The Molecular Mechanisms of Plant Polyploidization Revealed By Systems Analysis of the Genomes and Transcriptomes of Wheat, Cotton and Related Species

Polyploidization is a predominant process in flowering plant speciation and evolution. The genomes of most angiosperms are thought to have incurred one or more polyploidization events during their evolution. It is estimated that approximately 70% of flowering plants, including numerous agriculturally important crops such as wheat, cotton, potato, canola, oats, peanut, tobacco, coffee, banana and sugarcane, are late-evolution polyploids. However, little is known about the underlying molecular mechanisms of how a polyploid species forms and evolves. These questions are addressed by systems analysis of the genomes and transcriptomes of a total of 634 lines of polyploid wheat, polyploid cotton and their related diploid species, including 112 newly synthetic polyploid wheat lines. We first scrutinized the variations of contents, family sizes and interactions of 29 fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retro-transposable elements (RTE), simple sequence repeats (SSR) and low complexity repeats (LCR), in the processes of polyploidization from parental species to nascent polyploids to naturally-established polyploids. Then, we examined the variations of the transcriptomes of the species during the process. Finally, we investigated the variations of the contents and networks of the genes controlling cotton fiber length and wheat grain yield-related traits. The findings of this study have elucidated novel molecular mechanisms underlying plant polyploidization and significantly advanced our understanding of the process of plant speciation, variation and evolution.