidopsis. Methods Mol Biol 2023; 2686:3-38. [PMID: 37540352 DOI: 10.1007/978-1-0716-3299-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.
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Affiliation(s)
- Hicham Chahtane
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Institut de Recherche Pierre Fabre, Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Soual, France
| | - Xuelei Lai
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, China
| | | | - Philippe Rieu
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Coralie Cancé
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
| | - Claudius Marondedze
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Senga, Gweru, Zimbabwe
| | - François Parcy
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France.
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14
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Cirilli M, Rossini L, Chiozzotto R, Baccichet I, Florio FE, Mazzaglia A, Turco S, Bassi D, Gattolin S. Less is more: natural variation disrupting a miR172 gene at the di locus underlies the recessive double-flower trait in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2022; 22:318. [PMID: 35786350 PMCID: PMC9252053 DOI: 10.1186/s12870-022-03691-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND With the domestication of ornamental plants, artificial selective pressure favored the propagation of mutations affecting flower shape, and double-flower varieties are now readily available for many species. In peach two distinct loci control the double-flower phenotype: the dominant Di2 locus, regulated by the deletion of the binding site for miR172 in the euAP2 PETALOSA gene Prupe.6G242400, and the recessive di locus, of which the underlying factor is still unknown. RESULTS Based on its genomic location a candidate gene approach was used to identify genetic variants in a diverse panel of ornamental peach accessions and uncovered three independent mutations in Prupe.2G237700, the gene encoding the transcript for microRNA miR172d: a ~5.0 Kb LTR transposable element and a ~1.2 Kb insertion both positioned upstream of the sequence encoding the pre-miR172d within the transcribed region of Prupe.2G237700, and a ~9.5 Kb deletion encompassing the whole gene sequence. qRT-PCR analysis confirmed that expression of pre-miR172d was abolished in di/di genotypes homozygous for the three variants. CONCLUSIONS Collectively, PETALOSA and the mutations in micro-RNA miR172d identified in this work provide a comprehensive collection of the genetic determinants at the base of the double-flower trait in the peach germplasms.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy.
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Remo Chiozzotto
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Irina Baccichet
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Francesco Elia Florio
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | | | - Silvia Turco
- DAFNE Department - University of Tuscia, 01100, Viterbo, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Stefano Gattolin
- CNR - National Research Council of Italy, Institute of Agricultural Biology and Biotechnology (IBBA), 20133, Milan, Italy.
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15
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Müller-Xing R, Ardiansyah R, Xing Q, Faivre L, Tian J, Wang G, Zheng Y, Wang X, Jing T, de Leau E, Chen S, Chen S, Schubert D, Goodrich J. Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2385-2402. [PMID: 35045165 DOI: 10.1093/jxb/erac013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Polycomb group (PcG) protein-mediated histone methylation (H3K27me3) controls the correct spatiotemporal expression of numerous developmental regulators in Arabidopsis. Epigenetic silencing of the stem cell factor gene WUSCHEL (WUS) in floral meristems (FMs) depends on H3K27me3 deposition by PcG proteins. However, the role of H3K27me3 in silencing of other meristematic regulator and pluripotency genes during FM determinacy has not yet been studied. To this end, we report the genome-wide dynamics of H3K27me3 levels during FM arrest and the consequences of strongly depleted PcG activity on early flower morphogenesis including enlarged and indeterminate FMs. Strong depletion of H3K27me3 levels results in misexpression of the FM identity gene AGL24, which partially causes floral reversion leading to ap1-like flowers and indeterminate FMs ectopically expressing WUS and SHOOT MERISTEMLESS (STM). Loss of STM can rescue supernumerary floral organs and FM indeterminacy in H3K27me3-deficient flowers, indicating that the hyperactivity of the FMs is at least partially a result of ectopic STM expression. Nonetheless, WUS remained essential for the FM activity. Our results demonstrate that PcG proteins promote FM determinacy at multiple levels of the floral gene regulatory network, silencing initially floral regulators such as AGL24 that promotes FM indeterminacy and, subsequently, meristematic pluripotency genes such as WUS and STM during FM arrest.
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Affiliation(s)
- Ralf Müller-Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rhomi Ardiansyah
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Qian Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Léa Faivre
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Jingjing Tian
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Yucai Zheng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Xue Wang
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Tingting Jing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Erica de Leau
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Daniel Schubert
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
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16
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Tariq A, Jabeen Z, Farrakh S, Noreen K, Arshad W, Ahmed H, Haider W. Exploring the genetic potential of Pakistani soybean cultivars through RNA-seq based transcriptome analysis. Mol Biol Rep 2022; 49:2889-2897. [PMID: 35088376 DOI: 10.1007/s11033-021-07104-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Soybean is largely grown and considered among the top oilseed crops. Three Pakistani cultivars, NARC-II (N), Swat-84 (S), and Rawal-I (R) were employed for RNA-Seq based transcriptome analysis to explore their genetic potential and performance in our local environment. METHODS AND RESULTS We grew the plants in glass house at same conditions and sampled leaves for RNA-Seq analysis in triplicate for each variety. We retrieved 2225 differentially expressed genes (DEGs) between S vs R, 2591 DEGs between S vs N, and 1221 DEGs between R vs N cultvars. These genes consist of transcription factors representing Basic Helix-loop Helix, myeloblastosis, ethylene response factors, and WRKY amino acid motif (WRKY) type major families that were up-regulated. KEGG pathway analysis revealed that MAPK, plant hormone signal transduction, and Phenylpropanoid biosynthesis pathways were the most dominant pathways involved in plant defense and growth. Comparative analysis showed that Swat-84 (S) cultivar had better gene expression among these varieties having higher number of DEGs, where mostly genes related to important phenotypic traits were up regulated. CONCLUSIONS This is a pilot study to investigate and functionally characterise the DEG involved in the stress response in the cultivars studied.
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Affiliation(s)
- Arslan Tariq
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zahra Jabeen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kiran Noreen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Waleed Arshad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Haroon Ahmed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Waseem Haider
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
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17
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Tamayo-García R, Narváez-Zapata JA, Ku-González A, Aguilar-Espinosa M, Gutiérrez-Pacheco LC, Rivera-Madrid R. Gene expression analysis during the fruit development in dehiscent and indehiscent Bixa orellana L. accessions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:709-718. [PMID: 35592485 PMCID: PMC9110607 DOI: 10.1007/s12298-022-01180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/25/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Fruit morphology and dehiscence-related genes were analyzed in dehiscent N4P and dehiscent P12 Bixa orellana accessions. Fruit architecture (exocarp and pericarp cells, trichomes, vascular bundles, vesicles, and bixin cells) documented by Scanning electron microscopy (SEM) morphology, blue toluidine stain, and phloroglucinol and hydrochloric acid (PHCL) stain was similar in both accessions. Although, the dehiscent zone (DZ) was higher in the indehiscent P12 B. orellana accession, lignification values, obtained by phloroglucinol and hydrochloric acid stain, within the DZ remain was similar in both variants being lower at 34 days after floral anthesis in the dehiscent N4P B. orellana accession. Dehiscence-related genes APETALA (AP2), SHATTERPROOF (SHP), and SPATULA (SPT) were identified on the reported B. orellana transcriptome (SRX1117606). Real-time quantitative polymerase chain reaction primers build by using these genes allow observing a differential expression during six fruit development stages. In both B. orellana accessions, the AP2 transcripts have a reduced expression, whereas the SHP transcripts were significantly higher during the first two days and ten days of development. SPT transcripts show an expression differential between both accessions being significantly higher in the dehiscent N4P, peaking with 9.66% at 42 days after floral anthesis (DAFA) of development. SPT transcription profile suggested that this gene has an important role during the fruit opening in the dehiscent N4P B. orellana accession. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01180-w.
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Affiliation(s)
- R. Tamayo-García
- Unidad de Bioquímica Y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 # 130, Chuburná de Hidalgo, CP 97205 Mérida, Yucatán Mexico
| | - J. A. Narváez-Zapata
- Instituto Politécnico Nacional-Centro de Biotecnología Genómica, Blvd Del Maestro esq. Elias Piña, 88710 Reynosa, Tamaulipas Mexico
| | - A. Ku-González
- Unidad de Bioquímica Y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 # 130, Chuburná de Hidalgo, CP 97205 Mérida, Yucatán Mexico
| | - M. Aguilar-Espinosa
- Unidad de Bioquímica Y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 # 130, Chuburná de Hidalgo, CP 97205 Mérida, Yucatán Mexico
| | - L. C. Gutiérrez-Pacheco
- Unidad de Bioquímica Y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 # 130, Chuburná de Hidalgo, CP 97205 Mérida, Yucatán Mexico
| | - R. Rivera-Madrid
- Unidad de Bioquímica Y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 # 130, Chuburná de Hidalgo, CP 97205 Mérida, Yucatán Mexico
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18
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Transcriptomic Analysis of Sex-Associated DEGs in Female and Male Flowers of Kiwifruit (Actinidia deliciosa [A. Chev] C. F. Liang & A. R. Ferguson). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kiwifruit (Actinidia deliciosa [A. Chev.], C.V. Liang & A. R. Ferguson, 1984) is a perennial plant, with morphologically hermaphroditic and functionally dioecious flowers. Fruits of this species are berries of great commercial and nutritional importance. Nevertheless, few studies have analyzed the molecular mechanisms involved in sexual differentiation in this species. To determine these mechanisms, we performed RNA-seq in floral tissue at stage 60 on the BBCH scale in cultivar ‘Hayward’ (H, female) and a seedling from ‘Green Light’ × ‘Tomuri’ (G × T, male). From these analyses, we obtained expression profiles of 24,888 (H) and 27,027 (G × T) genes, of which 6413 showed differential transcript abundance. Genetic ontology (GO) and KEGG analysis revealed activation of pathways associated with the translation of hormonal signals, plant-pathogen interaction, metabolism of hormones, sugars, and nucleotides. The analysis of the protein-protein interaction network showed that the genes ERL1, AG, AGL8, LFY, WUS, AP2, WRKY, and CO, are crucial elements in the regulation of the hormonal response for the formation and development of anatomical reproductive structures and gametophytes. On the other hand, genes encoding four Putative S-adenosyl-L-methionine-dependent methyltransferases (Achn201401, Achn281971, Achn047771 and Achn231981) were identified, which were up-regulated mainly in the male flowers. Moreover, the expression profiles of 15 selected genes through RT-qPCR were consistent with the results of RNA-seq. Finally, this work provides gene expression-based interactions between transcription factors and effector genes from hormonal signaling pathways, development of floral organs, biological and metabolic processes or even epigenetic mechanisms which could be involved in the kiwi sex-determination. Thus, in order to decode the nature of these interactions, it could be helpful to propose new models of flower development and sex determination in the Actinidia genus.
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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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20
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Zhao J, Gong P, Liu H, Zhang M, He C. Multiple and integrated functions of floral C-class MADS-box genes in flower and fruit development of Physalis floridana. PLANT MOLECULAR BIOLOGY 2021; 107:101-116. [PMID: 34424500 DOI: 10.1007/s11103-021-01182-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
This work reveals potentially multiple and integrated roles in flower and fruit development of floral C-class MADS-box genes in Physalis. The Physalis fruit features a morphological novelty, the Chinese lantern. Floral C-class MADS-domain AGAMOUS-like (AG-like) proteins can interact with the identified regulators of this novel structure. However, the developmental role of the floral C-class genes is unknown in Physalis. Here, we characterized two AG-like genes from Physalis floridana, designated PFAG1 and PFAG2. The two paralogous genes shared around 61.0% of sequence identity and had similar expression domains, with different expression levels in the floral and berry development. However, the genes had distinct expression patterns in leaf and calyx development. Protein-protein interaction analyses revealed that PFAG1 and PFAG2 could commonly or specifically dimerize with certain floral MADS-domain proteins as well as non-MADS-domain proteins involved in various floral developmental processes. Gene downregulation analyses demonstrated that PFAG1 may repress PFAG2, but PFAG2 did not affect PFAG1. Downregulating PFAG1 led to incomplete floral homeotic variation in the stamens and carpels, and alteration of petal coloration pattern, while downregulating PFAG2 did not result in any floral homeotic variation. PFAG1 affected pollen maturation, while PFAG2 affected female fertility. However, simultaneously downregulating PFAG1 and PFAG2 caused loss of the complete C-function, indicating that the two PFAG genes interact to determine the identity and functionality of androecia and gynoecia organs. Their potential roles in regulating fruit size and the Chinese lantern are also discussed. Our results reveal functional divergence of floral C-class MADS-box genes in Physalis, demonstrating that they may play multiple and integrated roles in flower and fruit development.
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Affiliation(s)
- Jing Zhao
- Life Science College, Northwest Normal University, Lanzhou, 730070, Gansu, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hongyan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingshu Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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21
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Fernández-Piñán S, Boher P, Soler M, Figueras M, Serra O. Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation. Sci Rep 2021; 11:12053. [PMID: 34103550 PMCID: PMC8187341 DOI: 10.1038/s41598-021-90938-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/19/2021] [Indexed: 02/05/2023] Open
Abstract
The phellogen or cork cambium stem cells that divide periclinally and outwardly specify phellem or cork. Despite the vital importance of phellem in protecting the radially-growing plant organs and wounded tissues, practically only the suberin biosynthetic process has been studied molecularly so far. Since cork oak (Quercus suber) phellogen is seasonally activated and its proliferation and specification to phellem cells is a continuous developmental process, the differentially expressed genes during the cork seasonal growth served us to identify molecular processes embracing from phellogen to mature differentiated phellem cell. At the beginning of cork growth (April), cell cycle regulation, meristem proliferation and maintenance and processes triggering cell differentiation were upregulated, showing an enrichment of phellogenic cells from which phellem cells are specified. Instead, at maximum (June) and advanced (July) cork growth, metabolic processes paralleling the phellem cell chemical composition, such as the biosynthesis of suberin, lignin, triterpenes and soluble aromatic compounds, were upregulated. Particularly in July, polysaccharides- and lignin-related secondary cell wall processes presented a maximal expression, indicating a cell wall reinforcement in the later stages of cork formation, presumably related with the initiation of latecork development. The putative function of relevant genes identified are discussed in the context of phellem ontogeny.
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Affiliation(s)
- Sandra Fernández-Piñán
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Pau Boher
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Marçal Soler
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Mercè Figueras
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Olga Serra
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
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22
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Then There Were Plenty-Ring Meristems Giving Rise to Many Stamen Whorls. PLANTS 2021; 10:plants10061140. [PMID: 34205172 PMCID: PMC8228060 DOI: 10.3390/plants10061140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022]
Abstract
Floral meristems are dynamic systems that generate floral organ primordia at their flanks and, in most species, terminate while giving rise to the gynoecium primordia. However, we find species with floral meristems that generate additional ring meristems repeatedly throughout angiosperm history. Ring meristems produce only stamen primordia, resulting in polystemous flowers (having stamen numbers more than double that of petals or sepals), and act independently of the floral meristem activity. Most of our knowledge on floral meristem regulation is derived from molecular genetic studies of Arabidopsis thaliana, a species with a fixed number of floral organs and, as such of only limited value for understanding ring meristem function, regulation, and ecological value. This review provides an overview of the main molecular players regulating floral meristem activity in A. thaliana and summarizes our knowledge of ring primordia morphology and occurrence in dicots. Our work provides a first step toward understanding the significance and molecular genetics of ring meristem regulation and evolution.
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23
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MIR172d Is Required for Floral Organ Identity and Number in Tomato. Int J Mol Sci 2021; 22:ijms22094659. [PMID: 33925088 PMCID: PMC8124722 DOI: 10.3390/ijms22094659] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/29/2023] Open
Abstract
MicroRNA172 (miR172) functions as a central regulator of flowering time and flower development by post-transcriptional repression of APETALA2-LIKE transcription factors. In the model crop Solanum lycopersicum (tomato), the miR172 family is still poorly annotated and information about the functions of specific members is lacking. Here, de-novo prediction of tomato miR172 coding loci identified seven genes (SlMIR172a-g), that code for four unique species of miR172 (sly-miR172). During reproductive development, sly-miR172s are differentially expressed, with sly-miR172c and sly-miR172d being the most abundant members in developing flowers, and are predicted to guide the cleavage of eight APETALA2-LIKE transcription factors. By CRISPR-Cas9 co-targeting of SlMIR172c and SlMIR172d we have generated a battery of loss-of-function and hypomorphic mutants (slmir172c-dCR). The slmir172c-dCR plants developed normal shoot but their flowers displayed graded floral organ abnormalities. Whereas slmir172cCR loss-of-function caused only a slight greening of petals and stamens, hypomorphic and loss-of-function slmir172dCR alleles were associated with the conversion of petals and stamens to sepaloids, which were produced in excess. Interestingly, the degrees of floral organ identity alteration and proliferation were directly correlated with the reduction in sly-miR172d activity. These results suggest that sly-miR172d regulates in a dose-dependent manner floral organ identity and number, likely by negatively regulating its APETALA2-like targets.
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24
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Cucinotta M, Cavalleri A, Chandler JW, Colombo L. Auxin and Flower Development: A Blossoming Field. Cold Spring Harb Perspect Biol 2021; 13:a039974. [PMID: 33355218 PMCID: PMC7849340 DOI: 10.1101/cshperspect.a039974] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The establishment of the species-specific floral organ body plan involves many coordinated spatiotemporal processes, which include the perception of positional information that specifies floral meristem and floral organ founder cells, coordinated organ outgrowth coupled with the generation and maintenance of inter-organ and inter-whorl boundaries, and the termination of meristem activity. Auxin is integrated within the gene regulatory networks that control these processes and plays instructive roles at the level of tissue-specific biosynthesis and polar transport to generate local maxima, perception, and signaling. Key features of auxin function in several floral contexts include cell nonautonomy, interaction with cytokinin gradients, and the central role of MONOPTEROS and ETTIN to regulate canonical and noncanonical auxin response pathways, respectively. Arabidopsis flowers are not representative of the enormous angiosperm floral diversity; therefore, comparative studies are required to understand how auxin underlies these developmental differences. It will be of great interest to compare the conservation of auxin pathways among flowering plants and to discuss the evolutionary role of auxin in floral development.
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Affiliation(s)
- Mara Cucinotta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
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25
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Luong AM, Adam H, Gauron C, Affortit P, Ntakirutimana F, Khong NG, Le QH, Le TN, Fournel M, Lebrun M, Tregear J, Jouannic S. Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination. FRONTIERS IN PLANT SCIENCE 2021; 12:692955. [PMID: 34305984 PMCID: PMC8302143 DOI: 10.3389/fpls.2021.692955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 05/13/2023]
Abstract
Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like (euANT/PLT) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana. However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT-related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.
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Affiliation(s)
- Ai My Luong
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Carole Gauron
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Pablo Affortit
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | | | - Ngan Giang Khong
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
| | - Quang Hoa Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Thi Nhu Le
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
| | - Marie Fournel
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Michel Lebrun
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
- LSTM, University of Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France
| | - James Tregear
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
- *Correspondence: Stefan Jouannic,
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26
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Sun X, Zhu S, Li N, Cheng Y, Zhao J, Qiao X, Lu L, Liu S, Wang Y, Liu C, Li B, Guo W, Gao S, Yang Z, Li F, Zeng Z, Tang Q, Pan Y, Guan M, Zhao J, Lu X, Meng H, Han Z, Gao C, Jiang W, Zhao X, Tian S, Su J, Cheng Z, Liu T. A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis. MOLECULAR PLANT 2020; 13:1328-1339. [PMID: 32730994 DOI: 10.1016/j.molp.2020.07.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/26/2020] [Accepted: 07/27/2020] [Indexed: 05/21/2023]
Abstract
Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.
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Affiliation(s)
- Xiudong Sun
- Shandong Agricultural University, Tai'an 271018, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Ningyang Li
- Shandong Agricultural University, Tai'an 271018, China
| | - Yi Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xuguang Qiao
- Shandong Agricultural University, Tai'an 271018, China
| | - Li Lu
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Shiqi Liu
- Shandong Agricultural University, Tai'an 271018, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Benping Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wu Guo
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Shuang Gao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Yupeng Pan
- Northwest A&F University, Yangling 712100, China
| | - Mengjiao Guan
- Shandong Agricultural University, Tai'an 271018, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xiaoming Lu
- Shandong Agricultural University, Tai'an 271018, China
| | - Huanwen Meng
- Northwest A&F University, Yangling 712100, China
| | - Zhenlin Han
- Shandong Agricultural University, Tai'an 271018, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Zhihui Cheng
- Northwest A&F University, Yangling 712100, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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27
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Chang W, Guo Y, Zhang H, Liu X, Guo L. Same Actor in Different Stages: Genes in Shoot Apical Meristem Maintenance and Floral Meristem Determinacy in Arabidopsis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00089] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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28
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Wang Q, Zhang X, Lin S, Yang S, Yan X, Bendahmane M, Bao M, Fu X. Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1915-1927. [PMID: 31990971 PMCID: PMC7242084 DOI: 10.1093/jxb/erz558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/25/2020] [Indexed: 05/12/2023]
Abstract
The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.
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Affiliation(s)
- Qijian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Xiaoni Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Shaozong Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Xiuli Yan
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Mohammed Bendahmane
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan, China
- Correspondence:
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29
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Different MicroRNA Families Involved in Regulating High Temperature Stress Response during Cotton ( Gossypium hirsutum L.) Anther Development. Int J Mol Sci 2020; 21:ijms21041280. [PMID: 32074966 PMCID: PMC7072957 DOI: 10.3390/ijms21041280] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/26/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are small molecule RNAs widely involved in responses to plant abiotic stresses. We performed small RNA sequencing of cotton anthers at four developmental stages under normal and high temperature (NT and HT, respectively) conditions to investigate the stress response characteristics of miRNA to HT. A total of 77 miRNAs, including 33 known miRNAs and 44 novel miRNAs, were identified, and 41 and 28 miRNAs were differentially expressed under NT and HT stress conditions, respectively. The sporogenous cell proliferation (SCP), meiotic phase (MP), microspore release period (MRP), and pollen maturity (PM) stages had 10 (including 12 miRNAs), four (including six miRNAs), four (including five miRNAs), and seven (including 11 miRNAs) HT stress-responsive miRNA families, respectively, which were identified after removing the changes in genotype-specific miRNAs under NT condition. Seven miRNA families (miR2949, miR167, and miR160 at the SCP stage; miR156 and miR172 at the MP stage; miR156 at the MRP stage; and miR393 and miR3476 at the PM stage), which had expression abundance of more than 10% of the total expression abundance, served as the main regulators responding to HT stress with positive or negative regulation patterns. These miRNAs orchestrated the expression of the corresponding target genes and led to different responses in the HT-tolerant and the HT-sensitive lines. The results revealed that the HT stress response of miRNAs in cotton anthers were stage-specific and differed with the development of anthers. Our study may enhance the understanding of the response of miRNAs to HT stress in cotton anthers and may clarify the mechanism of plant tolerance to HT stress.
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30
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Jiang W, Zhang X, Song X, Yang J, Pang Y. Genome-Wide Identification and Characterization of APETALA2/Ethylene-Responsive Element Binding Factor Superfamily Genes in Soybean Seed Development. FRONTIERS IN PLANT SCIENCE 2020; 11:566647. [PMID: 33013987 PMCID: PMC7498640 DOI: 10.3389/fpls.2020.566647] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/17/2020] [Indexed: 05/15/2023]
Abstract
Glycine max is one of the most important grain and oil crops, and improvement of seed yield is one of the major objectives in soybean breeding. The AP2/ERF superfamily members are involved in regulating flower and seed development in many species, and therefore play key roles in seed yield. However, it is still unknown that how many AP2/ERF members were presented in the G. max genome and whether these AP2/ERF family members function in flower and seed development in G. max. Here, we identified 380 AP2/ERF superfamily genes in the G. max genome. Phylogenetic analysis showed that 323 members were grouped into the ERF family, and 49 into the AP2 family. Among the AP2 family, 14 members of the euAP2 lineage showed high identity with their orthologs, and eight member of the ANT lineage were expressed highly in the seeds. Furthermore, seven of them (GmAP2-1 to GmAP2-7) were successfully cloned and over-expressed in Arabidopsis thaliana. The transgenic Arabidopsis plants over-expressing these GmAP2 genes flowered earlier relative to the wild type control. The seed length and width, and seed area of these over-expression lines were increased compared with the wild type, and seed weight of over-expression lines of GmAP2-1, GmAP2-4, GmAP2-5, and GmAP2-6 were greater than those of the wild type. Furthermore, the seed number per silique of the over-expression lines for GmAP2 genes were not affected except GmAP2-5. Collectively, GmAP2-1, GmAP2-4, and GmAP2-6 played important roles in regulating seed weight by affecting seed length, width and area, and further controlling seed yield.
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Affiliation(s)
- Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuejing Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xuewei Song
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Junfeng Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yongzhen Pang,
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Solomon CU, Drea S. Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development. Genes (Basel) 2019; 10:genes10120994. [PMID: 31805740 PMCID: PMC6947164 DOI: 10.3390/genes10120994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.
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Affiliation(s)
- Charles U. Solomon
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu 441107, Nigeria
- Correspondence:
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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Fal K, Cortes M, Liu M, Collaudin S, Das P, Hamant O, Trehin C. Paf1c defects challenge the robustness of flower meristem termination in Arabidopsis thaliana. Development 2019; 146:dev.173377. [PMID: 31540913 PMCID: PMC6826038 DOI: 10.1242/dev.173377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 09/11/2019] [Indexed: 11/20/2022]
Abstract
Although accumulating evidence suggests that gene regulation is highly stochastic, genetic screens have successfully uncovered master developmental regulators, questioning the relationship between transcriptional noise and intrinsic robustness of development. To identify developmental modules that are more or less resilient to large-scale genetic perturbations, we used the Arabidopsis polymerase II-associated factor 1 complex (Paf1c) mutant vip3, which is impaired in several RNA polymerase II-dependent transcriptional processes. We found that the control of flower termination was not as robust as classically pictured. In angiosperms, the floral female organs, called carpels, display determinate growth: their development requires the arrest of stem cell maintenance. In vip3 mutant flowers, carpels displayed a highly variable morphology, with different degrees of indeterminacy defects up to wild-type size inflorescence emerging from carpels. This phenotype was associated with variable expression of two key regulators of flower termination and stem cell maintenance in flowers, WUSCHEL and AGAMOUS. The phenotype was also dependent on growth conditions. Together, these results highlight the surprisingly plastic nature of stem cell maintenance in plants and its dependence on Paf1c. Summary: Using a mutant with increased transcriptional noise, we reveal that stem cell maintenance is not as robust as anticipated in plants, even leading to major defects in essential developmental processes such as flower indeterminacy.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Matthieu Cortes
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mengying Liu
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Sam Collaudin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Pradeep Das
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Christophe Trehin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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Zhao Q, Shen J, Gao C, Cui Y, Wang Y, Cui J, Cheng L, Cao W, Zhu Y, Huang S, Zhou Q, Leong CK, Leung KP, Chen X, Jiang L. RST1 Is a FREE1 Suppressor That Negatively Regulates Vacuolar Trafficking in Arabidopsis. THE PLANT CELL 2019; 31:2152-2168. [PMID: 31221737 PMCID: PMC6751125 DOI: 10.1105/tpc.19.00003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/18/2019] [Accepted: 06/17/2019] [Indexed: 05/23/2023]
Abstract
FYVE domain protein required for endosomal sorting1 (FREE1), a plant-specific endosomal sorting complex required for transport-I component, is essential for the biogenesis of multivesicular bodies (MVBs), vacuolar degradation of membrane protein, cargo vacuolar sorting, autophagic degradation, and vacuole biogenesis in Arabidopsis (Arabidopsis thaliana). Here, we report the characterization of RESURRECTION1 (RST1) as a suppressor of free1 that, when mutated as a null mutant, restores the normal MVB and vacuole formation of a FREE1-RNAi knockdown line and consequently allows survival. RST1 encodes an evolutionarily conserved multicellular organism-specific protein, which contains two Domain of Unknown Function 3730 domains, showing no similarity to known proteins, and predominantly localizes in the cytosol. The depletion of FREE1 causes substantial accumulation of RST1, and transgenic Arabidopsis plants overexpressing RST1 display retarded seedling growth with dilated MVBs, and inhibition of endocytosed FM4-64 dye to the tonoplast, suggesting that RST1 has a negative role in vacuolar transport. Consistently, enhanced endocytic degradation of membrane vacuolar cargoes occurs in the rst1 mutant. Further transcriptomic comparison of rst1 with free1 revealed a negative association between gene expression profiles, demonstrating that FREE1 and RST1 have antagonistic functions. Thus, RST1 is a negative regulator controlling membrane protein homeostasis and FREE1-mediated functions in plants.
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Affiliation(s)
- Qiong Zhao
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University (SCNU), Guangzhou 510631, China
| | - Yong Cui
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yongyi Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jie Cui
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Lixin Cheng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Critical Care Medicine, Shenzhen People’s Hospital, The Second Clinical Medicine College of Ji’nan University, Shenzhen 518020, China
| | - Wenhan Cao
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Ying Zhu
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Shuxian Huang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Qianzi Zhou
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Cheuk Ka Leong
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - King Pong Leung
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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Chen P, Shi Q, Liang Z, Lu H, Li R. Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line. Genome 2019; 62:455-466. [DOI: 10.1139/gen-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Qiqi Shi
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhichen Liang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
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35
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Xu Y, Yamaguchi N, Gan ES, Ito T. When to stop: an update on molecular mechanisms of floral meristem termination. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1711-1718. [PMID: 30916342 DOI: 10.1093/jxb/erz048] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/06/2019] [Indexed: 05/17/2023]
Abstract
Flowers have fascinated humans for millennia, not only because of their beauty, but also because they give rise to fruits, from which most agricultural products are derived. In most angiosperms, the number and position of floral organs are morphologically and genetically defined, and their development is tightly controlled by complex regulatory networks to ensure reproductive success. How flower development is temporally initiated and spatially maintained has been widely researched. As the flower develops, the balance between proliferation and differentiation dynamically shifts towards organogenesis and termination of floral stem cell maintenance. In this review, we focus on recent findings that further reveal the intricate molecular mechanisms for precise timing of floral meristem termination.
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Affiliation(s)
- Yifeng Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Nara Institute of Science and Technology, Biological Sciences, Plant Stem Cell Regulation and Floral Patterning Laboratory, Takayama, Ikoma, Nara, Japan
| | - Nobutoshi Yamaguchi
- Nara Institute of Science and Technology, Biological Sciences, Plant Stem Cell Regulation and Floral Patterning Laboratory, Takayama, Ikoma, Nara, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Honcho, Kawaguchi-shi, Saitama, Japan
| | | | - Toshiro Ito
- Nara Institute of Science and Technology, Biological Sciences, Plant Stem Cell Regulation and Floral Patterning Laboratory, Takayama, Ikoma, Nara, Japan
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36
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Yang Y, Sun M, Yuan C, Han Y, Zheng T, Cheng T, Wang J, Zhang Q. Interactions between WUSCHEL- and CYC2-like Transcription Factors in Regulating the Development of Reproductive Organs in Chrysanthemum morifolium. Int J Mol Sci 2019; 20:ijms20061276. [PMID: 30875718 PMCID: PMC6471657 DOI: 10.3390/ijms20061276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
Chrysanthemum morifolium is a gynomonoecious plant that bears both female zygomorphic ray florets and bisexual actinomorphic disc florets in the inflorescence. This sexual system is quite prevalent in Asteraceae, but poorly understood. CYCLOIDEA (CYC) 2 subclade transcription factors, key regulators of flower symmetry and floret identity in Asteraceae, have also been speculated to function in reproductive organs and could be an entry point for studying gynomonoecy. However, the molecular mechanism is still unclear. On the other hand, the Arabidopsis WUSCHEL (WUS) transcription factor has been proven to play a vital role in the development of reproductive organs. Here, a WUS homologue (CmWUS) in C. morifolium was isolated and characterized. Overexpression of CmWUS in A. thaliana led to shorter siliques and fewer stamens, which was similar to CYC2-like genes reported before. In addition, both CmWUS and CmCYC2 were highly expressed in flower buds during floral organ differentiation and in the reproductive organs at later development stages, indicating their involvement in the development of reproductive organs. Moreover, CmWUS could directly interact with CmCYC2d. Thus, our data suggest a collaboration between CmWUS and CmCYC2 in the regulation of reproductive organ development in chrysanthemum and will contribute to a further understanding of the gynomonoecious sexual system in Asteraceae.
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Affiliation(s)
- Yi Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
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Jue D, Sang X, Liu L, Shu B, Wang Y, Liu C, Wang Y, Xie J, Shi S. Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition. BMC Genomics 2019; 20:126. [PMID: 30744552 PMCID: PMC6371577 DOI: 10.1186/s12864-019-5461-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
Background Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossoming is one of the most challenging issues. Perpetual flowering (PF) is a crucial trait for fruit trees and is directly linked to production potential. Therefore, studying the molecular regulatory mechanism of longan PF traits is crucial for understanding and solving problems related to flowering. In this study, comparative transcriptome analysis was performed using two longan cultivars that display opposite flowering phenotypes during floral induction. Results We obtained 853.72 M clean reads comprising 125.08 Gb. After comparing these data with the longan genome, 27,266 known genes and 1913 new genes were detected. Significant differences in gene expression were observed between the two genotypes, with 6150 and 6202 differentially expressed genes (DEGs) for ‘SJ’ and ‘SX’, respectively. The transcriptional landscape of floral transition at the early stage was very different in these two longan genotypes with respect to key hormones, circadian rhythm, sugar metabolism, and transcription factors. Almost all flowering-related DEGs identified are involved in photoperiod and circadian clock pathways, such as CONSTANS-like (COL), two-component response regulator-like (APRRs), gigantea (GI), and early flowering (EFL). In addition, the leafy (LFY) gene, which is the central floral meristem identity gene, may inhibit PF formation in ‘SJ’. Conclusion This study provides a platform for understanding the molecular mechanisms responsible for changes between PF and seasonal flowering (SF) longan genotypes and may benefit studies on PF trait mechanisms of evergreen fruit trees. Electronic supplementary material The online version of this article (10.1186/s12864-019-5461-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China.,School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Liqin Liu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Bo Shu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Yicheng Wang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Chengming Liu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yi Wang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China.
| | - Shengyou Shi
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China. .,School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China.
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39
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Abstract
In Arabidopsis, the floral meristem is essential for the production of floral organs. The floral meristem is initially maintained to contribute cells for floral organ formation. However, this stem cell activity needs be completely terminated at a certain floral developmental stage to ensure the proper development of floral reproductive organs. Here, we have reviewed recent findings on the complex regulation of floral meristem activities, which involve signaling cascades, transcriptional regulation, epigenetic mechanisms and hormonal control for floral meristem determinacy in Arabidopsis.
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Affiliation(s)
- Erlei Shang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Toshiro Ito
- Biological Science, Nara Institute of Science and Technology, Nara, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Bo Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- CONTACT Bo Sun State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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40
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Yamaguchi N, Huang J, Tatsumi Y, Abe M, Sugano SS, Kojima M, Takebayashi Y, Kiba T, Yokoyama R, Nishitani K, Sakakibara H, Ito T. Chromatin-mediated feed-forward auxin biosynthesis in floral meristem determinacy. Nat Commun 2018; 9:5290. [PMID: 30538233 PMCID: PMC6289996 DOI: 10.1038/s41467-018-07763-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/20/2018] [Indexed: 12/16/2022] Open
Abstract
In flowering plants, the switch from floral stem cell maintenance to gynoecium (female structure) formation is a critical developmental transition for reproductive success. In Arabidopsis thaliana, AGAMOUS (AG) terminates floral stem cell activities to trigger this transition. Although CRABS CLAW (CRC) is a direct target of AG, previous research has not identified any common targets. Here, we identify an auxin synthesis gene, YUCCA4 (YUC4) as a common direct target. Ectopic YUC4 expression partially rescues the indeterminate phenotype and cell wall defects that are caused by the crc mutation. The feed-forward YUC4 activation by AG and CRC directs a precise change in chromatin state for the shift from floral stem cell maintenance to gynoecium formation. We also showed that two auxin-related direct CRC targets, YUC4 and TORNADO2, cooperatively contribute to the termination of floral stem cell maintenance. This finding provides new insight into the CRC-mediated auxin homeostasis regulation for proper gynoecium formation. In Arabidopsis, the AG and CRC transcription factors terminate floral stem cells and allow the emergence of female floral organs. Here the authors show that AG and CRC form a feed-forward loop that controls local auxin biosynthesis via induction of YUCCA4 to ensure successful gynoecium formation.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi-shi, Saitama, 332-0012, Japan
| | - Jiangbo Huang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Yoshitaka Tatsumi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Masato Abe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Shigeo S Sugano
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi-shi, Saitama, 332-0012, Japan.,Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Shiga, 525-8577, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Takatoshi Kiba
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Ryusuke Yokoyama
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kazuhiko Nishitani
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.,Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
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Mulki MA, Bi X, von Korff M. FLOWERING LOCUS T3 Controls Spikelet Initiation But Not Floral Development. PLANT PHYSIOLOGY 2018; 178:1170-1186. [PMID: 30213796 PMCID: PMC6236595 DOI: 10.1104/pp.18.00236] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/30/2018] [Indexed: 05/18/2023]
Abstract
In many angiosperm plants, FLOWERING LOCUS T (FT)-like genes have duplicated and functionally diverged to control different reproductive traits or stages. Barley (Hordeum vulgare) carries several FT-like genes, the functions of which are not well understood. We characterized the role of HvFT3 in the vegetative and reproductive development of barley. Overexpression of HvFT3 accelerated the initiation of spikelet primordia and the early reproductive development of spring barley independently of the photoperiod. However, HvFT3 overexpression did not accelerate floral development, and inflorescences aborted under short days, suggesting that HvFT3 controls spikelet initiation but not floral development. Analysis of a nonfunctional HvFT3 allele supported the specific effects of this gene on spikelet initiation independent of the photoperiod. HvFT3 caused the up-regulation of the winter and spring alleles of the vernalization gene VERNALIZATION1 (VRN-H1) in nonvernalized plants and was therefore dominant over the repressive effects of the vernalization pathway. Global transcriptome analysis in developing main shoot apices of the transgenic lines showed that HvFT3 modified the expression of genes involved in hormone synthesis and response, of floral homeotic genes, and of barley row-type genes SIX-ROWED-SPIKE1 (VRS1), SIX-ROWED-SPIKE4 (VRS4), and INTERMEDIUM C Understanding the specific functions of individual FT-like genes will allow modification of individual phases of preanthesis development and thereby adaptation to different environments and improved yield.
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Affiliation(s)
- Muhammad Aman Mulki
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Xiaojing Bi
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules" 40225 Düsseldorf, Germany
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42
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Zhang Z, Li X. Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube. Sci Rep 2018; 8:15612. [PMID: 30353116 PMCID: PMC6199273 DOI: 10.1038/s41598-018-33744-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/07/2018] [Indexed: 02/06/2023] Open
Abstract
The Ethylene response factor (ERF) belongs to the APETALA2/ethylene response factor (AP2/ERF) superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes. Thus, identifying and charactering this transcription factor would be helpful to elucidate ethylene related fruit ripening regulation in Chinese jujube (Ziziphus jujuba Mill.). In the present study, 119 AP2/ERF genes, including 5 Related to ABI3/VPs (RAV), 17 AP2s, 57 ERFs, 39 dehydration-responsive element-binding (DREB) factors and 1 soloist gene, were identified from the jujube genome sequences. Genome localization, gene duplication, phylogenetic relationships and conserved motifs were simultaneously analysed. Using available transcriptomic data, 85 genes with differential transcripts in the flower, leaf and fruit were detected, suggesting a broad regulation of AP2/ERF genes in the growth and development of jujube. Among them, 44 genes were expressed in the fruit. As assessed by quantitative PCR, 15 up- and 23 downregulated genes corresponding to fruit full maturity were found, while in response to 100 μl l-1 ethylene, 6 up- and 16 downregulated genes were generated. By comparing the output, ZjERF54 and DREB39 were found to be the best candidate genes that positively participated in jujube fruit ripening, while ZjERF25 and ZjERF36, which had an ERF-associated amphiphilic repression (EAR) motif, were ripening repressors. These findings help to gain insights into AP2/ERF gene evolution and provide a useful resource to further understand the ethylene regulatory mechanisms underlying Chinese jujube fruit ripening.
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Affiliation(s)
- Zhong Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Research Centre for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Research Centre for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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43
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Su S, Shao X, Zhu C, Xu J, Tang Y, Luo D, Huang X. An AGAMOUS-like factor is associated with the origin of two domesticated varieties in Cymbidium sinense (Orchidaceae). HORTICULTURE RESEARCH 2018; 5:48. [PMID: 30181888 PMCID: PMC6119200 DOI: 10.1038/s41438-018-0052-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 05/15/2023]
Abstract
Cymbidium has been artificially domesticated for centuries in Asia, which produced numerous cultivated varieties. Flowers with stamenoid tepals or those with multiple tepals have been found in different species of Cymbidium; however, the molecular basis controlling the formation of these phenotypes is still largely unknown. Previous work demonstrated that AGAMOUS/AG lineage MADS genes function in floral meristem determinacy as well as in reproductive organs development in both dicots and monocots, indicating a possible relationship with the origin of two flower varieties in Cymbidium. Here, we characterized and analyzed two AG lineage paralogues, CsAG1 and CsAG2, from Cymbidium sinense, both of which were highly expressed in the gynostemium column of a standard C. sinense. Interestingly, we detected ectopic expression of CsAG1 rather than CsAG2 in all floral organs of a stamenoid-tepal variety and significant down-regulation of CsAG1 in a variety with multiple tepals. Over-expression of CsAG1 in wild type Arabidopsis resulted in petal-to-stamen homeotic conversion, suggesting a conserved C-function of CsAG1 in the development of Cymbidium flower. Altogether, our results supported a hypothesis that disruption of a single AG-like factor would be associated with the formation of two domesticated varieties in C. sinense.
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Affiliation(s)
- Shihao Su
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Aichi Japan
| | - Xiaoyu Shao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Changfa Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jiayin Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Yuhuan Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Da Luo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Xia Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
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44
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Lin Z, Damaris RN, Shi T, Li J, Yang P. Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera). BMC Genomics 2018; 19:554. [PMID: 30053802 PMCID: PMC6062958 DOI: 10.1186/s12864-018-4950-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/19/2018] [Indexed: 12/26/2022] Open
Abstract
Background Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure. Results Here, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus. Conclusions Taken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid. Electronic supplementary material The online version of this article (10.1186/s12864-018-4950-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhongyuan Lin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Juanjuan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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45
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Rong XF, Sang YL, Wang L, Meng WJ, Zou CH, Dong YX, Bie XM, Cheng ZJ, Zhang XS. Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2018; 59:756-764. [PMID: 29186581 PMCID: PMC6018948 DOI: 10.1093/pcp/pcx187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 05/13/2023]
Abstract
Plants are known for their capacity to regenerate organs, such as shoot, root and floral organs. Recently, a number of studies contributed to understanding the mechanisms of shoot and root regeneration. However, the mechanisms underlying floral organ regeneration are largely unknown. In this study, we established a carpel regeneration system in which two types of carpels were induced by exogenous cytokinin. For type I, all the floral organs in the regenerated inflorescence were transformed into carpels. For type II, carpels were generated directly from callus. The transcript level of AGAMOUS (AG), the carpel identity gene, was up-regulated during carpel induction. The expression signals of AG were detected in the initiating carpel primordia and regenerating carpels, and co-localized with those of two Type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs), ARR1 and ARR10. Repression of either AG or type-B ARRs reduced carpel regeneration. Binding analyses showed that ARR1 and ARR10 directly bound to transcriptional regulatory regions of AG and positively regulated its expression. In addition, the expression of type-B ARRs overlapped with that of AG in the floral primordia in planta. Defects in type-B ARRs reduced the number of carpels. The results indicate that type-B ARRs control carpel regeneration through activating AG expression. Our results provide new information for understanding the mechanism of carpel formation.
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Affiliation(s)
- Xiao Fei Rong
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ya Lin Sang
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | | | - Wen Jing Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Chun Hao Zou
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiao Min Bie
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Zhi Juan Cheng
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
- Corresponding authors: Xian S. Zhang, E-mail, ; Fax, +86-538-8226399; Zhi J. Cheng, E-mail,
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
- Corresponding authors: Xian S. Zhang, E-mail, ; Fax, +86-538-8226399; Zhi J. Cheng, E-mail,
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46
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Ren WL, Wen YJ, Dunwell JM, Zhang YM. pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study. Heredity (Edinb) 2018; 120:208-218. [PMID: 29234158 PMCID: PMC5836593 DOI: 10.1038/s41437-017-0007-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 11/08/2022] Open
Abstract
Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal-Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait. Finally, all the selected markers were placed into multi-locus model, these effects were estimated by empirical Bayes, and all the nonzero effects were further identified by a likelihood ratio test for true QTN detection. This method, named pKWmEB, was validated by a series of Monte Carlo simulation studies. As a result, pKWmEB effectively controlled false positive rate, although a less stringent significance criterion was adopted. More importantly, pKWmEB retained the high power of Kruskal-Wallis test, and provided QTN effect estimates. To further validate pKWmEB, we re-analyzed four flowering time related traits in Arabidopsis thaliana, and detected some previously reported genes that were not identified by the other methods.
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Affiliation(s)
- Wen-Long Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang-Jun Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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47
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Balanzà V, Martínez-Fernández I, Sato S, Yanofsky MF, Kaufmann K, Angenent GC, Bemer M, Ferrándiz C. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat Commun 2018. [PMID: 29422669 DOI: 10.1038/s41467-018-03065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover a genetic pathway regulating GPA in Arabidopsis that responds to age-dependent factors and acts in parallel to seed-derived signals. We show that FRUITFULL (FUL), a MADS-box gene involved in flowering and fruit development, has a key role in promoting meristem arrest, as GPA is delayed and fruit production is increased in ful mutants. FUL directly and negatively regulates APETALA2 expression in the shoot apical meristem and maintains the temporal expression of WUSCHEL which is an essential factor for meristem maintenance.
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Affiliation(s)
- Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Shusei Sato
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Martin F Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kerstin Kaufmann
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain.
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48
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Balanzà V, Martínez-Fernández I, Sato S, Yanofsky MF, Kaufmann K, Angenent GC, Bemer M, Ferrándiz C. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat Commun 2018; 9:565. [PMID: 29422669 PMCID: PMC5805735 DOI: 10.1038/s41467-018-03067-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 01/17/2018] [Indexed: 11/20/2022] Open
Abstract
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover a genetic pathway regulating GPA in Arabidopsis that responds to age-dependent factors and acts in parallel to seed-derived signals. We show that FRUITFULL (FUL), a MADS-box gene involved in flowering and fruit development, has a key role in promoting meristem arrest, as GPA is delayed and fruit production is increased in ful mutants. FUL directly and negatively regulates APETALA2 expression in the shoot apical meristem and maintains the temporal expression of WUSCHEL which is an essential factor for meristem maintenance. The lifespan of monocarpic plants is determined by coordinated arrest of shoot meristems. Here the authors show that this process is promoted by the FRUITFULL transcription factor which negatively regulates expression of the meristem maintenance factor WUSCHEL in an AP2-dependent manner.
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Affiliation(s)
- Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Shusei Sato
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Martin F Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kerstin Kaufmann
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands.,Bioscience, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain.
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49
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Zhang K, Wang R, Zi H, Li Y, Cao X, Li D, Guo L, Tong J, Pan Y, Jiao Y, Liu R, Xiao L, Liu X. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. THE PLANT CELL 2018; 30:324-346. [PMID: 29371438 PMCID: PMC5868698 DOI: 10.1105/tpc.17.00705] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/18/2017] [Accepted: 01/24/2018] [Indexed: 05/03/2023]
Abstract
Successful floral meristem (FM) determinacy is critical for subsequent reproductive development and the plant life cycle. Although the phytohormones cytokinin and auxin interact to coregulate many aspects of plant development, whether and how cytokinin and auxin function in FM determinacy remain unclear. Here, we show that in Arabidopsis thaliana, cytokinin homeostasis is critical for FM determinacy. In this developmental context, auxin promotes the expression of AUXIN RESPONSE FACTOR3 (ARF3) to repress cytokinin activity. ARF3 directly represses the expression of ISOPENTENYLTRANSFERASE (IPT) family genes and indirectly represses LONELY GUY (LOG) family genes, both of which encode enzymes required for cytokinin biosynthesis. ARF3 also directly inhibits the expression of ARABIDOPSIS HISTIDINE KINASE4, a cytokinin receptor gene, resulting in reduced cytokinin activity. Consequently, ARF3 controls cell division by regulating cell cycle gene expression through cytokinin. In flowers, we show that AGAMOUS (AG) dynamically regulates the expression of ARF3 and IPTs, resulting in coordinated regulation of FM maintenance and termination through cell division. Moreover, genome-wide transcriptional profiling revealed both repressive and active roles for ARF3 in early flower development. Our findings establish a molecular link between AG and auxin/cytokinin and shed light on the mechanisms of stem cell maintenance and termination in the FM.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, 410128 Changsha, China
| | - Hailing Zi
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Xiuwei Cao
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
| | - Dongming Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Lin Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, 410128 Changsha, China
| | - Yanyun Pan
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, 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 100101, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, 410128 Changsha, China
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
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50
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Abstract
Transcription factors that trigger major developmental decisions in plants and animals are termed "master regulators". Such master regulators are classically seen as acting on the top of a regulatory hierarchy that determines a complete developmental program, and they usually encode transcription factors. Here, we introduce master regulators of flowering time and flower development as examples to show how analysis of molecular interactions and gene-regulatory networks in plants has changed our view on the molecular mechanisms by which these factors control developmental processes. A picture has emerged that emphasizes a complex combinatorial interplay in determining cell-type transcriptional programs, and a high level of feedback control. The expression of master regulators themselves is usually regulated by multiple factors integrating environmental and endogenous spatiotemporal cues. Master regulatory transcription factors regulate gene expression by different mechanisms, including modifications in chromatin status in the bound regions. A poorly understood phenomenon is how developmental master regulators exert functions in different cell- and organ types. This is especially relevant for those factors that have important functions in several developmental processes.
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