Pooled whole‐genome sequencing of interspecific chestnut (Castanea) hybrids reveals loci associated with differences in caching behavior of fox squirrels (Sciurus niger L.)

• Published in: Ecology and evolution Vol. 8; no. 22; pp. 10638 - 10654
• Main Authors: LaBonte, Nicholas R., Woeste, Keith E.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.11.2018; John Wiley and Sons Inc
• Subjects: Annotations; Biological evolution; Caching; Carbohydrate metabolism; Carbohydrates; Castanea dentata; Castanea mollissima; Chestnut; coevolution; Dispersal; Dispersion; Divergence; Dormancy; Evolutionary genetics; Fagales; forest regeneration; Gene expression; Gene sequencing; Genes; Genomes; Genomics; Heredity; Hoarding behavior; Hybrids; Interspecific; Lipid metabolism; Lipids; Metabolism; mutualism; Original Research; Phenotypes; Phenotypic variations; Rodents; Sciurus niger; Seed dispersal; Seeds; Squirrels; Trees; forest regeneration; seed dispersal; Fagales; coevolution; mutualism
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.4336

Dispersal of seeds by scatter‐hoarding rodents is common among tropical and temperate tree species, including chestnuts in the genus Castanea. Backcrossed (BC) interspecific 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 handled differently by seed dispersers, phenotypic variation in BC trees is likely due to inheritance of genes that have undergone divergent evolution in the parent species. To identify candidate genomic regions for interspecific differences in seed dispersal, 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 annotations of candidate regions included predicted lipid metabolism, dormancy regulation, seed development, and carbohydrate metabolism genes. The results support the hypothesis that perception of seed dormancy is a predominant factor in squirrel caching decisions, and also indicate profitable directions for future work on the evolutionary genomics of trees and coevolved seed dispersers. We identified hybrid chestnut trees with variable seed traits and estimated the average seed dispersal distance (by squirrels) for each tree. By sequencing pooled genomes of trees with similar dispersal distance, we identified loci in the chestnut genome that may influence seed dispersal.