Natural variation for gene expression responses to abiotic stress in maize

• Published in: The Plant journal : for cell and molecular biology 2017-02, Vol.89 (4), p.706-717
• Main Authors: Waters, Amanda J., Makarevitch, Irina, Noshay, Jaclyn, Burghardt, Liana T., Hirsch, Candice N., Hirsch, Cory D., Springer, Nathan M.
• Format: Article
• Language: English
• Subjects: Abiotic stress; allele‐specific expression; Botany; Cold Temperature; Corn; Gene expression; Gene Expression Regulation, Plant - genetics; Gene Expression Regulation, Plant - physiology; Hot Temperature; regulatory variation; RNA, Plant - genetics; Seedlings - genetics; Seedlings - physiology; Sequence Analysis, RNA; Zea mays; Zea mays - genetics; Zea mays - physiology
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13414

Summary Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis‐ and trans‐regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14‐day‐old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele‐specific transcript abundance in the F1 hybrids, we were able to measure the abundance of cis‐ and trans‐regulatory variation between genotypes for both steady‐state and stress‐responsive expression differences. Although examples of trans‐regulatory variation were observed, cis‐regulatory variation was more common for both steady‐state and stress‐responsive expression differences. The genes with cis‐allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity. Significance Statement Plants rely on transcriptional responses to tolerate abiotic stress. Here we used transcriptional profiling of maize inbreds and hybrids to document regulatory variation for abiotic stress response. By monitoring allele‐specific gene expression in heterozygous plants, we found evidence for both cis‐ and trans‐regulatory variation. Our results provide a comprehensive picture of the genetic variation contributing to stress responses.