PS 71-137
Using next generation sequencing to detect evidence of selection on California oak seedlings growing in common gardens
Directional change in allele frequencies provides initial evidence of natural selection. In plant populations, seedlings with alleles conferring higher fitness in their environments should be favored by natural selection and thus more likely to survive. Through next generation sequencing, it is possible to detect evidence of natural selection by comparing genotypes of seedlings that survive to those that die within different environments. In this study, survival was tracked for Quercus douglasii (blue oak) and Quercus kelloggii (black oak) seedlings growing in common gardens across different climate zones in California. Our goals were to 1) test the hypothesis that the genotypes of seedlings that survive are significantly differentiated from those that die in different common gardens, and 2) identify SNPs associated with survival. To do this, we used genotyping-by-sequencing to randomly sample homologous loci across the genomes of 23 Q. douglasii and 24 Q. kelloggii seedlings, 8 of which eventually died in each species. We identified SNPs with Stacks software, and then used principal components analysis and MANOVA to test for overall genetic differentiation between surviving and dying seedlings. Additionally, we employed the mixed model approach, EMMAX, to detect SNPs associated with survival after controlling for relatedness and structure among samples.
Results/Conclusions
For both oak species, we identified over 8,000 SNPs in roughly 6,000 loci. For Q. douglasii, we did not detect genetic differentiation among surviving and dying seedlings, using 1 SNP per locus. However, for Q. kelloggii, we observed significant differentiation between surviving and dying seedlings, and a significant interaction between survival status and location of garden. After accounting for hidden kinship, population structure, and multiple testing, EMMAX detected 1 SNP in Q. douglasii and 3 SNPs in Q. kelloggii that were moderately to significantly associated with seedling survival. One SNP in Q. kelloggii fell within a gene encoding neutral non-lysosomal ceramidase, an enzyme found in cell membranes, whereas loci for the remaining SNPs lacked homology to known genes. These findings demonstrate that it is possible to detect evolutionary change through natural selection in seedling populations of non-model species using next generation sequencing tools. Future work that samples a larger portion of the genome will detect additional SNPs associated with seedling survival and allow tests of whether these SNPs are overrepresented in genes for response to climate.