Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

Abstract

Background Waterhemp ( Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause crippling yield losses for both maize ( Zea mays L.) and soybean ( Glycine max L. Merr). In 2011, 4-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicide resistance was first reported in two waterhemp populations. Since the discovery of HPPD-herbicide resistance, studies have identified the mechanism of resistance and described the inheritance of the herbicide resistance. However, no studies have examined genome-wide gene expression changes in response to herbicide treatment in herbicide resistant and susceptible waterhemp. Results We conducted RNA-sequencing (RNA-seq) analyses of two waterhemp populations (HPPD-herbicide resistant and susceptible), from herbicide-treated and mock-treated leaf samples at three, six, twelve, and twenty-four hours after treatment (HAT). We performed a de novo transcriptome assembly using all sample sequences. Following assessments of our assembly, individual samples were mapped to the de novo transcriptome allowing us to identify transcripts specific to a genotype, herbicide treatment, or time point. Our results indicate that the response of HPPD-herbicide resistant and susceptible waterhemp genotypes to HPPD-inhibiting herbicide is rapid, established as soon as 3 hours after herbicide treatment. Further, there was little overlap in gene expression between resistant and susceptible genotypes, highlighting dynamic differences in response to herbicide treatment. In addition, we used stringent analytical methods to identify candidate single nucleotide polymorphisms (SNPs) that distinguish the resistant and susceptible genotypes. Conclusions The waterhemp transcriptome, herbicide-responsive genes, and SNPs generated in this study provide valuable tools for future studies by numerous plant science communities. This collection of resources is essential to study and understand herbicide effects on gene expression in resistant and susceptible weeds. Understanding how herbicides impact gene expression could allow us to develop novel approaches for future herbicide development. Additionally, an increased understanding of the prolific traits intrinsic in weed success could lead to crop improvement. Electronic supplementary material The online version of this article (10.1186/s12870-019-1795-x) contains supplementary material, which is available to authorized users.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

“…Previous work has found evidence of gene expression changes in response to herbicide, often in genes not previously known to be important for herbicide response (An et al 2014;Leslie and Baucom 2014;Duhoux et al 2015;Serra et al 2015;Zhao et al 2017;Wright et al 2018) , but not directly investigated whether plastic responses appeared to be adaptive. One hint at the importance of maladaptive plasticity comes from the observation that a susceptible population of Amaranthus tuberculatus had increased rapid (3 hour) expression response to herbicide compared to a naturally resistant population (Kohlhase et al 2019) , suggesting that plastic expression changes could be maladaptive.…”

Herbicide resistance in Amaranthus tuberculatus†

“…76 Transcriptomic studies have been conducted recently to identify candidate genes contributing to HPPD-inhibitor resistance in A. tuberculatus, with the underlying assumption that such genes will be more abundantly expressed in resistant plants. 77,78 As is often the case with such studies, a large number of candidate genesbut no 'smoking gun'were identified, and much more work is needed for functional validation.…”

“…Furthermore, the emergence of -omics resources and capabilities provide promising opportunities not only to elucidate these mechanisms, but also to understand their regulation and evolution. For example, in the last 10 years, we have gone from generating a very rudimentary transcriptome 88 for A. tuberculatus to obtaining a very high quality transcriptome, 77 along with highquality reference genomes of both a female and male individual. 64,89 Recently, a herbicide-sensitive A. tuberculatus population has been isolated before becoming extinct and made publicly available (accession Ames 35 826 in the US National Plant Germplasm System).…”

Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance

“…2017 ; Shergill et al. 2018 ; Kohlhase et al. 2019 ) as well as for 2,4-D resistance ( Figueiredo et al.…”