Fig. 2

Allele distribution in a SNP in the 5′ UTR of CGR3 and its cis-regulated transcript abundance are correlated with the distance from the coast and temperature variability. A We explored an environmental cline in a SNP in the 5′ UTR of CGR3 (position chr5:26339736). Green indicates UTRs, orange indicates exons, and black indicates introns. B The map of Eurasia shows the geographical distribution of the allelic variants of this SNP. Blue dots show the distribution of accessions with the major allele (G), while red dots show the geographical distribution of accessions harboring the minor allele (A). C Given the geographic distribution of both alleles, the probability of encountering an accession with the minor allele increases in accessions more distant from the coastline. D Violin plots illustrating significantly different probability densities of CGR3 transcript abundance for the major and minor alleles of the SNP depicted in A. E Distance from the coast determines the temperature variability that accessions encounter in their local environment. (Note that these are the same data as in Fig. 1E, reproduced here for ease of comparison with the rest of Fig. 2). F, G As plants endure a higher degree of temperature variability inland (y-axis in F and G), the probability of harboring a minor allele (red dots) at site 26,339,736 increases. At the same time, the transcript abundance of CGR3 (x-axis in F and G) decreases, highlighting the regulatory effect of this SNP and its correlation with temperature variability. The regression is calculated using the transcript abundance data in the combined set of accessions (both major and minor alleles). Distance from the coast was derived from the NASA Ocean Biology processing group dataset. Climate variables are from the WorldClim 2.1 database. MAF, minor allele frequency; STDEV, standard deviatioon