Adaptation in two species of Phaseolus with contrasting mating systems

Abstract

For common bean, the loss of photoperiod sensitivity has been a major pre-requisite for domestication and further adaptation to European climates. Its self-pollinated mating system also makes it a good model for identifying genes that display enhanced levels of differentiation in gene expression, together with its closely related species, open-pollinated runner bean. We first use GWAS and haplotype structure tests to identify single nucleotide and structural variants strongly associated to the capacity to flower under neutral and long days. Gene-pool specific selective sweeps were identified that correspond to the independent domestication events in the Americas. A strong GWAS signal associated TFL-1 to the loss of photoperiod sensitivity in both Mesoamerican and Andean gene-pools, indicating its important function in this biological process. Then we investigated the genetic architecture of gene expression variation in common bean and runner bean, to determine if and how mating system has influenced patterns of adaptation and gene expression variation. We observe large differences in genomic characteristics between the two species. For the genetic architecture of gene expression, mating system appears to have minor effects and gene expression is likely under stabilizing selection in both species, regardless of mating system. We additionally found that in selfing species, connectivity in gene co-expression network played greater roles in regulating gene expression. To further investigate gene expression divergence and the underlying selection forces, we calculated the selection index. It is highly representative of gene expression divergence between two species. Although selective sweeps at the genomic level act less effectively on highly diverged genes, we found that DNA/RNA modification process may play an important role in conducting gene expression variation.