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Li P, He Y, Xiao L, Quan M, Gu M, Jin Z, Zhou J, Li L, Bo W, Qi W, Huang R, Lv C, Wang D, Liu Q, El-Kassaby YA, Du Q, Zhang D. Temporal dynamics of genetic architecture governing leaf development in Populus. New Phytol 2024; 242:1113-1130. [PMID: 38418427 DOI: 10.1111/nph.19649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/13/2024] [Indexed: 03/01/2024]
Abstract
Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome-wide association study (GWAS), time-ordered gene co-expression network (TO-GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus. We identified 42 time-specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO-GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO-GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.
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Affiliation(s)
- Peng Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuling He
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Xiao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Mingyang Quan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Mingyue Gu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhuoying Jin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxuan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lianzheng Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weina Qi
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rui Huang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenfei Lv
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dan Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT, 2601, Australia
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Qingzhang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Deqiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Li H, Feng H, Guo C, Yang S, Huang W, Xiong X, Liu J, Chen G, Liu Q, Xiong L, Liu K, Yang W. High-throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed. Plant Biotechnol J 2020; 18:2345-2353. [PMID: 32367649 PMCID: PMC7589443 DOI: 10.1111/pbi.13396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 05/21/2023]
Abstract
Rapeseed is the second most important oil crop species and is widely cultivated worldwide. However, overcoming the 'phenotyping bottleneck' has remained a significant challenge. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In addition, it is important to explore the dynamic genetic architecture underlying rapeseed plant growth and its contribution to final yield. In this work, a high-throughput phenotyping facility was used to dynamically screen a rapeseed intervarietal substitution line population during two growing seasons. We developed an automatic image analysis pipeline to quantify 43 dynamic traits across multiple developmental stages, with 12 time points. The time-resolved i-traits could be extracted to reflect shoot growth and predict the final yield of rapeseed. Broad phenotypic variation and high heritability were observed for these i-traits across all developmental stages. A total of 337 and 599 QTLs were identified, with 33.5% and 36.1% consistent QTLs for each trait across all 12 time points in the two growing seasons, respectively. Moreover, the QTLs responsible for yield indicators colocalized with those of final yield, potentially providing a new mechanism of yield regulation. Our results indicate that high-throughput phenotyping can provide novel insights into the dynamic genetic architecture of rapeseed growth and final yield, which would be useful for future genetic improvements in rapeseed.
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Affiliation(s)
- Haitao Li
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Hubei Collaborative Innovation Center for Green Transformation of Bio‐resourcesSchool of Life SciencesHubei UniversityWuhanChina
| | - Hui Feng
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Shanjing Yang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Wan Huang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Xiong Xiong
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhanChina
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Qian Liu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Kede Liu
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research, and Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanChina
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