|KOHLHASE, DANIEL - Iowa State University|
|OWEN, MICHEAL - Iowa State University|
Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2019
Publication Date: 5/6/2019
Citation: Kohlhase, D.R., O'Rourke, J.A., Owen, M.D.K., Graham, M.A. 2019. Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). Biomed Central (BMC) Plant Biology. 19:182. https://doi.org/10.1186/s12870-019-1795-x.
Interpretive Summary: Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause yield losses up to 74% and 56% in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.], respectively. P-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 126.96.36.199) inhibitor herbicides are commonly used in weed management programs. In 2011, HPPD resistance was discovered in two waterhemp populations. The evolution of herbicide resistant waterhemp poses a serious threat to agricultural production systems. Therefore, understanding the mechanisms of herbicide resistance is critically important. To identify genes recognizing and responding to HPPD herbicides, we measured gene expression across the entire waterhemp genome. The resources generated by this project will be valuable to the weed science community.
Technical Abstract: Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause yield losses up to 74% and 56% in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.], respectively. In 2011, p-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 188.8.131.52) inhibitor herbicide resistance was reported in two waterhemp populations. No previous studies have examined genome wide gene expression in herbicide resistant waterhemp. Therefore we conducted an RNA-sequencing (RNA-seq) de novo transcriptome assembly of waterhemp. We treated and mock-treated two waterhemp populations (HPPD-herbicide resistant and susceptible) and collected leaf samples at three, six, twelve, and twenty-four hours after treatment (HAT). We performed a de novo transcriptome assembly using all sample sequences to better represent the waterhemp transcriptome as well as allowing us to identify transcripts specific to a genotype, treatment, or time point. Our results indicate that the response of HPPD-herbicide resistant and susceptible waterhemp genotypes to HPPD-inhibiting herbicide is very rapid and established as soon as three hours after herbicide treatment. Further, the there was little overlap in gene expression between resistant and susceptible genotypes, highlighting dynamic differences in response to herbicide treatment. The waterhemp transcriptome, differentially expressed genes and single nucleotide polymorphisms (SNPs) generated in this study, will be a valuable to for the weed science community for future studies.