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Abstract
BackgroundGene 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.ResultsA 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.ConclusionsThis 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.
Highlights
Gene expression is a key determinant of cellular response
RNA-seq analysis of 224 maize accessions subjected to three water regimes To understand how genetic variants affect drought-responsive gene expression on a whole transcriptome scale in maize seedlings, a collection of 224 accessions was assembled from a previously characterized population that had been used for the genetic dissection of a number of agronomic traits [17, 22,23,24]
Watering was withheld from soil-growing seedlings at the Vegetative 2–3 stage, and the decline in relative leaf water content (RLWC) was recorded
Summary
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. Drought stress is a major environmental factor which limits crop production worldwide [4]; understanding the molecular mechanisms and identifying the functional variants underlying drought tolerance are critical for the trait improvement. Genome-wide association studies (GWAS) facilitate the detection of genetic and phenotypic associations, identification of the causal genes or DNA variants that mechanistically affect the trait is still challenging [5, 6]. Cumulative evidence suggests that genetic variants influence complex traits through modulating gene expression; highlighting the functional importance in regulatory variants. Genetic variations in ZmVPP1 and ZmNAC111I gene regulatory regions affect gene expression which are associated with the natural variation in drought tolerance [6, 10]. A 2-bp deletion, 9.5 kb upstream of ZmRAVL1, was identified as the causal variant responsible for the enlarged leaf angles in maize [11]
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