Accurate identification ofHelicoverpa armigera–Helicoverpa zeahybrids using genome admixture analysis: implications for genomic surveillance

Abstract

AbstractHelicoverpa armigera, the cotton bollworm moth, is one of the world’s most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasiveH.armigerahas been reported to hybridize with local populations ofHelicoverpa zea. The correct identification ofH.armigera-H.zeahybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitateH.zeapesticide resistance and host plant range via introgression ofH.armigeragenes. Here, we present a genome admixture analysis of high quality genome sequences generated from twoH.armigera-H.zeaF1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8 %H.armigerafor both F1 hybrids, confirming its accuracy. Genome sequences from fiveH.zeaand oneH.armigerathat were generated as part of the study show no evidence of hybridization. Interestingly, we show that fourH.zeagenomes generated from a previous study are predicted to possess a proportion ofH.armigeragenetic material. Using unsupervised clustering to identify non-hybridizedH.armigeraandH.zeagenomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minorH.armigeracomponent in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis ofH.armigera-H.zeahybrids, and suggest measures that will improve such analyses.