PMC

Homoeologous expression bias (HEB) in reciprocal Festuca × Lolium hybrids.
HEB in the F1 generation of Festuca × Lolium (F1 F × L) and Lolium × Festuca (F1 L × F) hybrids, the F2 generation of Festuca × Lolium (F2 F × L) and F1 and F2 generations of Festuca × Lolium hybrids after 4 years of cultivation (F1 F × L aging and F2 F × L aging, respectively). HEB was computed for 5790 genes. Three categories of relative homoeolog expression were defined: L = F (the expression of both homoeologs is not significantly different), L > F (Lolium homoeolog is significantly more expressed than Festuca homoeolog) and F > L (Festuca homoeolog is significantly more expressed than Lolium homoeolog).

a Scatter plot of δ¹³C and δ¹⁵N stable isotope natural abundances of leaves (circles), roots (downwards triangles), soil (squares), soil hyphae (diamonds) and mechanically isolated intraradical hyphae (upwards triangles) from the grass Festuca ovina (white symbols) and the legume Medicago sativa (black symbols) microcosms. FL Festuca leaves, ML Medicago leaves, FR Festuca roots, MR Medicago roots, FS Festuca soil, MS Medicago soil, FSH Festuca soil hyphae, FMH Festuca mechanically isolated hyphae, MSH Medicago soil hyphae, MMH Medicago mechanically isolated hyphae. Error bars indicate standard deviation (SD). b Whisker boxplot of δ¹³C values of AM fungal hyphae from the grass (left) and the legume (right), respectively, shown for the different isolation methods (soil hyphae; intraradical hyphae: mechanic vs enzymatic). FS Festuca soil hyphae, MS Medicago soil hyphae, FM Festuca mechanically isolated hyphae, MM Medicago mechanically isolated hyphae, FE Festuca enzymatically isolated hyphae, ME Medicago enzymatically isolated hyphae. The black line in the centre of the box indicates the median, box margins represent the 25th and 75th percentiles. The length of the box is the inter quartile range (IQR), whiskers indicate the minimum (25th percentile − 1.5 × IQR) and the maximum (75th percentile + 1.5 × IQR). Outliers are shown as circles

Number of genes with homoeolog‐specific silencing.
Silencing of homoeologs observed in the F1 generation of Festuca × Lolium (F1 F × L) and Lolium × Festuca (F1 L × F) hybrids, the F2 generation of Festuca × Lolium (F2 F × L) and the F1 and F2 generations of Festuca × Lolium hybrids after 4 years of cultivation (F1 F × L aging and F2 F × L aging, respectively). Homoeologs were considered silenced when the average count per million value in all samples (three plants, each with three biological replicates) was <1. F, Festuca pratensis homoeolog; L, Lolium multiflorum homoeolog.

Homoeologous expression bias in reciprocal Festuca × Lolium hybrids after cold stress.
Significant difference in homoeolog expression was computed for all 5790 genes and for the 468 genes differentially expressed after cold stress in both F1 and F2 generations. Three categories were defined: L = F (not significantly differentially expressed), L > F (Lolium homoeolog is significantly more expressed than Festuca homoeolog) and F > L (Festuca homoeolog is significantly more expressed than Lolium homoeolog). F, Festuca pratensis homoeolog; L, Lolium multiflorum homoeolog.