Waterhemp (Amaranthus tuberculatus) is an agronomic weed found throughout the Midwestern United States. Without proper management waterhemp has the potential to cause yield losses up to 74% and 56% in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.], respectively. There are various characteristics of waterhemp that contribute to increasing prevalence of waterhemp in agriculture including the ability to evolve herbicide resistance. There are six herbicide sites of action that have been evolved in waterhemp. In 2011, waterhemp was discovered to be resistant to p-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicides. The objectives of my research were to 1) identify the number of genes and describe the allelic expression involved with HPPD-herbicide resistance in waterhemp and 2) examine the transcriptomic expression response of HPPD-herbicide resistance in waterhemp.

To examine the inheritance of the resistance trait, we reciprocally crossed a known HPPD resistant waterhemp population with a known HPPD susceptible waterhemp population and established a pseudo-F2 generation. We challenged the parent, F1 and pseudo F2 generations against four rates of an HPPD-inhibiting herbicide. The HPPD-resistance trait was determined to be polygenic. Additionally, these data suggest the number of involved resistance genes was found to increase at higher rates of the herbicide with at least one dominant allele at each major locus. This study has confirmed previous reports describing the inheritance of HPPD resistance to be complex while introducing new descriptions of the response of HPPD resistant waterhemp to HPPD herbicides.

To examine the transcriptomic response of resistant waterhemp, we treated and mock-treated HPPD-herbicide resistant and susceptible waterhemp populations with mesotrione 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. This de novo assembly was then used to measure gene expression differences between genotypes, treatments and time points. These data suggest a rapid response of HPPD-herbicide resistant and susceptible waterhemp genotypes to the HPPD-inhibiting herbicide mesotrione. Furthermore, little overlap was found among the differentially expressed transcripts expressed by each genotype. We also identified the possibility of overlapping gene networks in response to other herbicides. We have made available the raw sequences, and assembled sequences with complete annotations for continued use by the weed science community.