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

Abstract

In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors in multiple states across the midwestern US. Two populations resistant to both mode-of-action groups, one from Nebraska (NEB) and one from Illinois (CHR), were studied using an RNA-seq approach on F2 mapping populations to identify the genes responsible for resistance. Using both an A. tuberculatus transcriptome assembly and a high-quality grain amaranth (A. hypochondriacus) genome as references, differential transcript and gene expression analyses were conducted to identify genes that were significantly over- or under-expressed in resistant plants. When these differentially expressed genes (DEGs) were mapped on the A. hypochondriacus genome, physical clustering of the DEGs was apparent along several of the 16 A. hypochondriacus scaffolds. Furthermore, single-nucleotide polymorphism (SNP) calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased towards R alleles overlapped with the DEG clusters. Within one of these clusters, allele-specific expression of cytochrome P450 81E8 was observed for 2,4-D resistance in both the CHR and NEB populations, and phylogenetic analysis indicated a common evolutionary origin of this R allele in the two populations.

Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action

“…As P450s normally cluster together on the same chromosome in plants (Nelson and Werck‐Reichhart, 2011; Liu et al , 2016), the existence of co‐regulated gene clusters involving different types of genes (such as P450s, GSTs and UGTs) in a metabolic pathway might occur, so that CYP72A71v1 could be potentially linked to these genes conferring herbicide resistance. Co‐ordinately regulated genes clusters have been reported for biosynthesis of allelochemicals such as DIMBOA and momilactone (see a recent paper by Batada et al ., 2007; Giacomini et al ., 2020; Mao et al ., 2020).…”

Genetic architecture underlying HPPD-inhibitor resistance in a Nebraska Amaranthus tuberculatus population

“…Furthermore, modification of transcription factors allows for trans-acting modulation of gene expression. Therefore, we suggest that the differential regulation observed by Giacomini et al is the result of regulation by distal factors 23 . In a different population, Kohlhase et al identified Scaffold 15 as enriched for SNP associated with HPPD-inhibitor resistance in A. tuberculatus 15 .…”

Genetic architecture underlying HPPD‐inhibitor resistance in a Nebraska Amaranthus tuberculatus population

“…Therefore, we suggest that the differential regulation observed by Giacomini et al . is the result of regulation by distal factors 23 . In a different population, Kohlhase et al .…”

“…Plants were grown to the 12‐leaf stage in the greenhouse, whereupon apical meristems were removed to promote branching. Clones were propagated from branches 23 and grown to approximately 15 cm in height in the growth chamber to dissuade flowering. Two clones from each of 16 and 12 plants from the NEB and WUS populations, respectively, were screened for their responses to the herbicide tembotrione (Laudis, Bayer Crop Science).…”

“…While an initial screening did not identify HPPD‐inhibitor resistance, 22 this was conducted at a single rate. Further analysis identified consistent HPPD‐inhibitor resistance 23 . Interestingly, the field from where the population was collected has no field‐use history of HPPD inhibitors.…”