Long-Term Population Studies Uncover the Genome Structure and Genetic Basis of Xenobiotic and Host Plant Adaptation in the HerbivoreTetranychus urticae

Abstract

Pesticide resistance arises rapidly in arthropod herbivores, as can host plant adaptation, and both are significant problems in agriculture. These traits have been challenging to study as both are often polygenic and many arthropods are genetically intractable. Here, we examined the genetic architecture of pesticide resistance and host plant adaptation in the two-spotted spider mite, Tetranychus urticae, a global agricultural pest. We show that the short generation time and high fecundity of T. urticae can be readily exploited in experimental evolution designs for high-resolution mapping of quantitative traits. As revealed by selection with spirodiclofen, an acetyl-CoA decarboxylase inhibitor, in populations from a cross between a spirodiclofen resistant and a susceptible strain, and which also differed in performance on tomato, we found that a limited number of loci could explain quantitative resistance to this compound. These were resolved to narrow genomic intervals, suggesting specific candidate genes, including acetyl-CoA decarboxylase itself, clustered and copy variable cytochrome P450 genes, and NADPH cytochrome P450 reductase, which encodes a redox partner for cytochrome P450s. For performance on tomato, candidate genomic regions for response to selection were distinct from those responding to the synthetic compound and were consistent with a more polygenic architecture. In accomplishing this work, we exploited the continuous nature of allele frequency changes across experimental populations to resolve the existing fragmented T. urticae draft genome to pseudochromosomes. This improved assembly was indispensable for our analyses, as it will be for future research with this model herbivore that is exceptionally amenable to genetic studies. .

Overexpression of an alternative allele of carboxyl/choline esterase 4 (CCE04) of Tetranychus urticae is associated with high levels of resistance to the keto‐enol acaricide spirodiclofen

“…In a recent study, using an SR‐VP‐derived inbred line, spirodiclofen resistance was mapped in high resolution to a number of genomic loci (QTL mapping), confirming its polygenic nature. None of the QTLs was associated with the CCE04 locus (located on pseudochromosome 1 at 2.39 Mb), but contained other interesting candidate genes: ACCase – the target of keto‐enol acaricides (on pseudochromosome 1 at 6.56 Mb), a region containing P450s (on pseudochromosome 1 at 24.13 Mb) belonging to the same P450 subfamily as CYP392E10, known to metabolize spirodiclofen and cytochrome P450 reductase (CPR) (on pseudochromosome 2 at 5.69 Mb) . On the other hand, it is still possible that these genomic loci harbor regulators (e.g.…”

“…In this study, we focus on the role of additional resistance mechanisms, more specifically the involvement of carboxyl/choline esterases (CCEs), for the following reasons: (i) classical genetics revealed that spirodiclofen resistance in T. urticae was not controlled by a single gene and suggested that additional mechanisms next to P450 metabolism are highly likely, which was confirmed by a recent quantitative trait locus (QTL) study; (ii) synergism experiments have previously pointed out the involvement of both P450s and CCEs in spirodiclofen resistance in spider mites, which was confirmed by enzymatic assays; and (iii) microarray analysis revealed that a single CCE gene ( CCE04 ) was highly overexpressed in two genetically distinct T. urticae strains (SR‐VP and SR‐TK), while transcriptome analysis of a spirodiclofen‐resistant P. ulmi strain revealed that the overexpression of a CCE was strongly associated with spirodiclofen resistance …”

High-resolution QTL mapping in Tetranychus urticae reveals acaricide-specific responses and common target-site resistance after selection by different METI-I acaricides

“…The two-spotted spider mite is a tractable organism for characterizing resistance mechanisms, as its haplodiploid breeding system (males are haploid while females are diploid) facilitates inbred line construction, its genome size is small (~90Mb), the generation time is as little as a week at optimal temperatures, and very large populations can be propagated (Van Leeuwen and Dermauw, 2016). Bulked segregant analysis (BSA) approaches have been used with T. urticae to identify monogenic loci (Bryon et al, 2017;Demaeght et al, 2014;Van Leeuwen et al, 2012), and these methods were recently extended to successfully describe polygenic resistance to a lipid-synthesis inhibiting acaricide, spirodiclofen (Wybouw et al, 2019). For genetic mapping of resistance with BSA methods, a resistant parent is crossed with a sensitive one, and resultant populations are expanded and selected with the pesticide.…”

Convergent evolution of cytochrome P450s underlies independent origins of keto-carotenoid pigmentation in animals

“…From the resulting 1,150,705 nucleotide positions, 196,214 single nucleotide polymorphisms (SNPs) within T. kanzawai were identified as fixed for contrasting differences between the two parents, and were retained. The locus responsible for the lemon phenotype was identified by comparing allele frequencies between the three lemon selected samples to the wild-type sample using previously published BSA genetic mapping methods with statistical testing for genotype-phenotype associations by permutation [22]; 75 kb windows with 5 kb offsets were used with the false discovery rate (FDR) set to 5%. Genome annotation of the BSA peak was based on Wybouw et al [22].…”

“…The locus responsible for the lemon phenotype was identified by comparing allele frequencies between the three lemon selected samples to the wild-type sample using previously published BSA genetic mapping methods with statistical testing for genotype-phenotype associations by permutation [22]; 75 kb windows with 5 kb offsets were used with the false discovery rate (FDR) set to 5%. Genome annotation of the BSA peak was based on Wybouw et al [22]. (f) De novo assemblies DNA sequence reads were imported into CLC Genomics Workbench 9.0.1 (https://www.qiagenbioinformatics.com/), trimmed using default settings, assembled into contigs using the default settings of the "De Novo Assembly" tool, and the contigs were aligned to the T. urticae genome assembly using BLASR (version 1.3.1) [30].…”