Maize Exhibits Differential Expression and Allelic Regulatory Variation in Response to Abiotic Stress

Plants can exhibit a variety of phenotypic and molecular responses to environmental stress. Many genes exhibit altered levels of expression in response to abiotic stress. Maize (Zea mays) provides a model system to study natural variation and potential allelic regulatory variation driving gene expression differences in response to abiotic stress. To study the frequency and molecular basis for natural variation in responsiveness to abiotic stress within maize, RNA sequencing was performed on 14 day old maize seedlings of inbreds B73, Mo17 and Oh43 as well as F1 hybrids B73xMo17, B73xOh43, and Mo17xOh43 under control, cold, and heat conditions. The analysis of gene expression levels in control and stress conditions identified many examples of stress-responsive expression in each of the inbred lines. Some of the genes show clear stress-responsive expression in some genotypes but no change in expression in other genotypes. The analysis of allele specific transcript abundance in the F1 hybrids was used to assess the contribution of cis- and trans-regulatory variation for stress-responsive expression. There were a number of examples of cis-regulatory control and current analyses are focused on characterization of the haplotype variation for these alleles. There were also examples of trans-regulatory variation that influence gene expression responses to abiotic stress that are being mapped by analysis of expression responses in recombinant inbred lines (RILs). In conclusion, maize exhibits a large amount of natural variation of gene expression in response to abiotic stress and understanding the sources of this regulatory variation may lead to improved strategies to improve abiotic stress tolerance in crops.