Coexpression clusters and allele-specific expression in metabolism-based herbicide resistance

Darci A. Giacomini, Eric L. Patterson, Anita Küpper, Roland Beffa, Todd A. Gaines, Patrick J. Tranel

Research output: Contribution to journalArticlepeer-review


In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphe-nylpyruvate dioxygenase inhibitors in multiple states across the midwestern United States. 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 underexpressed 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 calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased toward 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.

Original languageEnglish (US)
Pages (from-to)2267-2278
Number of pages12
JournalGenome biology and evolution
Issue number12
StatePublished - 2020


  • 2, 4-dichlorophenoxyacetic acid (2,4-D)
  • 4-hydroxyphenylpyruvate dioxygenase (HPPD)
  • Amaranthus tuberculatus
  • Differential expression analysis
  • Nontarget-site resistance (NTSR)
  • Single-nucleotide polymorphism (SNP) analysis

ASJC Scopus subject areas

  • General Medicine


Dive into the research topics of 'Coexpression clusters and allele-specific expression in metabolism-based herbicide resistance'. Together they form a unique fingerprint.

Cite this