Genomic basis underlying the metabolome-mediated drought adaptation of maize

Fei Zhang, Jinfeng Wu, Nir Sade, Si Wu, Aiman Egbaria, Alisdair R. Fernie, Jianbing Yan, Feng Qin, Wei Chen*, Yariv Brotman*, Mingqiu Dai*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Background: Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive. Results: Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance. Conclusion: Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits.

Original languageEnglish
Article number260
JournalGenome Biology
Issue number1
StatePublished - Dec 2021


FundersFunder number
111 Project Crop genomicsB20051
Beijing Outstanding Young Scientist ProgramBJJWZYJH01201910019026
College of Life Science and Technology
Wuhan Applied Foundational Frontier Project2020020601012258
National Natural Science Foundation of China32061143031
Chinese Academy of Sciences
Huazhong Agricultural University
Fundamental Research Funds for the Central Universities2662020SKY009


    • Drought tolerance
    • Maize
    • Metabolome
    • Natural variation
    • Stress responses


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