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Kangben F, Kumar S, Li Z, Sreedasyam A, Dardick C, Jones D, Saski CA. Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton. FRONTIERS IN PLANT SCIENCE 2024; 14:1320638. [PMID: 38356867 PMCID: PMC10864623 DOI: 10.3389/fpls.2023.1320638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024]
Abstract
Introduction Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity. Methods Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants. Results Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.
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Affiliation(s)
- Foster Kangben
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sonika Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Chris Dardick
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Don Jones
- Department of Agricultural Research, Cotton Incorporated, Cary, NC, United States
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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Tokuyama Y, Omachi M, Kushida S, Hikichi K, Okada S, Onishi K, Ishii T, Kishima Y, Koide Y. Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon). PLANTA 2023; 259:19. [PMID: 38085356 DOI: 10.1007/s00425-023-04300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.
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Affiliation(s)
- Yoshiki Tokuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Miku Omachi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shiori Kushida
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kiwamu Hikichi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shuhei Okada
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kazumitsu Onishi
- Research Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro-Shi, Hokkaido, 080-8555, Japan
| | - Takashige Ishii
- Graduate School of Agricultural Science, Kobe University, Kobe-Shi, Hyogo, 657-8501, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan.
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Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B. Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. FRONTIERS IN PLANT SCIENCE 2023; 14:1288826. [PMID: 37965014 PMCID: PMC10642751 DOI: 10.3389/fpls.2023.1288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.
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Affiliation(s)
- C. Robin Buell
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Christopher Dardick
- Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Breeanna Urbanowicz
- Center for Complex Carbohydrate Research, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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Li J, Sheng Y, Xu H, Li Q, Lin X, Zhou Y, Zhao Y, Song X, Wang J. Transcriptome and hormone metabolome reveal the mechanism of stem bending in water lily ( Nymphaea tetragona) cut-flowers. FRONTIERS IN PLANT SCIENCE 2023; 14:1195389. [PMID: 37746018 PMCID: PMC10515221 DOI: 10.3389/fpls.2023.1195389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Water lilies are popular ornamental cut-flowers with significant economic and cultural value. However, stem bending affects the preservation of cut-flowers during their vase life. To gain further insights into the molecular mechanisms of stem bending, transcriptome profiling, hormone measurement, and morphological analysis were performed using the stems of the 'Blue Bird' water lily. Transcriptome analysis revealed that 607 differentially expressed genes (DEGs) were associated with the dorsal and ventral stems of the water lily, of which 247 were up-regulated and 360 were down-regulated. Significant differences in genes associated with plant hormones, calcium ions, glucose metabolism, and photosynthesis pathways genes involved in the dorsal and ventral areas of the curved stem. In particular, DEGs were associated with the hormone synthesis, gravity response, starch granules, Ca2+ ions, and photosynthesis. The results of qRT-PCR were consistent with that of the transcriptome sequence analysis. A total of 12 hormones were detected, of which abscisic acid, indole-3-carboxaldehyde, indole-3-carboxaldehyde and jasmonic acid were significantly differentially expressed in the dorsal and ventral stems, and were significantly higher in the dorsal stem than in the ventral stem. The cell morphology in the dorsal and ventral areas of the curved stem clearly changed during vase life. The direction of starch granule settlement was consistent with the bending direction of the water lily stem, as well as the direction of gravity. In conclusion, stem bending in water lily cut-flowers is regulated by multiple factors and genes. This study provides an important theoretical basis for understanding the complex regulatory mechanism of water lily stem bending.
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Affiliation(s)
- Jie Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Yuhui Sheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
- College of Agricultural, Hengxing University, Qingdao, Shandong, China
| | - Huixian Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Qinxue Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Xiuya Lin
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Yang Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Ying Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Xiqiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Jian Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
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Wang H, Tu R, Ruan Z, Chen C, Peng Z, Zhou X, Sun L, Hong Y, Chen D, Liu Q, Wu W, Zhan X, Shen X, Zhou Z, Cao L, Zhang Y, Cheng S. Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:160. [PMID: 37347301 DOI: 10.1007/s00122-023-04404-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/11/2023] [Indexed: 06/23/2023]
Abstract
KEY MESSAGE TAC1 is involved in photoperiodic and gravitropic responses to modulate rice dynamic plant architecture likely by affecting endogenous auxin distribution, which could explain TAC1 widespread distribution in indica rice. Plants experience a changing environment throughout their growth, which requires dynamic adjustments of plant architecture in response to these environmental cues. Our previous study demonstrated that Tiller Angle Control 1 (TAC1) modulates dynamic changes in plant architecture in rice; however, the underlying regulatory mechanisms remain largely unknown. In this study, we show that TAC1 regulates plant architecture in an expression dose-dependent manner, is highly expressed in stems, and exhibits dynamic expression in tiller bases during the growth period. Photoperiodic treatments revealed that TAC1 expression shows circadian rhythm and is more abundant during the dark period than during the light period and under short-day conditions than under long-day conditions. Therefore, it contributes to dynamic plant architecture under long-day conditions and loose plant architecture under short-day conditions. Gravity treatments showed that TAC1 is induced by gravistimulation and negatively regulates shoot gravitropism, likely by affecting auxin distribution. Notably, the tested indica rice containing TAC1 displayed dynamic plant architecture under natural long-day conditions, likely explaining the widespread distribution of TAC1 in indica rice. Our results provide new insights into TAC1-mediated regulatory mechanisms for dynamic changes in rice plant architecture.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Ranran Tu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zheyan Ruan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Chi Chen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Zequn Peng
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xingpeng Zhou
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Lianping Sun
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Yongbo Hong
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Daibo Chen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Qunen Liu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Weixun Wu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xiaodeng Zhan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xihong Shen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Zhengping Zhou
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Liyong Cao
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
| | - Shihua Cheng
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
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Zhao L, Zheng Y, Wang Y, Wang S, Wang T, Wang C, Chen Y, Zhang K, Zhang N, Dong Z, Chen F. A HST1-like gene controls tiller angle through regulating endogenous auxin in common wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:122-135. [PMID: 36128872 PMCID: PMC9829390 DOI: 10.1111/pbi.13930] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 05/29/2023]
Abstract
Tiller angle is one of the most important agronomic traits and one key factor for wheat ideal plant architecture, which can both increase photosynthetic efficiency and greatly enhance grain yield. Here, a deacetylase HST1-like (TaHST1L) gene controlling wheat tiller angle was identified by the combination of a genome-wide association study (GWAS) and bulked segregant analysis (BSA). Ethyl methane sulfonate (EMS)-mutagenized tetraploid wheat lines with the premature stop codon of TaHST1L exhibited significantly smaller tiller angles than the wild type. TaHST1L-overexpressing (OE) plants exhibited significantly larger tiller angles and increased tiller numbers in both winter and spring wheat, while TaHST1L-silenced RNAi plants displayed significantly smaller tiller angles and decreased tiller numbers. Moreover, TaHST1L strongly interacted with TaIAA17 and inhibited its expression at the protein level, and thus possibly improved the content of endogenous auxin in the basal tissue of tillers. The transcriptomics and metabolomics results indicated that TaHST1L might change plant architecture by mediating auxin signal transduction and regulating endogenous auxin levels. In addition, a 242-bp insertion/deletion (InDel) in the TaHST1L-A1 promoter altered transcriptional activity and TaHST1L-A1b allele with the 242-bp insertion widened the tiller angle of TaHST1L-OE transgenic rice plants. Wheat varieties with TaHST1L-A1b allele possessed the increased tiller angle and grain yield. Further analysis in wheat and its progenitors indicated that the 242-bp InDel possibly originated from wild emmer and was strongly domesticated in the current varieties. Therefore, TaHST1L involved in the auxin signalling pathway showed the big potential to improve wheat yield by controlling plant architecture.
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Affiliation(s)
- Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Yueting Zheng
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Ying Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Shasha Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Tongzhu Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Canguan Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Yue Chen
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Kunpu Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Zhongdong Dong
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
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Kawamoto N, Morita MT. Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle. THE NEW PHYTOLOGIST 2022; 236:1637-1654. [PMID: 36089891 PMCID: PMC9828789 DOI: 10.1111/nph.18474] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Gravity is one of the fundamental environmental cues that affect plant development. Indeed, the plant architecture in the shoots and roots is modulated by gravity. Stems grow vertically upward, whereas lateral organs, such as the lateral branches in shoots, tend to grow at a specific angle according to a gravity vector known as the gravitropic setpoint angle (GSA). During this process, gravity is sensed in specialised gravity-sensing cells named statocytes, which convert gravity information into biochemical signals, leading to asymmetric auxin distribution and driving asymmetric cell division/expansion in the organs to achieve gravitropism. As a hypothetical offset mechanism against gravitropism to determine the GSA, the anti-gravitropic offset (AGO) has been proposed. According to this concept, the GSA is a balance of two antagonistic growth components, that is gravitropism and the AGO. Although the nature of the AGO has not been clarified, studies have suggested that gravitropism and the AGO share a common gravity-sensing mechanism in statocytes. This review discusses the molecular mechanisms underlying gravitropism as well as the hypothetical AGO in the control of the GSA.
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Affiliation(s)
- Nozomi Kawamoto
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
| | - Miyo Terao Morita
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
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9
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Dutt M, Mahmoud LM, Nehela Y, Grosser JW, Killiny N. The Citrus sinensis TILLER ANGLE CONTROL 1 (CsTAC1) gene regulates tree architecture in sweet oranges by modulating the endogenous hormone content. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111401. [PMID: 35905898 DOI: 10.1016/j.plantsci.2022.111401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Citrus is a major fruit crop cultivated on a global scale. Citrus trees are long lived perennials with a large canopy. Understanding the genetic control of tree architecture could provide tools for breeding and selection of citrus cultivars suitable for high density planting with improved light exposure. Tree architecture is modulated by the TILLER ANGLE CONTROL 1 (TAC1) gene which plays an important role in the regulation of the shoot angle. Herein, we used CRISPR/Cas9 technology to knockout the CsTAC1 gene for the biochemical and molecular analysis of its function. Nine transgenic lines were obtained, and five edited plants were confirmed based on T7EI mismatch detection assay and Sanger sequencing. The transgenic citrus lines exhibited pleiotropic phenotypes, including differences in branch angle and stem growth. Additionally, silencing CsTAC1 led to enhanced CsLAZY1 transcript levels in the tested lines. Analysis of the phytohormonal profile revealed that TAC1-edited plants exhibited lower auxin contents and increased cytokinin levels in the leaves compared to the wild-type plants. The GA7 gibberellin level was enhanced in most of the edited lines. Collectively, TAC1 affects branch angle in association with hormone signals in citrus.
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Affiliation(s)
- Manjul Dutt
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA.
| | - Lamiaa M Mahmoud
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Yasser Nehela
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31512, Egypt
| | - Jude W Grosser
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA
| | - Nabil Killiny
- Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA
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10
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Yang H, Liao H, Xu F, Zhang W, Xu B, Chen X, Zhu B, Pan W, Yang X. Integrated transcriptomic and gibberellin analyses reveal genes related to branch development in Eucalyptus urophylla. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:69-79. [PMID: 35661587 DOI: 10.1016/j.plaphy.2022.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Tree branches affect the planting density and basal scab, which act as important attributes in the yield and quality of trees. Eucalyptus urophylla is an important pioneer tree with characteristics of strong adaptability, fast growth, short rotation period, and low disease and pest pressures. In this study, we collected ZQUC14 and LDUD26 clones and compared their transcriptomes and metabolomes from mature xylem, phloem, and developing tissues to identify factors that may influence branch development. In total, 32,809 differentially expressed genes (DEGs) and 18 gibberellin (GA) hormones were detected in the five sampled tissues. Searches of the kyoto Encyclopedia of Genes and Genomes pathways identified mainly genes related to diterpenoid biosynthesis, plant MAPK signaling pathways, plant hormone signal transduction, glycerolipid metabolism, peroxisome, phenylpropanoid biosynthesis, ABC transporters, and brassinosteroid biosynthesis. Furthermore, gene expression trend analysis and weighted gene co-expression network analysis revealed 13 genes likely involved in diterpenoid biosynthesis, including five members of the 2OG-Fe(II) oxygenase superfamily, four cytochrome P450 genes, and four novel genes. In GA signal transduction pathways, 24 DEGs were found to positively regulate branch formation. These results provide a comprehensive analysis of branch development based on the transcriptome and metabolome, and help clarify the molecular mechanisms of E. urophylla.
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Affiliation(s)
- Huixiao Yang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Huanqin Liao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Fang Xu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Weihua Zhang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Bin Xu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Xinyu Chen
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Baozhu Zhu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Wen Pan
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China.
| | - Xiaohui Yang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, 510520, China.
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11
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Moulia B, Badel E, Bastien R, Duchemin L, Eloy C. The shaping of plant axes and crowns through tropisms and elasticity: an example of morphogenetic plasticity beyond the shoot apical meristem. THE NEW PHYTOLOGIST 2022; 233:2354-2379. [PMID: 34890051 DOI: 10.1111/nph.17913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Shoot morphogenetic plasticity is crucial to the adaptation of plants to their fluctuating environments. Major insights into shoot morphogenesis have been compiled studying meristems, especially the shoot apical meristem (SAM), through a methodological effort in multiscale systems biology and biophysics. However, morphogenesis at the SAM is robust to environmental changes. Plasticity emerges later on during post-SAM development. The purpose of this review is to show that multiscale systems biology and biophysics is insightful for the shaping of the whole plant as well. More specifically, we review the shaping of axes and crowns through tropisms and elasticity, combining the recent advances in morphogenetic control using physical cues and by genes. We focus mostly on land angiosperms, but with growth habits ranging from small herbs to big trees. We show that generic (universal) morphogenetic processes have been identified, revealing feedforward and feedback effects of global shape on the local morphogenetic process. In parallel, major advances have been made in the analysis of the major genes involved in shaping axes and crowns, revealing conserved genic networks among angiosperms. Then, we show that these two approaches are now starting to converge, revealing exciting perspectives.
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Affiliation(s)
- Bruno Moulia
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
| | - Eric Badel
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
| | - Renaud Bastien
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
- INSERM U1284, Center for Research and Interdisciplinarity (CRI), Université de Paris, F-75004, Paris, France
| | - Laurent Duchemin
- Physique et Mécanique des Milieux Hétérogenes, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, F-75005, Paris, France
| | - Christophe Eloy
- Aix Marseille Univ, CNRS, Centrale Marseille, IRPHE, F-13013, Marseille, France
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12
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Li Y, Tan X, Guo J, Hu E, Pan Q, Zhao Y, Chu Y, Zhu Y. Functional Characterization of MdTAC1a Gene Related to Branch Angle in Apple ( Malus x domestica Borkh.). Int J Mol Sci 2022; 23:1870. [PMID: 35163793 PMCID: PMC8836888 DOI: 10.3390/ijms23031870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022] Open
Abstract
The Tiller Angle Control 1 (TAC1) gene belongs to the IGT family, which mainly controls plant branch angle, thereby affecting plant form. Two members of MdTAC1 are identified in apple; the regulation of apple branch angle by MdTAC1 is still unclear. In this study, a subcellular localization analysis detected MdTAC1a in the nucleus and cell membrane, but MdTAC1b was detected in the cell membrane. Transgenic tobacco by overexpression of MdTAC1a or MdTAC1b showed enlarged leaf angles, the upregulation of several genes, such as GA 2-oxidase (GA2ox), and a sensitive response to light and gravity. According to a qRT-PCR analysis, MdTAC1a and MdTAC1b were strongly expressed in shoot tips and vegetative buds of weeping cultivars but were weakly expressed in columnar cultivars. In the MdTAC1a promoter, there were losses of 2 bp in spur cultivars and 6 bp in weeping cultivar compared with standard and columnar cultivars. An InDel marker specific to the MdTAC1a promoter was developed to distinguish apple cultivars and F1 progeny. We identified a protein, MdSRC2, that interacts with MdTAC1a, whose encoding gene which was highly expressed in trees with large branch angles. Our results indicate that differences in the MdTAC1a promoter are major contributors to branch-angle variation in apple, and the MdTAC1a interacts with MdSRC2 to affect this trait.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuandi Zhu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China; (Y.L.); (X.T.); (J.G.); (E.H.); (Q.P.); (Y.Z.); (Y.C.)
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13
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Wang W, Gao H, Liang Y, Li J, Wang Y. Molecular basis underlying rice tiller angle: Current progress and future perspectives. MOLECULAR PLANT 2022; 15:125-137. [PMID: 34896639 DOI: 10.1016/j.molp.2021.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
Crop plant architecture is an important agronomic trait that contributes greatly to crop yield. Tiller angle is one of the most critical components that determine crop plant architecture, which in turn substantially affects grain yield mainly owing to its large influence on plant density. Gravity is a fundamental physical force that acts on all organisms on earth. Plant organs sense gravity to control their growth orientation, including tiller angle in rice (Oryza sativa). This review summarizes recent research advances made using rice tiller angle as a research model, providing insights into domestication of rice tiller angle, genetic regulation of rice tiller angle, and shoot gravitropism. Finally, we propose that current discoveries in rice can shed light on shoot gravitropism and improvement of plant tiller/branch angle in other species, thereby contributing to agricultural production in the future.
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Affiliation(s)
- Wenguang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Hengbin Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yan Liang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Jiayang Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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14
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Li D, Zhao M, Yu X, Zhao L, Xu Z, Han X. Over-Expression of Rose RrLAZY1 Negatively Regulates the Branch Angle of Transgenic Arabidopsis Inflorescence. Int J Mol Sci 2021; 22:ijms222413664. [PMID: 34948467 PMCID: PMC8709306 DOI: 10.3390/ijms222413664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Branch angle is a key shoot architecture trait that strongly influences the ornamental and economic value of garden plants. However, the mechanism underlying the control of branch angle, an important aspect of tree architecture, is far from clear in roses. In the present study, we isolated the RrLAZY1 gene from the stems of Rosa rugosa ‘Zilong wochi’. Sequence analysis showed that the encoded RrLAZY1 protein contained a conserved GΦL (A/T) IGT domain, which belongs to the IGT family. Quantitative real-time PCR (qRT-PCR) analyses revealed that RrLAZY1 was expressed in all tissues and that expression was highest in the stem. The RrLAZY1 protein was localized in the plasma membrane. Based on a yeast two-hybrid assay and bimolecular fluorescence complementation experiments, the RrLAZY1 protein was found to interact with auxin-related proteins RrIAA16. The over-expression of the RrLAZY1 gene displayed a smaller branch angle in transgenic Arabidopsis inflorescence and resulted in changes in the expression level of genes related to auxin polar transport and signal transduction pathways. This study represents the first systematic analysis of the LAZY1 gene family in R. rugosa. The results of this study will provide a theoretical basis for the improvement of rose plant types and molecular breeding and provide valuable information for studying the regulation mechanism of branch angle in other woody plants.
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Affiliation(s)
| | | | | | | | - Zongda Xu
- Correspondence: (Z.X.); (X.H.); Tel.: +86-0538-824-2216 (Z.X. & X.H.)
| | - Xu Han
- Correspondence: (Z.X.); (X.H.); Tel.: +86-0538-824-2216 (Z.X. & X.H.)
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15
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Targeted CRISPR/Cas9-Based Knock-Out of the Rice Orthologs TILLER ANGLE CONTROL 1 (TAC1) in Poplar Induces Erect Leaf Habit and Shoot Growth. FORESTS 2021. [DOI: 10.3390/f12121615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pyramidal-, erect- or upright-growing plant forms are characterized by narrow branch angles of shoots and leaves. The putative advantage of upright-leaf and shoot habit could be a more efficient penetration of light into lower canopy layers. Pyramidal genotypes have already been reported for various tree genotypes including peach. The paralogous rice ortholog TILLER ANGLE CONTROL 1 (TAC1) has been proposed to be the responsible gene for upright growth. However, it has not really been demonstrated for any of the pyramidal tree genotypes that a knock-out mutation of the TAC1 gene is causing pyramidal plant growth. By in silico analyses, we have identified a putative rice TAC1 ortholog (Potri.014G102600, “TAC-14”) and its paralog (Potri.002G175300, “TAC-2”) in the genome of P. trichocarpa. Two putative PcTAC1 orthologs in the P. × canescens clone INRA 717-1B4 were successfully knocked-out by applying a transgenic CRISPR/Cas9-approach. The mutants were molecularly analyzed and phenotyped over a period of three years in a glasshouse. Our results indicate that the homozygous knock-out of “TAC-14” is sufficient to induce pyramidal plant growth in P. × canescens. If up to twice as many pyramidal individuals were planted on short rotation coppices (SRCs), this could lead to higher wood yield, without any breeding, simply by increasing the number of trees on a default field size.
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16
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Montesinos Á, Dardick C, Rubio-Cabetas MJ, Grimplet J. Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars. PLoS One 2021; 16:e0252001. [PMID: 34644299 PMCID: PMC8513883 DOI: 10.1371/journal.pone.0252001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a shared conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. To our knowledge, this is the first effort to analyze the diversity of IGT family proteins in members of the same tree species. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation could be established between the expression profile of these genes and the variability observed in the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that neither the expression nor the genetic polymorphism of IGT family genes are correlated to diversity of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.
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Affiliation(s)
- Álvaro Montesinos
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Hortofruticultura, Gobierno de Aragón, Avda. Montañana, Zaragoza, Spain
- Instituto Agroalimentario de Aragón–IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet, Zaragoza, Spain
| | - Chris Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States of America
| | - María José Rubio-Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Hortofruticultura, Gobierno de Aragón, Avda. Montañana, Zaragoza, Spain
- Instituto Agroalimentario de Aragón–IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet, Zaragoza, Spain
| | - Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Hortofruticultura, Gobierno de Aragón, Avda. Montañana, Zaragoza, Spain
- Instituto Agroalimentario de Aragón–IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet, Zaragoza, Spain
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Xia X, Mi X, Jin L, Guo R, Zhu J, Xie H, Liu L, An Y, Zhang C, Wei C, Liu S. CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis). BMC PLANT BIOLOGY 2021; 21:243. [PMID: 34049485 PMCID: PMC8164267 DOI: 10.1186/s12870-021-03044-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Branch angle is a pivotal component of tea plant architecture. Tea plant architecture not only affects tea quality and yield but also influences the efficiency of automatic tea plant pruning. However, the molecular mechanism controlling the branch angle, which is an important aspect of plant architecture, is poorly understood in tea plants. RESULTS In the present study, three CsLAZY genes were identified from tea plant genome data through sequence homology analysis. Phylogenetic tree displayed that the CsLAZY genes had high sequence similarity with LAZY genes from other plant species, especially those in woody plants. The expression patterns of the three CsLAZYs were surveyed in eight tissues. We further verified the expression levels of the key CsLAZY1 transcript in different tissues among eight tea cultivars and found that CsLAZY1 was highly expressed in stem. Subcellular localization analysis showed that the CsLAZY1 protein was localized in the plasma membrane. CsLAZY1 was transferred into Arabidopsis thaliana to investigate its potential role in regulating shoot development. Remarkably, the CsLAZY1 overexpressed plants responded more effectively than the wild-type plants to a gravity inversion treatment under light and dark conditions. The results indicate that CsLAZY1 plays an important role in regulating shoot gravitropism in tea plants. CONCLUSIONS The results provide important evidence for understanding the functions of CsLAZY1 in regulating shoot gravitropism and influencing the stem branch angle in tea plants. This report identifies CsLAZY1 as a promising gene resource for the improvement of tea plant architecture.
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Affiliation(s)
- Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Ling Jin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Hui Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Lu Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Cao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China.
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, China.
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18
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Waite JM, Dardick C. The roles of the IGT gene family in plant architecture: past, present, and future. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101983. [PMID: 33422965 DOI: 10.1016/j.pbi.2020.101983] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 05/03/2023]
Abstract
Genetic improvement of architectural traits offers tremendous opportunities to dramatically improve crop densities, productivity, and ultimately sustainability. Among these, the orientation, or gravitropic set point angle (GSA), of plant organs is critical to optimize crop profiles, light capture, and nutrient acquisition. Mutant GSA phenotypes have been studied in plants since the 1930's but only recently have the underlying genes been identified. Many of these genes have turned out to fall within the IGT (LAZY1/DRO1/TAC1) family, which initially was not previously recognized due to the lack of sequence conservation of homologous genes across species. Here we discuss recent progress on IGT family genes in various plant species over the past century, review possible functional mechanisms, and provide further analysis of their evolution in land plants and their past and future roles in crop domestication.
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Affiliation(s)
- Jessica Marie Waite
- USDA Tree Fruit Research Laboratory, 1104 N Western Avenue, Wenatchee, WA, USA
| | - Christopher Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA.
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19
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Li L, Zhang Y, Zheng T, Zhuo X, Li P, Qiu L, Liu W, Wang J, Cheng T, Zhang Q. Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. Sci Rep 2021; 11:2675. [PMID: 33514804 PMCID: PMC7846751 DOI: 10.1038/s41598-021-81892-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/13/2021] [Indexed: 11/23/2022] Open
Abstract
Prunus mume (also known as Mei) is an important ornamental plant that is popular with Asians. The weeping trait in P. mume has attracted the attention of researchers for its high ornamental value. However, the formation of the weeping trait of woody plants is a complex process and the molecular basis of weeping stem development is unclear. Here, the morphological and histochemical characteristics and transcriptome profiles of upright and weeping stems from P. mume were studied. Significant alterations in the histochemical characteristics of upright and weeping stems were observed, and the absence of phloem fibres and less xylem in weeping stems might be responsible for their inability to resist gravity and to grow downward. Transcriptome analysis showed that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and phytohormone signal transduction pathways. To investigate the differential responses to hormones, upright and weeping stems were treated with IAA (auxin) and GA3 (gibberellin A3), respectively, and the results revealed that weeping stems had a weaker IAA response ability and reduced upward bending angles than upright stems. On the contrary, weeping stems had increased upward bending angles than upright stems with GA3 treatment. Compared to upright stems, interestingly, DEGs associated with diterpenoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched after being treated with IAA, and expression levels of genes associated with phenylpropanoid biosynthesis, ABC transporters, glycosylphosphatidylinositol (GPI)—anchor biosynthesis were altered after being treated with GA3 in weeping stems. Those results reveal that multiple molecular mechanisms regulate the formation of weeping trait in P. mume, which lays a theoretical foundation for the cultivation of new varieties.
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Affiliation(s)
- Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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 Advanced Innovation Center for Tree Breeding By Molecular Design, 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.
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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
| | - Like Qiu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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
| | - Weichao Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, 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 Advanced Innovation Center for Tree Breeding By Molecular Design, 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 Advanced Innovation Center for Tree Breeding By Molecular Design, 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 Advanced Innovation Center for Tree Breeding By Molecular Design, 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.
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20
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Jiao Z, Du H, Chen S, Huang W, Ge L. LAZY Gene Family in Plant Gravitropism. FRONTIERS IN PLANT SCIENCE 2021; 11:606241. [PMID: 33613583 PMCID: PMC7893674 DOI: 10.3389/fpls.2020.606241] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/01/2020] [Indexed: 05/26/2023]
Abstract
Adapting to the omnipresent gravitational field was a fundamental basis driving the flourishing of terrestrial plants on the Earth. Plants have evolved a remarkable capability that not only allows them to live and develop within the Earth's gravity field, but it also enables them to use the gravity vector to guide the growth of roots and shoots, in a process known as gravitropism. Triggered by gravistimulation, plant gravitropism is a highly complex, multistep process that requires many organelles and players to function in an intricate coordinated way. Although this process has been studied for several 100 years, much remains unclear, particularly the early events that trigger the relocation of the auxin efflux carrier PIN-FORMED (PIN) proteins, which presumably leads to the asymmetrical redistribution of auxin. In the past decade, the LAZY gene family has been identified as a crucial player that ensures the proper redistribution of auxin and a normal tropic response for both roots and shoots upon gravistimulation. LAZY proteins appear to be participating in the early steps of gravity signaling, as the mutation of LAZY genes consistently leads to altered auxin redistribution in multiple plant species. The identification and characterization of the LAZY gene family have significantly advanced our understanding of plant gravitropism, and opened new frontiers of investigation into the novel molecular details of the early events of gravitropism. Here we review current knowledge of the LAZY gene family and the mechanism modulated by LAZY proteins for controlling both roots and shoots gravitropism. We also discuss the evolutionary significance and conservation of the LAZY gene family in plants.
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Affiliation(s)
- Zhicheng Jiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Huan Du
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Shu Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
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21
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Guo W, Chen L, Herrera-Estrella L, Cao D, Tran LSP. Altering Plant Architecture to Improve Performance and Resistance. TRENDS IN PLANT SCIENCE 2020; 25:1154-1170. [PMID: 32595089 DOI: 10.1016/j.tplants.2020.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.
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Affiliation(s)
- Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Luis Herrera-Estrella
- The Unidad de Genomica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico; Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, TX, USA
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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22
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Opposing influences of TAC1 and LAZY1 on Lateral Shoot Orientation in Arabidopsis. Sci Rep 2020; 10:6051. [PMID: 32269265 PMCID: PMC7142156 DOI: 10.1038/s41598-020-62962-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
TAC1 and LAZY1 are members of a gene family that regulates lateral shoot orientation in plants. TAC1 promotes outward orientations in response to light, while LAZY1 promotes upward shoot orientations in response to gravity via altered auxin transport. We performed genetic, molecular, and biochemical assays to investigate possible interactions between these genes. In Arabidopsis they were expressed in similar tissues and double mutants revealed the wide-angled lazy1 branch phenotype, indicating it is epistatic to the tac1 shoot phenotype. Surprisingly, the lack of TAC1 did not influence gravitropic shoot curvature responses. Combined, these results suggest TAC1 might negatively regulate LAZY1 to promote outward shoot orientations. However, additional results revealed that TAC1- and LAZY1 influence on shoot orientation is more complex than a simple direct negative regulatory pathway. Transcriptomes of Arabidopsis tac1 and lazy1 mutants compared to wild type under normal and gravistimulated conditions revealed few overlapping differentially expressed genes. Overexpression of each gene did not result in major branch angle differences. Shoot tip hormone levels were similar between tac1, lazy1, and Col, apart from exceptionally elevated levels of salicylic acid in lazy1. The data presented here provide a foundation for future study of TAC1 and LAZY1 regulation of shoot architecture.
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23
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Antioxidant and the Dwarfing Candidate Gene of "Nantongxiaofangshi" ( Diospyros kaki Thunb.). OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1629845. [PMID: 31885771 PMCID: PMC6899303 DOI: 10.1155/2019/1629845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022]
Abstract
The aims of this work were to identify genes related to dwarfing for subsequent dwarfing-related research in persimmon and evaluate the relationship between antioxidant activity, dwarf, and hormones of persimmon trees for analyzing the possible dwarf mechanism oxidation factors. In the present study, a transcriptome analysis of “Nantongxiaofangshi” was used to identify and clone 22 candidate genes related to gibberellin signal transduction pathways and synthetic pathway. The expression of these genes was assessed in two persimmon cultivars, “Dafangshi” and “Nantongxiaofangshi,” by RT-qPCR at different phenological stages and in response to the exogenous application of GA3 (GA treatment) and PAZ (paclobutrazol, a plant growth inhibitor, also called PP333). The results revealed differential expression of 14 of these 22 genes in the two varieties. Subsequently, endogenous hormone levels were assessed of the two varieties, along with the number of internodes and internode length. The results suggested that the persimmon could be used as a valuable and powerful natural candidate for providing information on the functional role of dwarfing.
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Zhang W, Tan L, Sun H, Zhao X, Liu F, Cai H, Fu Y, Sun X, Gu P, Zhu Z, Sun C. Natural Variations at TIG1 Encoding a TCP Transcription Factor Contribute to Plant Architecture Domestication in Rice. MOLECULAR PLANT 2019; 12:1075-1089. [PMID: 31002981 DOI: 10.1016/j.molp.2019.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/24/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
The modification of plant architecture is a crucial target in rice domestication and modern genetic improvement. Although several genes regulating rice plant architecture have been characterized, the molecular mechanisms underlying rice plant architecture domestication remain largely unclear. Here we show that the inclined tiller growth in wild rice is controlled by a single dominant gene, TILLER INCLINED GROWTH 1 (TIG1), which is located on chromosome 8 and encodes a TCP transcriptional activator. TIG1 is primarily expressed in the adaxial side of the tiller base, promotes cell elongation, and enlarges the tiller angle in wild rice. Variations in the TIG1 promoter of indica cultivars (tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle, leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice domestication. TIG1 positively regulates the expression of EXPA3, EXPB5, and SAUR39 to promote cell elongation and increase the tiller angle. Selective sweep analysis revealed that the tig1 allele was selected in indica cultivars by human beings. The cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.
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Affiliation(s)
- Weifeng Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Lubin Tan
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Hongying Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xinhui Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Hongwei Cai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Yongcai Fu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xianyou Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Ping Gu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Zuofeng Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China.
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25
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Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis. Proc Natl Acad Sci U S A 2019; 116:5653-5658. [PMID: 30833384 PMCID: PMC6431163 DOI: 10.1073/pnas.1820513116] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Utilization of heterosis has greatly increased productivity of many crops globally. Allele-specific expression (ASE) has been suggested as a mechanism for causing heterosis. We performed a genome-wide analysis of ASE in three tissues of an elite rice hybrid grown under four conditions. The analysis identified 3,270 genes showing various patterns of ASE in response to developmental and environmental cues, which provides a glimpse of the ASE landscape in the hybrid genome. We showed that the ASE patterns may have distinct implications in the genetic basis of heterosis, especially in light of the classical dominance and overdominance hypotheses. The genes showing ASE provide the candidates for future studies of the genetic and molecular mechanism of heterosis. Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.
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Hill JL, Hollender CA. Branching out: new insights into the genetic regulation of shoot architecture in trees. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:73-80. [PMID: 30339931 DOI: 10.1016/j.pbi.2018.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 05/03/2023]
Abstract
Directional growth in all plants involves both phototropic and gravitropic responses. Accordingly, mechanisms controlling shoot architecture throughout the plant kingdom are likely similar. However, as forms vary between species due in part to gene copy number and functional divergence, some aspects of how plants predetermine and regulate architecture can differ. This is especially true when comparing annual herbaceous species (e.g. model plants) to woody perennials such as trees. In the past decade, inexpensive genomic sequencing and technological advances enabled gene discovery and functional analyses in trees. This led to the identification of genes associated with tree shoot architecture control. Here, we present recent discoveries on the regulation of shoot architectures for which causative genes have been identified, including dwarf, weeping, columnar, and pillar growth habits. We also discuss potential applications of these findings.
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Affiliation(s)
- Joseph L Hill
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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27
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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28
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Busov VB. Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production. FRONTIERS IN PLANT SCIENCE 2018; 9:1505. [PMID: 30459780 PMCID: PMC6232754 DOI: 10.3389/fpls.2018.01505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Growth and architectural traits in trees are economically and environmentally important and thus of considerable importance to the improvement of forest and fruit trees. These traits are complex and result from the operation of a number of molecular mechanisms. This review will focus on the regulation of crown architecture, secondary woody growth and adventitious rooting. These traits and processes have significant impact on deployment, management, and productivity of tree crops. The majority of the described work comes from experiments in model plants, poplar, apple, peach, and plum because these species allow functional analysis of the involved genes and have significant genomics resources. However, these studies convincingly show conserved mechanisms for elaboration of specific growth and architectural traits. The conservation of these mechanisms suggest that they can be used as a blueprint for the improvement of these traits and processes in phylogenetically diverse tree crops. We will specifically consider the involvement of flowering time, transcription factors and hormone-associated genes. The review will also discuss the impact of recent technological advances as well as the challenges to the dissection of these traits in trees.
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29
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Waite JM, Dardick C. TILLER ANGLE CONTROL 1 modulates plant architecture in response to photosynthetic signals. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4935-4944. [PMID: 30099502 DOI: 10.1093/jxb/ery253] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/02/2018] [Indexed: 05/11/2023]
Abstract
Light serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under continuous dark or far-red growth conditions, but did not drop to these low levels during a diurnal time course. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon red/far-red or blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1). Overexpression of TAC1 partially prevented the narrowing of branch angles in the dark or under far-red light. Treatment with the carotenoid biosynthesis inhibitor norflurazon or the PSII inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) led to loss of TAC1 expression similar to dark or far-red conditions, but expression increased in response to the PSI inhibitor paraquat. Treatment of adult plants with norflurazon resulted in upward growth angle of branch tips. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.
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Affiliation(s)
- Jessica M Waite
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, Kearneysville, WV, USA
| | - Chris Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, Kearneysville, WV, USA
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