1
|
Zhu C, Zhao L, Zhao S, Niu X, Li L, Gao H, Liu J, Wang L, Zhang T, Cheng R, Shi Z, Zhang H, Wang G. Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet. Int J Biol Macromol 2024; 277:134288. [PMID: 39079238 DOI: 10.1016/j.ijbiomac.2024.134288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024]
Abstract
Drought stress is a major constraint on crop development, potentially causing huge yield losses and threatening global food security. Improving Crop's stress tolerance is usually associated with a yield penalty. One way to balance yield and stress tolerance is modification specific gene by emerging precision genome editing technology. However, our knowledge of yield-related drought-tolerant genes is still limited. Foxtail millet (Setaria italica) has a remarkable tolerance to drought and is considered to be a model C4 crop that is easy to engineer. Here, we have identified 46 drought-responsive candidate genes by performing a machine learning-based transcriptome study on two drought-tolerant and two drought-sensitive foxtail millet cultivars. A total of 12 important drought-responsive genes were screened out by principal component analysis and confirmed experimentally by qPCR. Significantly, by investigating the haplotype of these genes based on 1844 germplasm resources, we found two genes (Seita.5G251300 and Seita.8G036300) exhibiting drought-tolerant haplotypes that possess an apparent advantage in 1000 grain weight and main panicle grain weight without penalty in grain weight per plant. These results demonstrate the potential of Seita.5G251300 and Seita.8G036300 for breeding drought-tolerant high-yielding foxtail millet. It provides important insights for the breeding of drought-tolerant high-yielding crop cultivars through genetic manipulation technology.
Collapse
Affiliation(s)
- Chunhui Zhu
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China.
| | - Ling Zhao
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Shaoxing Zhao
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Xingfang Niu
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China; College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Lin Li
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Hui Gao
- Hebei Key Laboratory of Crop Stress Biology, Department of Life Science and Technology, College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Jiaxin Liu
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China; Hebei Key Laboratory of Crop Stress Biology, Department of Life Science and Technology, College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Litao Wang
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China; College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ting Zhang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Zhigang Shi
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Haoshan Zhang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China.
| | - Genping Wang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China.
| |
Collapse
|
2
|
Yoo JY, Ko KS, Vu BN, Lee YE, Choi HN, Lee YN, Fanata WID, Harmoko R, Lee SK, Chung WS, Hong JC, Lee KO. IRE1 is implicated in protein synthesis regulation under ER stress conditions in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108963. [PMID: 39084166 DOI: 10.1016/j.plaphy.2024.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/14/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
The unfolded protein response (UPR) is a crucial cellular mechanism for maintaining protein folding homeostasis during endoplasmic reticulum (ER) stress. In this study, the role of IRE1, a key component of the UPR, was investigated in protein translation regulation under ER stress conditions in Arabidopsis. We discovered that the loss of IRE1A and IRE1B leads to diminished protein translation, indicating a significant role for IRE1 in this process. However, this regulation was not solely dependent on the interaction with bZIP60, a key transcription factor in the UPR. Interestingly, while chemical chaperones TUDCA and PBA effectively alleviated the translation inhibition observed in ire1a ire1b mutants, this effect was more pronounced than the mitigation observed from suppressing GCN2 expression or introducing a non-phosphorylatable eIF2α variant. Additionally, the kinase and ribonuclease activities of IRE1B were demonstrated to be crucial for plant adaptation and protein synthesis regulation under ER stress conditions. Overall, this study not only highlights the complex regulatory mechanisms of IRE1 in plant ER stress responses but also provides insights into its multifaceted roles in protein translation regulation.
Collapse
Affiliation(s)
- Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Bich Ngoc Vu
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Young Eun Lee
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Ha Na Choi
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Yoo Na Lee
- Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Wahyu Indra Duwi Fanata
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Department of Agrotechnology, Faculty of Agriculture, University of Jember, Jember, 68121, Indonesia
| | - Rikno Harmoko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Research Center for Genetic Engineering, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor, Cibinong, Bogor, 16911, Indonesia
| | - Sang-Kyu Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Woo Sik Chung
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science, Division of Applied Life Sciences (BK4 Program) Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea.
| |
Collapse
|