Received: 3 April 2018 | Revised: 7 June 2018 | Accepted: 10 June 2018 DOI: 10.1002/ece3.4336 ORIGINAL RESEARCH Pooled whole- genome sequencing of interspecific chestnut (Castanea) hybrids reveals loci associated with differences in caching behavior of fox squirrels (Sciurus niger L.) Nicholas R. LaBonte1 | Keith E. Woeste2 1Department of Crop Sciences, University of Illinois, Urbana, Illinois Abstract 2USDA Forest Service, Northern Research Dispersal of seeds by scatter- hoarding rodents is common among tropical and tem- Station, Hardwood Tree Improvement perate tree species, including chestnuts in the genus Castanea. Backcrossed (BC) in- and Regeneration Center, West Lafayette, Indiana terspecific hybrid chestnuts exhibit wide variation in seed traits: as the parent species (Castanea dentata and C. mollissima) have distinct seed phenotypes and tend to be Correspondence Nicholas R. LaBonte, Department of Crop handled differently by seed dispersers, phenotypic variation in BC trees is likely due Sciences, University of Illinois, 1201 W to inheritance of genes that have undergone divergent evolution in the parent spe- Gregory Drive, Urbana, IL 61801. Email:
[email protected] cies. To identify candidate genomic regions for interspecific differences in seed dis- persal, we used tagged seeds to measure average dispersal distance for seeds of third- generation BC chestnuts and sequenced pooled whole genomes of mother trees with contrasting seed dispersal: high caching rate/long distance; low caching rate/short distance; no caching. Candidate regions affecting seed dispersal were identified as loci with more C. mollissima alleles in the high caching rate/ long- distance pool than expected by chance and observed in the other two pools. Functional an- notations of candidate regions included predicted lipid metabolism, dormancy regu- lation, seed development, and carbohydrate metabolism genes.