Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in Synthetic Brassica napus and Derivatives (AC, AAC, CCA, CCAA)

Abstract

Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of Brassica rapa and Brassica oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes and mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations and mostly facilitated dosage compensation. More protein-protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expressions.

Keywords: Brassica; cis/trans effects; dosage imbalance; gene expression; polyploids.

Figure 1

Phenotype and cytology of synthetic B. napus and derivatives. (A) Pedigrees of the plant materials. (B) Young plants, leaves and flowers of AA, CC, CCAA, AAC, and CCA. Scale bars = 5 cm. (C) DAPI, BAC-FISH, and merged images for each mitotic cell. Scale bars = 5 μm.

Figure 2

Gene expression changes in synthetic B. napus and derivatives. (A) The number of expressed genes (FPKM > 0) diversity between A- and C-subgenome genes in MPV, AC, CCAA, AAC, and CCA. (B) Global gene expression levels diversity between A- and C-subgenome genes in MPV, AC, CCAA, AAC, and CCA. (C) The distribution of fold change (FC) of AC, CCAA, AAC, and CCA, compared with progenitors.

Figure 3

Genome-wide dosage regulation of homeologous expression in synthetic B. napus. (A) Number of genes with positive (R > 0) and negative (R < 0) correlation between dosage and expression of A (left) and C (right) homeologous genes at significant (FDR < 0.05) and insignificant (FDR > 0.05) levels. (B) The distribution of coefficient of determination (R²) in A and C homeologous. X axis: R² value bins divided; Y axis: number of genes in each bin. Gray lines separate genes with dosage-dependent and dosage-independent expression. (C) Number of Ad, Ai, Cd, and Ci genes. (D) Numbers of genes with fold-change (FC) distribution of in A and C homeologous genes at “0.5–1.5” and “>1.5 or <0.5” levels in CCAA. Ad, Ai, Cd, and Ci means dosage dependent A, dosage independent A, dosage dependent C, and dosage independent C, respectively.

Figure 4

Dosage-dependent and dosage-independent expressions of homeologous in B. napus. (A) Number and percentage of AdCd, AdCi, AiCd, and AiCi genes. (B) Percentages of Ad (red), Ai (blue), Cd (black), Ci (green) genes that contain absolute expression levels (FPKM) within a range of distances. X axis: a range of bins contains FPKM values ranking from low to high; Y axis: percentage of genes in each bin. Dash lines represent the expected levels. (C) Enrichment of AdCd and AiCi genes in GO groups. Ad, Ai, Cd, and Ci represent dosage dependent A, dosage independent A, dosage dependent C, and dosage independent C, respectively.

Figure 5

Cis and trans effects on gene expressions of dosage-balance regulatory. (A,B) The distributions of “cis effects” and “trans effects” in CCAA and AAC, respectively. (C,D) The percentages of “only cis effects” and “only trans effects” diversities between A and C homeologous genes in AC, CCAA, AAC, and CCA. Ad, Ai, Cd, and Ci means dosage dependent A, dosage independent A, dosage dependent C and dosage independent C, respectively.

Figure 6

The degrees of protein interactions for dosage-dependent and dosage-independent genes. (A) The number of protein interactions for dosage-dependent and dosage-independent in AdCd and AiCi of B. napus. (B) The number of protein interactions for dosage-dependent and dosage-independent in TdAd and TiAi of Arabidopsis. Dosage-independent genes have significantly more protein interactions. Asterisks indicate p < 0.05. Ad, Ai, Cd, and Ci means dosage dependent A, dosage independent A, dosage dependent C, and dosage independent C, respectively.