View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Polyploidy or whole genome duplication (WGD) is a prominent evolutionary feature for all flowering plants and many animals. Most crop plants including wheat, cotton, and oilseed rape are polyploids, and many other crops such as maize and soybean are ancient polyploids. In allopolyploids, interspecific hybridization can induce “genome shock,” leading to genomic and epigenomic changes, the effects of which can be amplified by genome doubling (ploidy changes). Moreover, heterozygosity between hybridizing parents is permanently fixed in allopolyploids. However, many polyploid plants and crops were formed long time ago, and their exact progenitors may become extinct. To replay the evolutionary type, we resynthesized Arabidopsis suecicaallotetraploids between A. thaliana and A. arenosa and compared them with natural A. suecica that was formed ~300,000 years ago. Using the trackable Arabidopsis allotetraploid system and allotetraploid cotton crop model, we employed integrated approaches of genomics, epigenomics, and computational biology to investigate genomic variation, gene expression changes, and epigenomic modifications that have shaped phenotypic diversification in plant polyploids. Here, I will update recent findings and perspectives of comparative genomics and epigenomics that have uncovered the molecular bases for nonadditive gene expression, altered genetic recombination, morphological diversity, and adaptive evolution in Arabidopsis and cotton allopolyploids. These conceptual advances and genomic and epigenomic resources will help us better understand polyploid genome evolution and improve the production of polyploid crops for food security and carbon capture and storage.

Genomic and Epigenomic Insights into Formation and Evolution of Polyploid Plants and Crops