Poster Presentation Society for Molecular Biology and Evolution Conference 2016

Finding needles in a genomic haystack: targeted capture to identify signatures of selection in a non-model plant species (#399)

Matthew J Christmas 1 , Ed Biffin 2 , Martin F Breed 1 , Andrew J Lowe 1
  1. University of Adelaide, Adelaide, SA, Australia
  2. State Herbarium of South Australia, Adelaide, SA, Australia

Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for non-model species lacking a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation practices, especially for the management of species in the face of contemporary and future climate change. Here, I present on assessing adaptive genomic variation within a non-model plant species, the narrow-leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid-capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. 8,462 single-nucleotide polymorphisms (SNPs) were analysed for FST outliers as well as associations with environmental variables. Using these methods we found 50 SNPs with significant correlations to temperature and water availability, and 24 SNPs to elevation. Genes containing SNPs identified as under environmental selection were diverse, including aquaporin and abscisic acid (ABA) genes, as well as genes with ontologies relating to environmental responses. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for non-model organisms.