Mapping regulatory variants controlling gene expression in drought response and tolerance in maize.
Shengxue Liu, Cuiping Li, Hongwei Wang, Shuhui Wang, Shiping Yang, Xiaohu Liu, Jianbing Yan, Bailin Li, Mary Beatty, Gina Zastrow-Hayes, Shuhui Song, Feng Qin
Author Information
- Shengxue Liu: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Cuiping Li: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China.
- Hongwei Wang: Agricultural College, Yangtze University, Jingzhou, 434025, China.
- Shuhui Wang: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Shiping Yang: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Xiaohu Liu: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Jianbing Yan: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Bailin Li: Corteva Agriscience, Johnston, IA, 50131, USA.
- Mary Beatty: Corteva Agriscience, Johnston, IA, 50131, USA.
- Gina Zastrow-Hayes: Corteva Agriscience, Johnston, IA, 50131, USA.
- Shuhui Song: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China. songshh@big.ac.cn.
- Feng Qin: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. qinfeng@cau.edu.cn. ORCID
BACKGROUND: Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a major environmental threat of crop production worldwide, is of great value for drought-tolerant gene identification.
RESULTS: A total of 627 RNA-seq analyses are performed for 224 maize accessions which represent a wide genetic diversity under three water regimes; 73,573 eQTLs are detected for about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting a comprehensive and dynamic genetic architecture of gene expression in response to drought. The regulatory variants controlling the gene expression constitutively or drought-dynamically are unraveled. Focusing on dynamic regulatory variants resolved to genes encoding transcription factors, a drought-responsive network reflecting a hierarchy of transcription factors and their target genes is built. Moreover, 97 genes are prioritized to associate with drought tolerance due to their expression variations through the Mendelian randomization analysis. One of the candidate genes, Abscisic acid 8'-hydroxylase, is verified to play a negative role in plant drought tolerance.
CONCLUSIONS: This study unravels the effects of genetic variants on gene expression dynamics in drought response which allows us to better understand the role of distal and proximal genetic effects on gene expression and phenotypic plasticity. The prioritized drought-associated genes may serve as direct targets for functional investigation or allelic mining.
Abscisic Acid
Droughts
Gene Expression Regulation, Plant
Genome-Wide Association Study
Mendelian Randomization Analysis
Osmoregulation
Quantitative Trait Loci
Regulatory Elements, Transcriptional
Transcription Factors
Water
Zea mays
Transcription Factors
Water
Abscisic Acid
