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Tibbs-Cortes LE, Guo T, Andorf CM, Li X, Yu J. Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize. Genome Res 2024; 34:1253-1263. [PMID: 39271292 PMCID: PMC11444181 DOI: 10.1101/gr.279027.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024]
Abstract
Maize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region are challenging. In this study, we conducted systematic analysis to identify environmental indices that strongly influence 19 traits (including flowering time, plant architecture, and yield component traits) measured in the maize nested association mapping (NAM) population grown in 11 environments. Identified environmental indices based on day length, temperature, moisture, and combinations of these are biologically meaningful. Next, we leveraged a total of more than 20 million SNP and SV markers derived from recent de novo sequencing of the NAM founders for trait prediction and dissection. When combined with identified environmental indices, genomic prediction enables accurate performance predictions. Genome-wide association studies (GWASs) detected genetic loci associated with the plastic response to the identified environmental indices for all examined traits. By systematically uncovering the major environmental and genomic factors underlying phenotypic plasticity in a wide variety of traits and depositing our results as a track on the MaizeGDB genome browser, we provide a community resource as well as a comprehensive analytical framework to facilitate continuing complex trait dissection and prediction in maize and other crops. Our findings also provide a conceptual framework for the genetic architecture of phenotypic plasticity by accommodating two alternative models, regulatory gene model and allelic sensitivity model, as special cases of a continuum.
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Affiliation(s)
- Laura E Tibbs-Cortes
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington 99164, USA
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
| | - Tingting Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
- Department of Computer Science, Iowa State University, Ames, Iowa 50011, USA
| | - Xianran Li
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington 99164, USA;
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA;
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Chen L, Wu X, Zhang M, Yang L, Ji Z, Chen R, Cao Y, Huang J, Duan Q. Genome-Wide Identification of BrCMF Genes in Brassica rapa and Their Expression Analysis under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:1118. [PMID: 38674527 PMCID: PMC11054530 DOI: 10.3390/plants13081118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]
Abstract
CCT MOTIF FAMILY (CMF) genes belong to the CCT gene family and have been shown to play a role in diverse processes, such as flowering time and yield regulation, as well as responses to abiotic stresses. CMF genes have not yet been identified in Brassica rapa. A total of 25 BrCMF genes were identified in this study, and these genes were distributed across eight chromosomes. Collinearity analysis revealed that B. rapa and Arabidopsis thaliana share many homologous genes, suggesting that these genes have similar functions. According to sequencing analysis of promoters, several elements are involved in regulating the expression of genes that mediate responses to abiotic stresses. Analysis of the tissue-specific expression of BrCMF14 revealed that it is highly expressed in several organs. The expression of BrCMF22 was significantly downregulated under salt stress, while the expression of BrCMF5, BrCMF7, and BrCMF21 was also significantly reduced under cold stress. The expression of BrCMF14 and BrCMF5 was significantly increased under drought stress, and the expression of BrCMF7 was upregulated. Furthermore, protein-protein interaction network analysis revealed that A. thaliana homologs of BrCMF interacted with genes involved in the abiotic stress response. In conclusion, BrCMF5, BrCMF7, BrCMF14, BrCMF21, and BrCMF22 appear to play a role in responses to abiotic stresses. The results of this study will aid future investigations of CCT genes in B. rapa.
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Affiliation(s)
- Luhan Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Xiaoyu Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Meiqi Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Lin Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Zhaojing Ji
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Rui Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Yunyun Cao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
| | - Jiabao Huang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China; (L.C.); (X.W.); (M.Z.); (L.Y.); (Z.J.); (R.C.); (Y.C.)
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Fan X, Wang P, Qi F, Hu Y, Li S, Zhang J, Liang L, Zhang Z, Liu J, Xiong L, Xing Y. The CCT transcriptional activator Ghd2 constantly delays the heading date by upregulating CO3 in rice. J Genet Genomics 2023; 50:755-764. [PMID: 36906137 DOI: 10.1016/j.jgg.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
CONSTANS, CO-like, and TOC1 (CCT) family genes play important roles in regulating heading date, which exerts a large impact on the regional and seasonal adaptation of rice. Previous studies have shown that Grain number, plant height, and heading date2 (Ghd2) exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date. However, the target gene of Ghd2 regulating heading date is still unknown. In this study, CO3 is identified by analyzing Ghd2 ChIP-seq data. Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain. EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2. A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1, Hd3a, and RFT1. In addition, the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data. Taken together, these results suggest that Ghd2 directly binds to the downstream gene CO3, and the Ghd2-CO3 module constantly delays heading date via the Ehd1-mediated pathway.
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Affiliation(s)
- Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Feixiang Qi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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