Fig. 1

Allele distribution in a synonymous SNP in ZR3 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 with a synonymous effect in ZR3 (position chr3:20310479). Green indicates UTRs, orange indicates exons, and black indicates the sole intron. 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,” for guanine), while red dots show the geographical distribution of accessions harboring the minor allele (“A,” for adenine). 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 ZR3 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. 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 20,310,479 increases. At the same time, the transcript abundance of ZR3 (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 deviation