Genomic prediction in insects: a case study on wing morphology traits in the jewel wasp Nasonia vitripennis

Biological control is a sustainable strategy to combat agricultural pests. Yet, legislation increasingly restricts importing non-native biocontrol agents. Thus, selective breeding of biocontrol traits is suggested to enhance performance of existing biocontrol agents. Genomic prediction, where genomic data is used to estimate the genetic merit of an individual for specific traits, is an alternative to exploit genetic variation for the improvement of native biocontrol agents. This study aims to establish proof-of-principle for genomic prediction in insect biocontrol agents, using wing morphology traits in the model parasitoid Nasonia vitripennis Walker (Pteromalidae). We performed genomic prediction using a Genomic Best Linear Unbiased Prediction (GBLUP) model, using 1,230 individuals with 8,639 SNPs generated by genotyping-by-sequencing (GBS). We used individuals from two generations from the outbred HVRx population, 717 individuals from generation G169 and 513 from generation G172. To assess genomic prediction accuracy, we used across-generation validation: forward validation for G172 from G169, backward validation for G169 from G172, and also 5-fold cross-validation. For size-related traits, including tibia length, wing length, width, and second moment wing area, the accuracy of genomic prediction was close to zero in both across-generation validations, but much higher in 5-fold cross-validation (ranging 0.54-0.68). For the shape-related trait wing aspect ratio, a high accuracy was found for all three validation strategies, with 0.47 for across-generation forward validation, 0.65 for across-generation backward validation, and 0.54 for 5-fold cross-validation. Overall, genomic selection in insect biocontrol agents with a relative small effective population size seems promising. However, factors such as the biology of insects, phenotyping techniques, and large-scale genotyping costs still challenge the application of genomic selection to biocontrol agents.