Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet.

Journal: International journal of biological macromolecules
PMID: 39079238

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.

Authors

  • Chunhui Zhu
    College of Physics, Hebei Normal University, Shijiazhuang 050024, China. Electronic address: chunhuizhu@hebtu.edu.cn.
  • Ling Zhao
    School of Acu-Mox and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, 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
    Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany.
  • Hui Gao
    Department of Pharmaceuticals, Affiliated Hospital of Yan'an University, Yan'an 716000, Shaanxi, China.
  • Jiaxin Liu
    Department of Pulmonary Medicine, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian 361000, People's Republic of China.
  • Litao Wang
    College of Physics, Hebei Normal University, Shijiazhuang 050024, China; College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
  • Ting Zhang
    Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, 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. Electronic address: zhanghaoshan@caas.cn.
  • 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. Electronic address: wang521wgp@163.com.

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