Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana

Abstract

The evolutionary processes and genetics underlying local adaptation at a specieswide level are largely unknown. Recent work has indicated that a frameshift mutation in a member of a family of transcription factors, C-repeat binding factors or CBFs, underlies local adaptation and freezing tolerance divergence between two European populations of Arabidopsis thaliana. To ask whether the specieswide evolution of CBF genes in Arabidopsis is consistent with local adaptation, we surveyed CBF variation from 477 wild accessions collected across the species' range. We found that CBF sequence variation is strongly associated with winter temperature variables. Looking specifically at the minimum temperature experienced during the coldest month, we found that Arabidopsis from warmer climates exhibit a significant excess of nonsynonymous polymorphisms in CBF genes and revealed a CBF haplotype network whose structure points to multiple independent transitions to warmer climates. We also identified a number of newly described mutations of significant functional effect in CBF genes, similar to the frameshift mutation previously indicated to be locally adaptive in Italy, and find that they are significantly associated with warm winters. Lastly, we uncover relationships between climate and the position of significant functional effect mutations between and within CBF paralogs, suggesting variation in adaptive function of different mutations. Cumulatively, these findings support the hypothesis that disruption of CBF gene function is adaptive in warmer climates, and illustrate how parallel evolution in a transcription factor can underlie adaptation to climate.

Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution

“…To further address the generality of this finding , Monroe et al. () surveyed CBF variation from 477 wild accessions collected across the species' range. They found that CBF sequence variation is strongly associated with winter temperature variables, thus suggesting that the disruption of CBF gene function is adaptive only in warm climate.…”

Advances in physiological and molecular aspects of plant cold tolerance

“…CBF3/DREB1A and CBF/DREB1B are induced at the same time and earlier than CBF2/DREB1C (Medina et al 2011). More recently Monroe et al (2016) screened 477 wild accession from Arabidopsis for the variation in CBF genes; they found that CBF sequences variation is strongly associated with winter temperatures. The types that come from warmer winters showed significant access to the CBF polymorphisms.…”

Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization

“…In humans, 19 UGT isoforms have been identified, and these UGTs have been classified into two families (UGT1 and UGT2) based on their sequence identity [9]. In the model plant, Arabidopsis thaliana , more than 120 UGTs encoding genes have been identified, with five UGTs found to be correlated with flavonoid biosynthetic [10–12]. A total of 253 UGTs were found in Panax ginseng transcriptome, and recent works have confirmed the function of UGTs in ginsenoside biosynthesis [13–15].…”