Data from: Investigation of the geographic scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana
| Main Authors: | Brachi, Benjamin, Villoutreix, Romain, Faure, Nathalie, Hautekèete, Nina-Coralie, Piquot, Yves, Pauwels, Maxime, Roby, Dominique, Cuguen, Joel, Bergelson, Joy, Roux, Fabrice |
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| Format: | info dataset Journal |
| Terbitan: |
, 2013
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4937644 |
Daftar Isi:
- Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into the spatial scale of adaptive variation by identifying the putative selective agents responsible for this selection. Forty-nine natural stands from four climatically contrasted French regions were characterized (i) phenologically for six traits, (ii) genetically using 135 SNP markers and (iii) ecologically for 42 variables. Up to 63% of phenological variation could be explained by neutral genetic diversity. The remaining phenological variation displayed stronger associations with ecological variation within regions than among regions, suggesting the importance of local selective agents in shaping adaptive phenological variation. Although climatic conditions have often been suggested as the main selective agents acting on phenology in A. thaliana, both edaphic conditions and interspecific competition appear to be strong selective agents in some regions. In a first attempt to identify the genetics of phenological variation at different geographical scales, we phenotyped worldwide accessions and local polymorphic populations from the French RegMap in a genome-wide association (GWA) mapping study. The genomic regions associated with phenological variation depended upon the geographical scale considered, stressing the need to account for the scale of adaptive phenotypic variation when choosing accession panels for GWAS.
- Ecological_variablesEcological data measured for each A. thaliana stands sampled for this study. Refer to material and method section for acquisition methods and Figure S2 for variable description.phenologyPhenological data measured in the greenhouse experiment. Number: Line number. Block: Experimental block. Treatment: Simulated Fall and Spring treatments. Tray: Number of the 66-well trays in which plant grew. Line and Column: Coordinates of the plants in the 66-well trays the plants were grown in. Type: French_stand: 49 natural stands of this study, accessions; worldwide and French accessions. Region: Four regions of France where stands have been sampled. Stand: Name of stands. For accessions, numbers correspond to the accession_ID used for GWA mapping (see Table S1.B). Name: Individual family or accession name. BT: Bolting time. FT: Flowering time. INT: Interval between bolting and flowering. FP: Flowering period. RP: Reproductive Period. FRR: Ration between flowering and reproductive reproductive period.genotypes of the french familiesGenotypes for the french families used in this study. The column "sample" corresponds to families from the french populations. "." stands for missing data. Heterozygotes are coded as follow: W for AT, M for AC, R for AG, Y for TC, K for TG and S for CG.genotypes.txt