Genome‐wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

Abstract

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.

Adaptation genomics: The angel is in the details

“…Dispersal barriers have important consequences for population dynamics, allelic and species distributions, and community compositions (Caplat et al, ). Tabas‐Madrid et al () directly confirmed this effect by reporting the presence of four distinct genetic groups around Iberia and even provide evidence and speculation about their life history.…”

“…The study by Tabas‐Madrid et al () also illustrates the importance of studying plants at the regional scale and taking environmental variables into account when breeding crops with genomics‐based strategies. All life adapts to selective pressures imposed on it by their environment through natural selection (Figure ).…”

“…Adaptive genotypes pass through environmental selection, but the environment also influences the development of individual plants. This question of the extent of “nature versus nurture” is addressed in this issue of Plant, Cell and Environment by Tabas‐Madrid et al (). Here, they report their observations about the correlation between flowering time and both the genomics of local A. thaliana populations and the climatic variations of their native environments.…”

“…After characterizing the genomic composition of the Iberian A. thaliana populations, Tabas‐Madrid et al () moved on to discern the effects temperature and climate have on their flowering time. The authors were able to confirm flowering time is a highly heritable trait by comparing the phenotypic variances recorded from field grown plants with plants grown in a greenhouse.…”

“…They were, however, also able to confirm that flowering time was affected by significant GxE interactions. When they investigated this interaction further with genome‐wide association (GWA) studies, the authors, unsurprisingly, found genes associated with temperature adaptation like PIF4 (Quint et al, ) and flowering time like FRL1 (Tabas‐Madrid et al, ). Furthermore, they were able to identify genes in certain populations that have not previously been attributed to flowering time.…”