Population Genomics of Tropical Tree Species: Implications for Identification of Genetic Components of Disease Resistance in Theobroma Cacao

In tropical forests, rarer species show increased sensitivity to species-specific soil pathogens and more negative effects of conspecific density on seedling survival (negative density dependence, NDD). Small population size is expected to disproportionately reduce genetic diversity of hyperdiverse loci such as immunity genes. We generated root transcriptome data for six tropical tree species from Barro Colorado Island, Panama, that varied widely in their local abundance, and tested defense gene induction with live soil and salicylic acid. Initial results support the hypothesis that smaller local tree populations have reduced R gene diversity and recognition-dependent immune responses, along with greater co-susceptibility to species-specific pathogens that may facilitate disease transmission and NDD. We then asked whether population variation in orthologs of predicted defense genes in Theobroma cacao also showed evidence of diversifying selection in wild populations. T. cacao orthologs were sequenced from multiple accessions from Ecuador, Peru and French Guiana. Genetic polymorphism revealed differences between populations in extent of polymorphism and evidence of diversifying selection; prior knowledge from unrelated species enabled prediction of genes with elevated polymorphism. Our new project, funded by NSF-PGRP, will leverage population genomic data, transcriptome responses, and indicators of adaptive evolution to help identify functional disease resistance genes in wild populations that can be integrated into commercial Theobroma cacao lines.

Claude W. dePamphilis¹, James H. Marden¹, Andrew Fister¹, Liza S. Comita^2,3, Scott A. Mangan^3,4, Mark Peterson¹, Eric Wafula¹, Joshua P. Der^1,5, Howard W. Fescemyer¹, Dapeng Zhang⁶, Peter Tiffin⁷, Siela N. Maximova¹, and Mark J. Guiltinan¹. ¹Penn State University, University Park, PA; ²Yale University, New Haven, CT; ³Smithsonian Tropical Research Institute, Panama; ⁴Washington University in St. Louis, St. Louis MO; ⁵California State University, Fullerton, CA; ⁶U.S. Department of Agriculture ARS, Beltsville MD; ⁷University of Minnesota, St. Paul, MN