Fig. 7: Analysis of chromosomal regions and loci potentially related to rye domestication.

a, Putative selection sweeps revealed using three different methods, with dashed lines indicating thresholds for significant selection sweeps (top 5% outliers). ScBC1, ScBtr, ScGW2, ScMOC1, ScID1 and ScWx were found in the putative sweeps. b, Specific and shared selection sweeps (SLS) uncovered by different methods. c, Selection sweeps associated with ScBC1, ScBtr, ScMOC1 or ScID1 uncovered by joint DRI and XP-CLR analysis. d, Microsynteny analysis of collinear ID1 loci in rye and related Triticeae genomes. Red and gray lines connect orthologous ID1 or flanking genes. e, Different expression profiles of ScID1.1 and ScID1.2 genes in Weining and Jingzhou rye plants at 3 DAS, revealed by RT–qPCR. Each value is the mean (±s.d.) of five samples taken from n = 5 plants, and the results shown were reproducible in n = 3 separate assays. f, Boxplots for days to heading, based on the genotype of the ScID1 locus in the Weining × Jingzhou F₂ population (n = 66 for WN/WN, n = 161 for WN/JZ and n = 64 for JZ/JZ). Box edges represent 0.25 and 0.75 quantiles, respectively, with the median values shown by bold lines. The lower and upper whiskers correspond to the minima values, at most the first quartile − 1.5 × interquartile range (IQR) or the maxima values no further than the third quartile + 1.5 × IQR. All data are shown by gray dots, with statistical analysis performed using two-tailed t-tests.