Isolation, characterization and PCR multiplexing of microsatellite loci for a mite crop pest, Tetranychus urticae (Acari: Tetranychidae)

Abstract

BackgroundTetranychus urticae is a highly polyphagous species with a cosmopolitan distribution that has the status of pest in more than 100 economically significant crops all over the world. Despite a number of previous efforts to isolate genetic markers, only a reduced set of microsatellite loci has been published. Taking advantage of the whole genome sequence of T. urticae that recently became available; we isolated and characterized a new set of microsatellite loci and tested the level of polymorphism across populations originating from a wide geographical area.ResultsA total of 42 microsatellite sequences widespread in the T. urticae genome were identified, the exact position in the genome recorded, and PCR amplification of microsatellite loci tested with primers defined here. Fourteen loci showed unambiguous genotype patterns and were further characterized. Three multiplex polymerase chain reaction sets were optimized in order to genotype a total of 24 polymorphic loci, including 10 previously published Tetranychus-specific loci. The microsatellite kits successfully amplified 686 individuals from 60 field populations for which we assessed the level of genetic diversity. The number of alleles per locus ranged from 3 to 16 and the expected heterozygosity values ranged from 0.12 to 0.81. Most of the loci displayed a significant excess of homozygous and did not model the Hardy–Weinberg equilibrium. This can be explained by the arrhenotokous mode of reproduction of T. urticae.ConclusionsThese primers represent a valuable resource for robust studies on the genetic structure, dispersal and population biology of T. urticae, that can be used in managing this destructive agricultural pest.

Independently evolved and gene flow‐accelerated pesticide resistance in two‐spotted spider mites

“…Overall, we found that nearby populations of TSSM are likely to belong to the same genetic cluster, although the IBD analysis of pairwise genetic differentiation (F ST ) and geographic distance of TSSM populations showed no significant correlation when the entire data set was considered. Here, we used five microsatellite loci for population genetic analysis due to rare microsatellite loci in the small genome of TSSM (Grbic et al, 2011;Saune et al, 2015) and limited Note. S05, S19, S65, S158, and S167 represent five microsatellite loci, respectively, which are referred in previous work about microsatellite development in TSSM (Ge et al, 2013).…”

Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections

“…Nuclear microsatellite loci have been preferred as markers of geographic origin for high impact plant pests [3,[20][21][22], but their design requires species-specific priming sites and genomic locations. Even with improvements in technology [23] and greater availability of genome sequences [24] that make finding such loci easier, testing them to confirm suitable population-level heterogeneity is extremely time-consuming. They are also not trivial to use because of a complex evolution [25,26] and the potential for crossamplification of non-orthologous loci [27].…”