Analysis of gene expression level dominance and homoeologous expression bias in different tissues of a new synthetic amphidiploid, Raphanobrassica (Brassica rapa × Raphanus sativus)

• The progeny plants AR(2n=19) harboring the genomes of radish (Raphanus sativus, RR, 2n=18) and cabbage (Brassica pekinensis, AA, 2n=20) were identified by fluorescence in situ hybridization. • The gene expression bias of AR leaf and flower tissues was in favor of A genome, and the proportion was 26.03 % and 32.74 %. ELD results showed that all of them were favorable to R genome, and the proportion was 15.41 % and 18.61 %. • Gene silencing and expression of new genes in the two tissues were observed in the progeny AR. Polyploidization is an evolutionarily and mechanistically intriguing process, that requires harmonization of genomic and regulatory interactions among divergent genome groups. Here, we examined gene expression pattern changes in the leaves and petals of Raphanobrassica, a new synthetic amphidiploid generated by a distant cross between radish (RR, 2n = 18) and purple cabbage (AA, 2n = 20). The degree and direction of expression level dominance (ELD), defined as the total expression level of two homoeologous genes, was assessed, and homoeologous expression bias (HEB) analyzed, to assess the relative contributions of homoeologous genes to the transcriptome. Comparative analysis between Raphanobrassica and its parental species revealed that most differentially expressed genes were additive (leaves, 81.63 %; flowers, 82.71 %). ELD favors the R genome in both Raphanobrassica tissues, primarily driven by up- or down-regulation of non-dominant parent genes, with radish (RR) as the dominant parent in ELD-R and cabbage (AA) in ELD-A HEB indicated a preference for the A genome in both tissues (leaves, 26.03 %; flowers, 32.74 %). To further elucidate the ELD phenomenon, we compared expression levels of individual homoeologous genes with those in the diploid parents. ELD toward genes expressed at higher levels in parents was mediated either by down-regulation of genes from the dominant parent or up-regulation of those from the non-dominant parent, whereas ELD toward genes expressed at lower levels in parents was attributable solely to down-regulation of non-dominant parent homoeologous genes. Our findings provide novel insights into gene expression changes in heterodiploids generated by hybridization prior to polyploidization, laying a foundation for understanding genome-wide expression pattern alterations during polyploid formation.