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Cao C, Guo S, Deng P, Yang S, Xu J, Hu T, Hu Z, Chen D, Zhang H, Navea IP, Chin JH, Zhang W, Jing W. The BEL1-like homeodomain protein OsBLH4 regulates rice plant height, grain number, and heading date by repressing the expression of OsGA2ox1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1369-1385. [PMID: 38824648 DOI: 10.1111/tpj.16857] [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: 11/09/2023] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/04/2024]
Abstract
Gibberellins (GAs) play crucial roles in regulating plant architecture and grain yield of crops. In rice, the inactivation of endogenous bioactive GAs and their precursors by GA 2-oxidases (GA2oxs) regulates stem elongation and reproductive development. However, the regulatory mechanisms of GA2ox gene expression, especially in rice reproductive organs, are unknown. The BEL1-like homeodomain protein OsBLH4, a negative regulatory factor for the rice OsGA2ox1 gene, was identified in this study. Loss of OsBLH4 function results in decreased bioactive GA levels and pleiotropic phenotypes, including reduced plant height, decreased grain number per panicle, and delayed heading date, as also observed in OsGA2ox1-overexpressing plants. Consistent with the mutant phenotype, OsBLH4 was predominantly expressed in shoots and young spikelets; its encoded protein was exclusively localized in the nucleus. Molecular analysis demonstrated that OsBLH4 directly bound to the promoter region of OsGA2ox1 to repress its expression. Genetic assays revealed that OsBLH4 acts upstream of OsGA2ox1 to control rice plant height, grain number, and heading date. Taken together, these results indicate a crucial role for OsBLH4 in regulating rice plant architecture and yield potential via regulation of bioactive GA levels, and provide a potential strategy for genetic improvements of rice.
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Affiliation(s)
- Chengjuan Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shuaiqiang Guo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ping Deng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Xianghu Laboratory, Hangzhou, China
| | - Shiyi Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jing Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tengfei Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhijuan Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Di Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hongsheng Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | - Wenhua Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wen Jing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Tsuda K, Maeno A, Otake A, Kato K, Tanaka W, Hibara KI, Nonomura KI. YABBY and diverged KNOX1 genes shape nodes and internodes in the stem. Science 2024; 384:1241-1247. [PMID: 38870308 DOI: 10.1126/science.adn6748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/03/2024] [Indexed: 06/15/2024]
Abstract
Plant stems comprise nodes and internodes that specialize in solute exchange and elongation. However, their boundaries are not well defined, and how these basic units arise remains elusive. In rice with clear nodes and internodes, we found that one subclade of class I knotted1-like homeobox (KNOX1) genes for shoot meristem indeterminacy restricts node differentiation and allows internode formation by repressing YABBY genes for leaf development and genes from another node-specific KNOX1 subclade. YABBYs promote nodal vascular differentiation and limit stem elongation. YABBY and node-specific KNOX1 genes specify the pulvinus, which further elaborates the nodal structure for gravitropism. Notably, this KNOX1 subclade organization is specific to seed plants. We propose that nodes and internodes are distinct domains specified by YABBY-KNOX1 cross-regulation that diverged in early seed plants.
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Affiliation(s)
- Katsutoshi Tsuda
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Akiteru Maeno
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ayako Otake
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kae Kato
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo 656-0484, Japan
| | - Ken-Ichi Nonomura
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
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Dong X, Liu X, Cheng L, Li R, Ge S, Wang S, Cai Y, Liu Y, Meng S, Jiang CZ, Shi CL, Li T, Fu D, Qi M, Xu T. SlBEL11 regulates flavonoid biosynthesis, thus fine-tuning auxin efflux to prevent premature fruit drop in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:749-770. [PMID: 38420861 DOI: 10.1111/jipb.13627] [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: 10/24/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024]
Abstract
Auxin regulates flower and fruit abscission, but how developmental signals mediate auxin transport in abscission remains unclear. Here, we reveal the role of the transcription factor BEL1-LIKE HOMEODOMAIN11 (SlBEL11) in regulating auxin transport during abscission in tomato (Solanum lycopersicum). SlBEL11 is highly expressed in the fruit abscission zone, and its expression increases during fruit development. Knockdown of SlBEL11 expression by RNA interference (RNAi) caused premature fruit drop at the breaker (Br) and 3 d post-breaker (Br+3) stages of fruit development. Transcriptome and metabolome analysis of SlBEL11-RNAi lines revealed impaired flavonoid biosynthesis and decreased levels of most flavonoids, especially quercetin, which functions as an auxin transport inhibitor. This suggested that SlBEL11 prevents premature fruit abscission by modulating auxin efflux from fruits, which is crucial for the formation of an auxin response gradient. Indeed, quercetin treatment suppressed premature fruit drop in SlBEL11-RNAi plants. DNA affinity purification sequencing (DAP-seq) analysis indicated that SlBEL11 induced expression of the transcription factor gene SlMYB111 by directly binding to its promoter. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay showed that S. lycopersicum MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG111 (SlMYB111) induces the expression of the core flavonoid biosynthesis genes SlCHS1, SlCHI, SlF3H, and SlFLS by directly binding to their promoters. Our findings suggest that the SlBEL11-SlMYB111 module modulates flavonoid biosynthesis to fine-tune auxin efflux from fruits and thus maintain an auxin response gradient in the pedicel, thereby preventing premature fruit drop.
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Affiliation(s)
- Xiufen Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xianfeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Lina Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Ruizhen Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Siqi Ge
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Sai Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Yue Cai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Yang Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Sida Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture Agricultural Research Service, Washington, DC, 20250, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Daqi Fu
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
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4
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Ma B, Zhu J, Huang X. Diversification of plant SUPPRESSOR OF MAX2 1 (SMAX1)-like genes and genome-wide identification and characterization of cotton SMXL gene family. BMC PLANT BIOLOGY 2023; 23:419. [PMID: 37691127 PMCID: PMC10494346 DOI: 10.1186/s12870-023-04421-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Strigolactones (SLs) are a recently discovered class of plant hormones. SUPPRESSOR OF MAX2 1 (SMAX1)-like proteins, key component of the SL signaling pathway, have been studied extensively for their roles in regulating plant growth and development, such as plant branching. However, systematic identification and functional characterization of SMXL genes in cotton (Gossypium sp.), an important fiber and oil crop, has rarely been conducted. RESULTS We identified 210 SMXL genes from 21 plant genomes and examined their evolutionary relationships. The structural characteristics of the SMXL genes and their encoded proteins exhibited both consistency and diversity. All plant SMXL proteins possess a conserved Clp-N domain, P-loop NTPase, and EAR motif. We identified 63 SMXL genes in cotton and classified these into four evolutionary branches. Gene expression analysis revealed tissue-specific expression patterns of GhSMXL genes, with some upregulated in response to GR24 treatment. Protein co-expression network analysis showed that GhSMXL6, GhSMXL7-1, and GhSMXL7-2 mainly interact with proteins functioning in growth and development, while virus-induced gene silencing revealed that GhSMAX1-1 and GhSMAX1-2 suppress the growth and development of axillary buds. CONCLUSIONS SMXL gene family members show evolutionary diversification through the green plant lineage. GhSMXL6/7-1/7-2 genes play critical roles in the SL signaling pathway, while GhSMXL1-1 and GhSMXL1-2 function redundantly in growth of axillary buds. Characterization of the cotton SMXL gene family provides new insights into their roles in responding to SL signals and in plant growth and development. Genes identified in this study could be used as the candidate genes for improvement of plant architecture and crop yield.
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Affiliation(s)
- Bin Ma
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China
| | - Jianbo Zhu
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China.
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5
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Jia P, Sharif R, Li Y, Sun T, Li S, Zhang X, Dong Q, Luan H, Guo S, Ren X, Qi G. The BELL1-like homeobox gene MdBLH14 from apple controls flowering and plant height via repression of MdGA20ox3. Int J Biol Macromol 2023; 242:124790. [PMID: 37169049 DOI: 10.1016/j.ijbiomac.2023.124790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
Apple growth and yield are largely dependent on plant height and flowering characteristics. The BELL1-like homeobox (BLH) transcription factors regulate extensive plant biological processes. However, the BLH-mediated regulation of plant height and flowering in apple remains elusive. In the current study, 19 members of the MdBLH family were identified in the apple genome. Segmental duplication and purifying selection are the main reasons for the evolution of the MdBLH genes. A BLH1-like gene, MdBLH14, was isolated and functionally characterized. The MdBLH14 was preferentially expressed in flower buds, and downregulated during the floral induction period. The subcellular localization in tobacco leaves indicated that MdBLH14 is a nuclear protein. Overexpression of MdBLH14 in Arabidopsis led to a significant dwarfing and late-flowering phenotype by hindering active GA accumulation. Additionally, MdKNOX19, another member of the TALE superfamily, physically interacts with MdBLH14 and synergistically inhibits the expression of MdGA20ox3. This is the first report on the function of the MdBLH14 from apple, and its mechanism involving plant flower induction and growth. The data presented here provide a theoretical basis for genetically breeding new apple varieties.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China.
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youmei Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China; Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tianbo Sun
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Shikui Li
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xuemei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Qinglong Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Haoan Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Suping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xiaolin Ren
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China.
| | - Guohui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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Yoon J, Baek G, Pasriga R, Tun W, Min CW, Kim ST, Cho LH, An G. Homeobox transcription factors OsZHD1 and OsZHD2 induce inflorescence meristem activity at floral transition in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1327-1339. [PMID: 36120845 DOI: 10.1111/pce.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/04/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Floral transition starts in the leaves when florigens respond to various environmental and developmental factors. Among several regulatory genes that are preferentially expressed in the inflorescence meristem during the floral transition, this study examines the homeobox genes OsZHD1 and OsZHD2 for their roles in regulating this transition. Although single mutations in these genes did not result in visible phenotype changes, double mutations in these genes delayed flowering. Florigen expression was not altered in the double mutants, indicating that the delay was due to a defect in florigen signaling. Morphological analysis of shoot apical meristem at the early developmental stage indicated that inflorescence meristem development was significantly delayed in the double mutants. Overexpression of ZHD2 causes early flowering because of downstream signals after the generation of florigens. Expression levels of the auxin biosynthesis genes were reduced in the mutants and the addition of indole-3-acetic acid recovered the defect in the mutants, suggesting that these homeobox genes play a role in auxin biosynthesis. A rice florigen, RICE FLOWERING LOCUS T 1, binds to the promoter regions of homeobox genes. These results indicate that florigens stimulate the expression of homeobox genes, enhancing inflorescence development in the shoot apex.
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Affiliation(s)
- Jinmi Yoon
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
| | - Richa Pasriga
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Win Tun
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Sun-Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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8
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Chen Y, Guo Y, Guan P, Wang Y, Wang X, Wang Z, Qin Z, Ma S, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Guo W, Peng H. A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. MOLECULAR PLANT 2023; 16:393-414. [PMID: 36575796 DOI: 10.1016/j.molp.2022.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/28/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Panfeng Guan
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaobo Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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9
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Gao Y, Yuan Y, Zhang X, Song H, Yang Q, Yang P, Gao X, Gao J, Feng B. Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet ( Setaria italica). Int J Mol Sci 2022; 23:11824. [PMID: 36233125 PMCID: PMC9569614 DOI: 10.3390/ijms231911824] [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: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.
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Affiliation(s)
- Yongbin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
- Dexing Township Agro-Pastoral Comprehensive Service Center, Nyingchi 860700, China
| | - Yuhao Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiongying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Hui Song
- Anyang Academy of Agricultural Sciences, Anyang 455099, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Pu Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Jinfeng Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
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10
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Niu X, Fu D. The Roles of BLH Transcription Factors in Plant Development and Environmental Response. Int J Mol Sci 2022; 23:3731. [PMID: 35409091 PMCID: PMC8998993 DOI: 10.3390/ijms23073731] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Despite recent advancements in plant molecular biology and biotechnology, providing enough, and safe, food for an increasing world population remains a challenge. The research into plant development and environmental adaptability has attracted more and more attention from various countries. The transcription of some genes, regulated by transcript factors (TFs), and their response to biological and abiotic stresses, are activated or inhibited during plant development; examples include, rooting, flowering, fruit ripening, drought, flooding, high temperature, pathogen infection, etc. Therefore, the screening and characterization of transcription factors have increasingly become a hot topic in the field of plant research. BLH/BELL (BEL1-like homeodomain) transcription factors belong to a subfamily of the TALE (three-amino-acid-loop-extension) superfamily and its members are involved in the regulation of many vital biological processes, during plant development and environmental response. This review focuses on the advances in our understanding of the function of BLH/BELL TFs in different plants and their involvement in the development of meristems, flower, fruit, plant morphogenesis, plant cell wall structure, the response to the environment, including light and plant resistance to stress, biosynthesis and signaling of ABA (Abscisic acid), IAA (Indoleacetic acid), GA (Gibberellic Acid) and JA (Jasmonic Acid). We discuss the theoretical basis and potential regulatory models for BLH/BELL TFs' action and provide a comprehensive view of their multiple roles in modulating different aspects of plant development and response to environmental stress and phytohormones. We also present the value of BLHs in the molecular breeding of improved crop varieties and the future research direction of the BLH gene family.
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Affiliation(s)
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China;
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11
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Genome-Wide Identification, Expression, and Interaction Analysis of BEL-Like Homeodomain Gene Family in Peach. Biochem Genet 2022; 60:2037-2051. [PMID: 35230561 DOI: 10.1007/s10528-022-10203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 02/09/2022] [Indexed: 11/02/2022]
Abstract
BEL1-like homeodomain (BLH) family genes as homeodomain transcription factors are found ubiquitously in plants to play important regulatory roles in reproductive development, morphological development, and stress response. Although BLH proteins have been reported in some species, there is little information about BLH genes in peach. In this study, we identified 11 peach PpBLH genes based on the conserved domain. Phylogenetic analysis suggested that the PpBLH proteins could be divided into five groups, which might be involved in different aspects of morphogenesis. Genomics structure analysis revealed that there were four exons in the PpBLH gene, and the length of the third exon was 61 bp. Chromosomal location analysis showed that the PpBLH genes were not distributed uniformly on six chromosomes. Promoter analysis showed that the promoter sequences of six PpBLH genes contained multiple cis-acting elements for hormones and stress. Six PpBLH genes were cloned by RT-PCR, and PpBLH1, PpBLH4, and PpBLH7 showed different expression patterns in the tested fruits under common temperature and high temperature. Y2H results indicated that PpBLH7 andPpBLH10 interacted with the PpOFP6 protein, and PpBLH1 interacted with the PpOFP1, PpOFP2, PpOFP4, and PpOFP13 proteins. These results provide new insight for further study of PpBLH genes, and construction of regulatory networks of PpBLH proteins in the growth, development, and stress response of peach.
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12
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He Y, Yang T, Yan S, Niu S, Zhang Y. Identification and characterization of the BEL1-like genes reveal their potential roles in plant growth and abiotic stress response in tomato. Int J Biol Macromol 2022; 200:193-205. [PMID: 34995657 DOI: 10.1016/j.ijbiomac.2021.12.175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/05/2022]
Abstract
BEL1-like (BELL) transcription factors, belonging to three-amino acid-loop-extension (TALE) superfamily, are ubiquitous in plants. BELLs regulate a wide range of plant biological processes, but the understanding of the BELL family in tomato (Solanum lycopersicum) remains fragmentary. In this study, a total of 14 members of the SlBELL family were identified in tomato. SlBELL proteins contained the conserved BELL and SKY domains that served as typical structures of the BELL family. Syntenic analysis indicated that the BELL orthologs between tomato and other dicots had close evolutionary relationships. Furthermore, the promoters of SlBELLs contained numerous cis-elements related to plant growth, development, and stress response. The SlBELL genes exhibited different tissue-specific expression profiles and responded to cold, heat, and drought stresses, implying their potential functions in regulating multiple aspects of plant growth, as well as in response to abiotic stresses. Through the interaction network prediction, we found that most SlBELL proteins displayed probable interactions with the KNOTTED1-like (KNOX) proteins, another kind of transcription factor in the TALE superfamily. These findings laid foundations for further dissection of the functions of SlBELL genes in tomato, as well as for exploration of the evolutionary relationships of BELL homologs among different plant species.
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Affiliation(s)
- Yu He
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Tongwen Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Siwei Yan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Shaobo Niu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Yan Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
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13
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VPB1 Encoding BELL-like Homeodomain Protein Is Involved in Rice Panicle Architecture. Int J Mol Sci 2021; 22:ijms22157909. [PMID: 34360677 PMCID: PMC8348756 DOI: 10.3390/ijms22157909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022] Open
Abstract
Inflorescence architecture in rice (Oryza sativa) is mainly determined by spikelets and the branch arrangement. Primary branches initiate from inflorescence meristem in a spiral phyllotaxic manner, and further develop into the panicle branches. The branching patterns contribute largely to rice production. In this study, we characterized a rice verticillate primary branch 1(vpb1) mutant, which exhibited a clustered primary branches phenotype. Gene isolation revealed that VPB1 was a allele of RI, that it encoded a BELL-like homeodomain (BLH) protein. VPB1 gene preferentially expressed in the inflorescence and branch meristems. The arrangement of primary branch meristems was disturbed in the vpb1 mutant. Transcriptome analysis further revealed that VPB1 affected the expression of some genes involved in inflorescence meristem identity and hormone signaling pathways. In addition, the differentially expressed gene (DEG) promoter analysis showed that OsBOPs involved in boundary organ initiation were potential target genes of VPB1 protein. Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter system further verified that VPB1 protein bound to the promoter of OsBOP1 gene. Overall, our findings demonstrate that VPB1 controls inflorescence architecture by regulating the expression of genes involved in meristem maintenance and hormone pathways and by interacting with OsBOP genes.
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14
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Wang L, Ming L, Liao K, Xia C, Sun S, Chang Y, Wang H, Fu D, Xu C, Wang Z, Li X, Xie W, Ouyang Y, Zhang Q, Li X, Zhang Q, Xiao J, Zhang Q. Bract suppression regulated by the miR156/529-SPLs-NL1-PLA1 module is required for the transition from vegetative to reproductive branching in rice. MOLECULAR PLANT 2021; 14:1168-1184. [PMID: 33933648 DOI: 10.1016/j.molp.2021.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/06/2021] [Accepted: 04/27/2021] [Indexed: 05/04/2023]
Abstract
Reproductive transition of grasses is characterized by switching the pattern of lateral branches, featuring the suppression of outgrowth of the subtending leaves (bracts) and rapid formation of higher-order branches in the inflorescence (panicle). However, the molecular mechanisms underlying such changes remain largely unknown. Here, we show that bract suppression is required for the reproductive branching in rice. We identified a pathway involving the intrinsic time ruler microRNA156/529, their targets SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes, NECK LEAF1 (NL1), and PLASTOCHRON1 (PLA1), which regulates the bract outgrowth and thus affects the pattern switch between vegetative and reproductive branching. Suppression of the bract results in global reprogramming of transcriptome and chromatin accessibility following the reproductive transition, while these processes are largely dysregulated in the mutants of these genes. These discoveries contribute to our understanding of the dynamic plant architecture and provide novel insights for improving crop yields.
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Affiliation(s)
- Lei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Keyan Liao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyuan Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongkai Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Conghao Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Yin X. Phyllotaxis: from classical knowledge to molecular genetics. JOURNAL OF PLANT RESEARCH 2021; 134:373-401. [PMID: 33550488 DOI: 10.1007/s10265-020-01247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Plant organs are repetitively generated at the shoot apical meristem (SAM) in recognizable patterns. This phenomenon, known as phyllotaxis, has long fascinated scientists from different disciplines. While we have an enriched body of knowledge on phyllotactic patterns, parameters, and transitions, only in the past 20 years, however, have we started to identify genes and elucidate genetic pathways that involved in phyllotaxis. In this review, I first summarize the classical knowledge of phyllotaxis from a morphological perspective. I then discuss recent advances in the regulation of phyllotaxis, from a molecular genetics perspective. I show that the morphological beauty of phyllotaxis we appreciate is the manifestation of many regulators, in addition to the critical role of auxin as a patterning signal, exerting their respective effects in a coordinated fashion either directly or indirectly in the SAM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Japan Society for the Promotion of Science, Tokyo, Japan.
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16
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Wang C, Yang X, Li G. Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops. Int J Mol Sci 2021; 22:3508. [PMID: 33805287 PMCID: PMC8037405 DOI: 10.3390/ijms22073508] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.
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Affiliation(s)
- Chengyu Wang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
| | - Gang Li
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
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17
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He L, Liu Y, He H, Liu Y, Qi J, Zhang X, Li Y, Mao Y, Zhou S, Zheng X, Bai Q, Zhao B, Wang D, Wen J, Mysore KS, Tadege M, Xia Y, Chen J. A molecular framework underlying the compound leaf pattern of Medicago truncatula. NATURE PLANTS 2020; 6:511-521. [PMID: 32393879 DOI: 10.1038/s41477-020-0642-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
Compound leaves show more complex patterns than simple leaves, and this is mainly because of a specific morphogenetic process (leaflet initiation and arrangement) that occurs during their development. How the relevant morphogenetic activity is established and modulated to form a proper pattern of leaflets is a central question. Here we show that the trifoliate leaf pattern of the model leguminous plant Medicago truncatula is controlled by the BEL1-like homeodomain protein PINNATE-LIKE PENTAFOLIATA1 (PINNA1). We identify PINNA1 as a determinacy factor during leaf morphogenesis that directly represses transcription of the LEAFY (LFY) orthologue SINGLE LEAFLET1 (SGL1), which encodes an indeterminacy factor key to the morphogenetic activity maintenance. PINNA1 functions alone in the terminal leaflet region and synergizes with another determinacy factor, the C2H2 zinc finger protein PALMATE-LIKE PENTAFOLIATA1 (PALM1), in the lateral leaflet regions to define the spatiotemporal expression of SGL1, leading to an elaborate control of morphogenetic activity. This study reveals a framework for trifoliate leaf-pattern formation and sheds light on mechanisms generating diverse leaf forms.
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Affiliation(s)
- Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China
| | - Hua He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Ye Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jinfeng Qi
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaojia Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Youhan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zheng
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Dongfa Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | | | | | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, USA
| | - Yongmei Xia
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, China.
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18
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Hojsgaard D. Apomixis Technology: Separating the Wheat from the Chaff. Genes (Basel) 2020; 11:E411. [PMID: 32290084 PMCID: PMC7231277 DOI: 10.3390/genes11040411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University of Göttingen, Untere Karspüle 2, D-37073-1 Göttingen, Germany
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