Abstract
BackgroundWaterhemp (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.ResultsWe 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.ConclusionsThe 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.
Highlights
Phenotypic assessment of mesotrione responses in resistant and susceptible waterhemp genotypes Samples used for RNA-seq were harvested prior to the development of visual mesotrione treatment symptoms; herbicide-treated and mock-treated control plants were maintained in the greenhouse for 3 weeks after mesotrione application to assess phenotype responses
The resistant population initially displayed the major HPPD-inhibiting herbicide characteristics of chlorosis and bleached meristematic growth followed by necrosis but recovered by the third week after application
We provide a comprehensive resource for waterhemp genomics, including the first waterhemp transcriptome, identification of differentially expressed transcripts (DETs) responding to herbicide treatment in HPPD-resistant and susceptible genotypes and candidate single nucleotide polymorphism (SNP) for future marker development
Summary
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 In 2011, 4-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicide resistance was first reported in two waterhemp populations. Over the past 30 years, waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) has evolved into a major problem weed species in agricultural production systems across the Midwestern United States [1]. Fields infested with waterhemp can suffer yield losses up to 74% in maize (Zea mays L.) and 56% in soybean (Glycine max (L.) Merr.) [2, 3]. Obligatory outcrossing facilitates the movement of ecologically valuable traits, such as herbicide resistance, among and between waterhemp populations. Additional biological traits that contribute to the weediness of waterhemp include prolific seed production [4], extended and opportunistic germination [5], and rapid growth rate [6]
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