Fig. 4

Characteristics of ASE genes in switchgrass. a ASE gene numbers increase with the quantity of RNA-seq samples. The specified number sets were selected randomly from 23 ASE gene sets with three replicates. b Dominant expressed alleles in two haplotype genomes. c Ka/Ks of ASE and non-ASE genes. Minima and maxima are present in the lower and upper bounds of the whiskers, respectively, and the width of the violin are densities of the Ka/Ks value. P values were calculated with a two-sided Student’s t test. d SNP density in ASE genes and equivalently expressed alleles (EEAs). The y axis represents SNP numbers every 100 bp. P values were calculated with two-sided Student’s t test. *** indicates P < 0.0005. e Number of ASE genes identified in JJ31 (left) and Alamo (right) under control (room temperature) and cold stress (4 °C). P values were calculated with two-sided Student’s t test. NS indicates not significant. f The expression changes of 67 COR alleles enriched in JJ31-specific ASE genes under control (room temperature) and cold stress (4 °C) conditions. The suffixes “L” and “R” represent leaves and roots, respectively. g The expression levels (TPM) of two alleles of the CBF gene (PVA_6 K02793.1 and PVB_6 K02781.1) across different transcriptome samples in JJ31 and Alamo. ** indicates adjusted P-value < 0.01. h Pattern diagram of PVB_6 K02781.1 advantage expression. Red and blue indicate the allele IDs, corresponding bases, and encoded amino acid types in “JJ31-A” and “JJ31-B,” respectively. “RNA-seq reads” represents the proportion of reads containing different SNP types that map to “JJ31-B.” From left to right, RNA-seq reads aligned to the SNP sites are as follows: 79 reads (C: 92%, G: 8%), 100 reads (G: 45%, C: 55%), and 67 reads each for the third and fourth sites (T: 81%, A: 19%; G: 85%, T: 13%)