Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host‐affiliated sibling species

Abstract

It has recently been shown that the European corn borer, a major pest of maize crops, is actually composed of two genetically differentiated and reproductively isolated taxa, which are found in sympatry over a wide geographical range in Eurasia. Each taxon is adapted to specific host plants: Ostrinia nubilalis feeds mainly on maize, while O. scapulalis feeds mainly on hop or mugwort. Here, we present a genome scan approach as a first step towards an integrated molecular analysis of the adaptive genomic divergence between O. nubilalis and O. scapulalis. We analysed 609 AFLP marker loci in replicate samples of sympatric populations of Ostrinia spp. collected on maize, hop and mugwort, in France. Using two genome scan methods based on the analysis of population differentiation, we found a set of 28 outlier loci that departed from the neutral expectation in one or the other method (of which a subset of 14 loci were common to both methods), which showed a significantly increased differentiation between O. nubilalis and O. scapulalis, when compared to the rest of the genome. A subset of 12 outlier loci were sequenced, of which 7 were successfully re-amplified as target candidate loci. Three of these showed homology with annotated lepidopteran sequences from public nucleotide databases.

Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: lessons from an ocellated lizard genome scan

“…However, fragments with repetitive elements can easily achieve larger sizes, as in mk209 (303 bp) or mk245 (250 bp). Although some AFLP genome scan studies have tested for linkage disequilibrium among AFLP markers to control for non-independent markers (Murray and Hare, 2006;Paris et al, 2010;Poncet et al, 2010;Midamegbe et al, 2011;Paris and Despres, 2012), it might be difficult to detect linkage disequilibrium when the same AFLP locus generates 42 length-variable alleles potentially classified as different markers. Therefore, interpretation of results from AFLP outlier detection should be made with caution and special efforts should be taken to investigate the sequence content of outliers in order to validate their selection signature (Butlin, 2010).…”

“…Our attempts to isolate and sequence specific outliers from AFLP profiles and to convert them into codominant markers highlighted some pitfalls and technical challenges that are probably common to similar follow-up studies. We isolated outlier AFLP bands from agarose gels, but other higher resolution alternatives have been used to isolate outlier AFLPs, such as polyacrylamide (Midamegbe et al, 2011) or Spreadex gels (Minder and Widmer, 2008). Agarose gels were chosen for this study because it was the easiest and the most affordable solution to separate dense AFLP profiles, using CE to confirm the sizes of fragments recovered from gel slices and the sizes of clone inserts.…”

“…We could learn much more from such studies if AFLP markers detected as outliers were brought out from anonymity and further research were conducted toward the identification of genes linked with such outliers and their implications for local adaptation. Unfortunately, and despite 425 AFLP genome scans for selection in non-model species available in the literature, only a few studies report their attempts to isolate and sequence AFLP markers identified as candidate loci under selection (Minder and Widmer, 2008;Wood et al, 2008, Midamegbe et al, 2011Paris and Despres, 2012). The isolation of a particular AFLP fragment can be technically demanding and time consuming, often involving the need for fragment cloning.…”

Crop domestication, global human-mediated migration, and the unresolved role of geography in pest control

“…Native herbivore populations that shift onto agricultural crops can become genetically differentiated from populations that remain on the original host plant (Vialatte et al, 2005;Michel et al, 2010;Lavandero et al, 2011 Midamegbe et al, 2011;Barman et al, 2012;Bourguet et al, 2014). Because host shifts create new ecological opportunities for herbivores, population can diverge via ecological speciation in sympatry (Bush, 1969;Berlocher and Feder, 2002).…”

Genetic mapping of two components of reproductive isolation between two sibling species of moths, Ostrinia nubilalis and O. scapulalis

“…DNA concentration was assessed by fluorimetric quantification of dsDNA with the PicoGreen Kit (Life Technologies, Carlsbad, CA, USA). AFLP analyses were conducted as described by Midamegbe et al (2011). Briefly, we digested B100 ng of genomic DNA with EcoRI and BamHI (Promega, Madison, WI, USA) enzymes, and then carried out two successive selective PCRs with the EcoRI (5 0 -GACTGCGTACCAATTC-3 0 ) and BamHI þ A (5 0 -ATGAGTCCTGATGATCCA-3 0 ) primers for the first reaction and the EcoRI þ 2 and BamHI þ 3 primers for the second reaction.…”