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Tang H, Jing D, Liu C, Xie X, Zhang L, Chen X, Li C. Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize. Curr Issues Mol Biol 2024; 46:430-449. [PMID: 38248329 PMCID: PMC10814199 DOI: 10.3390/cimb46010027] [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: 12/04/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.
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Affiliation(s)
- Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - De Jing
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Lei Zhang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xunji Chen
- Institute of Nuclear and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Changyu Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
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Zhang P, Zhu W, He Y, Fan J, Shi J, Fu R, Hu J, Li L, Zhang D, Liang W. THERMOSENSITIVE BARREN PANICLE (TAP) is required for rice panicle and spikelet development at high ambient temperature. THE NEW PHYTOLOGIST 2023; 237:855-869. [PMID: 36263719 DOI: 10.1111/nph.18551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
In cereal plants, the size of the panicle (inflorescence) is a critical factor for yield. Panicle size is determined by a complex interplay of genetic and environmental factors, but the mechanisms underlying adaptations to temperature stress during panicle development remain largely unknown. We identify the rice THERMOSENSITIVE BARREN PANICLE (TAP) gene, which encodes a transposase-derived FAR1-RELATED SEQUENCE (FRS) protein and is responsible for regulating panicle and spikelet development at high ambient temperature. The tap mutants display high temperature-dependent reproductive abnormalities, including compromised secondary branch and spikelet initiation and pleiotropic floral organ defects. Consistent with its thermosensitive phenotype, TAP expression is induced by high temperature. TAP directly promotes the expression of OsYABBY3 (OsYAB3), OsYAB4, and OsYAB5, which encode key transcriptional regulators in panicle and spikelet development. In addition, TAP physically interacts with OsYAB4 and OsYAB5 proteins; phenotypic analysis of osyab4 tap-1 and osyab5 tap-1 double mutants indicates that TAP-OsYAB4/OsYAB5 complexes act to maintain normal panicle and spikelet development. Taken together, our study reveals the novel role of a TE-derived transcription factor in controlling rice panicle development under high ambient temperatures, shedding light on the molecular mechanism underlying the adaptation of cereal crops to increasing environmental temperatures.
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Affiliation(s)
- Peng Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Yi He
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Junyi Fan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Ruifeng Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
| | - Li Li
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
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Zhang H, Cao Y, Wang Z, Ye M, Wu R. Functional Mapping of Genes Modulating Plant Shade Avoidance Using Leaf Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:608. [PMID: 36771692 PMCID: PMC9920004 DOI: 10.3390/plants12030608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Shade avoidance syndrome (SAS) refers to a set of plant responses that increases light capture in dense stands. This process is crucial for plants in natural and agricultural environments as they compete for resources and avoid suboptimal conditions. Although the molecular, biochemical, and physiological mechanisms underlying the SAS response have been extensively studied, the genetic basis of developmental variation in leaves in regard to leaf area, petiole length, and leaf length (i.e., their allometric relationships) remains unresolved. In this study, with the recombinant inbred line (RIL) population, the developmental traits of leaves of Arabidopsis were investigated under two growth density conditions (high- and low-density plantings). The observed changes were then reconstructed digitally, and their allometric relationships were modelled. Taking the genome-wide association analysis, the SNP genotype and the dynamic phenotype of the leaf from both densities were combined to explore the allometry QTLs. Under different densities, leaf change phenotype was analyzed from two core ecological scenarios: (i) the allometric change of the leaf area with leaf length, and (ii) the change of the leaf length with petiole length. QTLs modulating these two scenarios were characterized as 'leaf shape QTLs' and 'leaf position QTLs'. With functional mapping, results showed a total of 30 and 24 significant SNPs for shapeQTLs and positionQTLs, respectively. By annotation, immune pathway genes, photosensory receptor genes, and phytohormone genes were identified to be involved in the SAS response. Interestingly, genes modulating the immune pathway and salt tolerance, i.e., systemic acquired resistance (SAR) regulatory proteins (MININ-1-related) and salt tolerance homologs (STH), were reported to mediate the SAS response. By dissecting and comparing QTL effects from low- and high-density conditions, our results elucidate the genetic control of leaf formation in the context of the SAS response. The mechanism with leaf development × density interaction can further aid the development of density-tolerant crop varieties for agricultural practices.
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Affiliation(s)
- Han Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yige Cao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Zijian Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
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Walla A, Wilma van Esse G, Kirschner GK, Guo G, Brünje A, Finkemeier I, Simon R, von Korff M. An Acyl-CoA N-Acyltransferase Regulates Meristem Phase Change and Plant Architecture in Barley. PLANT PHYSIOLOGY 2020; 183:1088-1109. [PMID: 32376761 PMCID: PMC7333700 DOI: 10.1104/pp.20.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/19/2020] [Indexed: 05/04/2023]
Abstract
The modification of shoot architecture and increased investment into reproductive structures is key for crop improvement and is achieved through coordinated changes in the development and determinacy of different shoot meristems. A fundamental question is how the development of different shoot meristems is genetically coordinated to optimize the balance between vegetative and reproductive organs. Here we identify the MANY NODED DWARF1 (HvMND1) gene as a major regulator of plant architecture in barley (Hordeum vulgare). The mnd1.a mutant displayed an extended vegetative program with increased phytomer, leaf, and tiller production but a reduction in the number and size of grains. The induction of vegetative structures continued even after the transition to reproductive growth, resulting in a marked increase in longevity. Using mapping by RNA sequencing, we found that the HvMND1 gene encodes an acyl-CoA N-acyltransferase that is predominately expressed in developing axillary meristems and young inflorescences. Exploration of the expression network modulated by HvMND1 revealed differential expression of the developmental microRNAs miR156 and miR172 and several key cell cycle and developmental genes. Our data suggest that HvMND1 plays a significant role in the coordinated regulation of reproductive phase transitions, thereby promoting reproductive growth and whole plant senescence in barley.
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Affiliation(s)
- Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
| | - G Wilma van Esse
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Laboratory for Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Gwendolyn K Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
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5
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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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