Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance
| Autor: | Todd A. Gaines, Anita Küpper, Darci A. Giacomini, Patrick J. Tranel, Eric L. Patterson, Roland Beffa |
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| Rok vydání: | 2020 |
| Předmět: |
AcademicSubjects/SCI01140
0106 biological sciences single-nucleotide polymorphism (SNP) analysis Plant Weeds 01 natural sciences Genome Transcriptome 03 medical and health sciences Cytochrome P-450 Enzyme System Polymorphism (computer science) Gene expression Genetics Allele 2 4-dichlorophenoxyacetic acid (2 4-D) Gene Ecology Evolution Behavior and Systematics 030304 developmental biology 0303 health sciences Amaranthus biology Phylogenetic tree AcademicSubjects/SCI01130 biology.organism_classification nontarget-site resistance (NTSR) 4-hydroxyphenylpyruvate dioxygenase (HPPD) differential expression analysis Multigene Family Amaranthus tuberculatus Herbicide Resistance Research Article 010606 plant biology & botany |
| Zdroj: | Genome Biology and Evolution |
| ISSN: | 1759-6653 |
| Popis: | In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate 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. |
| Databáze: | OpenAIRE |
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