|
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
|
Gao Q, Liu Y, Liu Y, Dai C, Zhang Y, Zhou F, Zhu Y. Salicylic Acid Modulates the Osmotic System and Photosynthesis Rate to Enhance the Drought Tolerance of Toona ciliata. PLANTS (BASEL, SWITZERLAND) 2023; 12:4187. [PMID: 38140515 PMCID: PMC10747095 DOI: 10.3390/plants12244187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
Toona ciliata M. Roem. is a valuable and fast-growing timber species which is found in subtropical regions; however, drought severely affects its growth and physiology. Although the exogenous application of salicylic acid (SA) has been proven to enhance plant drought tolerance by regulating the osmotic system and photosynthesis rate, the physiological processes involved in the regulation of drought tolerance by SA in various plants differ. Therefore, drought mitigation techniques tailored for T. ciliata should be explored or developed for the sustainable development of the timber industry. We selected 2-year-old T. ciliata seedlings for a potting experiment, set the soil moisture at 45%, and subjected some of the T. ciliata seedlings to a moderate drought (MD) treatment; to others, 0.5 mmol/L exogenous SA (MD + SA) was applied as a mitigation test, and we also conducted a control using a normal water supply at 70% soil moisture (CK). Our aim was to investigate the mitigating effects of exogenous SA on the growth condition, osmotic system, and photosynthesis rate of T. ciliata under drought stress conditions. OPLS-VIP was used to analyze the main physiological factors that enable exogenous SA to alleviate drought-induced injury in T. ciliata. The results indicated that exogenous SA application increased the growth of the ground diameter, plant height, and leaf blades and enhanced the drought tolerance of the T. ciliata seedlings by maintaining the balance of their osmotic systems, improving their gas exchange parameters, and restoring the activity of their PSII reaction centers. The seven major physiological factors that enabled exogenous SA to mitigate drought-induced injury in the T. ciliata seedlings were the soluble proteins (Sp), net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), stomatal opening window (Sow), activity of the photosystem II reaction center (ΦPSII), and electron transfer rate (ETR). Of these, Sp was the most dominant factor. There was a synergistic effect between the osmotic system and the photosynthetic regulation of drought injury in the T. ciliata seedlings. Overall, our study confirms that exogenous SA enhances the drought tolerance of T. ciliata by modulating the osmotic system and photosynthesis rate.
Collapse
Affiliation(s)
- Qi Gao
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Yamin Liu
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Yumin Liu
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Chongwen Dai
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Yulin Zhang
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Fanbo Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Yating Zhu
- College of Resources and Environment, Southwest University, Chongqing 400715, China; (Q.G.); (Y.L.); (C.D.); (Y.Z.); (F.Z.); (Y.Z.)
- Key Laboratory of Ecological Environment in Three Gorges Reservoir Area, Ministry of Education, Southwest University, Chongqing 400715, China
| |
Collapse
|
|
3
|
Mehra P, Fairburn R, Leftley N, Banda J, Bennett MJ. Turning up the volume: How root branching adaptive responses aid water foraging. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102405. [PMID: 37379661 DOI: 10.1016/j.pbi.2023.102405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/06/2023] [Accepted: 05/20/2023] [Indexed: 06/30/2023]
Abstract
Access to water is critical for all forms of life. Plants primarily access water through their roots. Root traits such as branching are highly sensitive to water availability, enabling plants to adapt their root architecture to match soil moisture distribution. Lateral root adaptive responses hydropatterning and xerobranching ensure new branches only form when roots are in direct contact with moist soil. Root traits are also strongly influenced by atmospheric humidity, where a rapid drop leads to a promotion of root growth and branching. The plant hormones auxin and/or abscisic acid (ABA) play key roles in regulating these adaptive responses. We discuss how these signals are part of a novel "water-sensing" mechanism that couples hormone movement with hydrodynamics to orchestrate root branching responses.
Collapse
Affiliation(s)
- Poonam Mehra
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
| | - Rebecca Fairburn
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Nicola Leftley
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jason Banda
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Malcolm J Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
| |
Collapse
|