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Su J, Zeng J, Wang S, Zhang X, Zhao L, Wen S, Zhang F, Jiang J, Chen F. Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum. PLANT CELL REPORTS 2024; 43:84. [PMID: 38448703 DOI: 10.1007/s00299-024-03172-4] [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: 12/22/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
KEY MESSAGE The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51-75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1, ACA10, and FOP1. Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Junwei Zeng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Siyue Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Xuefeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Limin Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Shiyun Wen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China.
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Zhang YM, Jia Z, Xie SQ, Wen J, Wang S, Zhang YW. Editorial: Advances in statistical methods for the genetic dissection of complex traits in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1357564. [PMID: 38287980 PMCID: PMC10822929 DOI: 10.3389/fpls.2024.1357564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024]
Affiliation(s)
- Yuan-Ming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Shang-Qian Xie
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, United States
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Ya-Wen Zhang
- International Genome Center, Jiangsu University, Zhenjiang, China
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