Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

BACKGROUND: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (A(n)A(n)C(n)C(n)) relative to its two diploid progenitors, B. rapa (A(r)A(r)) and B. oleracea (C(o)C(o)), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. RESULTS: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (A(n)A(n)C(n)C(n) vs A(r)A(r) and A(n)A(n)C(n)C(n) vs C(o)C(o)), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. CONCLUSIONS: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.