Fractionization of Polyploid Duplicated Genes: Gene Loss, Expression Divergence, and Epigenetic Regulation in Brassica napus

Abstract

Plant genome polyploidization and subsequent evolution is a crucial process for trait innovation and new species formation. Recurrent whole-genome duplication (WGD) existing in Brassica napus created abundant genetic variation, which make it an ideal model for studying the patterns and mechanism of polyploid genome evolution. Based on the availability of reference genomes and high-throughput ‘omics’ data, the duplicated genes derived from different WGD events were identified, enabling investigation of their expression divergence and epigenetic regulation. This chapter introduced generation and loss of duplicated genes in multiple cycles of whole-genome duplication and described expression divergence of duplicates, particularly those homeologous genes. Alternative splicing events may play an important role in expression divergence of the duplicate genes. Expression divergence of duplicated genes may be regulated by epigenetic mechanisms, especially subgenome interaction-related small RNA produced from transposable elements in the case that the two subgenomes have asymmetrical transposable elements and their abundance. In the future, the new ‘omics’ technologies could be used to accurately quantify expression divergence and its regulatory mechanisms of duplicated genes in relation to phenotypic changes to uncover polyploid genome evolution.