Whole-Genome Resequencing of the VGSC Reveals the Evolutionary Mechanism of Pesticide Resistance in Liriomyza trifolii in Hainan

TL;DR

This study uses whole-genome resequencing to identify genetic mutations in Liriomyza trifolii linked to pesticide resistance in Hainan Province.

Contribution

The study identifies specific nonsynonymous SNPs in the VGSC gene associated with pyrethroid and indoxacarb resistance in L. trifolii.

Findings

Six nonsynonymous SNPs and thirty-one synonymous SNPs were identified in five L. trifolii populations.

Four nonsynonymous SNPs (M918T, L1014F, T933I, V1845I) are linked to pesticide resistance.

Cross-resistance between pyrethroids and indoxacarb was observed in L. trifolii populations.

Abstract

The extended application of pesticides has intensified the resistance problem in Liriomyza trifolii within Hainan Province. This study aimed to elucidate the underlying mechanisms contributing to the elevated resistance observed in this pest by employing Whole-Genome Re-sequencing (WGR) technology. Through the analysis and comparison of WGR data focusing on voltage-gated sodium channel (VGSC) from diverse regions and LT-S of L. trifolii in Hainan Province, we identified a total of six nonsynonymous single nucleotide polymorphisms (nsSNPs) and thirty-one synonymous single nucleotide polymorphisms (sSNPs) in five wild populations MY, TS, DA, TY, and JY. Among the six nsSNPs, three (PyR1: M918T, L1014F, and PyR2: T933I) have been confirmed as linked to pyrethroid resistance, while one (D IVS6: V1845I) was associated with resistance to indoxacarb. Moreover, the frequency of these four mutations generally increases with decreasing latitude. Additionally, under sustained pesticide selection pressure, L. trifolii exhibits an evolutionary pattern characterized by a dN/dS ratio (nsSNP/sSNP = 6/31 ≈ 0.19) of less than 1. Among the 31 sSNPs that held an absolute quantitative advantage, the highest occurrence frequency reached 94.44% (G2033: JY), and this sSNP occurred in all populations. In contrast, among a limited number of 6 nsSNPs, the highest occurrence frequency attained 100% (L1014F: all populations). This study substantiates that the elevated resistance observed in L. trifolii within Hainan Province can be ascribed to the presence of four nsSNPs-M922T, T933I, L1018F, and V1845I in their VGSC. Furthermore, the emergence of cross-resistance between pyrethroids and indoxacarb has been identified. This research offers a novel theoretical foundation for future investigations into the resistance mechanisms of L. trifolii.

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