Epigenetic perspectives on the evolution and domestication of polyploid plant and crops

Abstract

Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.

Extensive allele‐level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies

“…Gene expression in an F 1 hybrid is regulated by the independent actions, as well as interactions, of its subgenomes. Epiallelic interactions and remodeling may play a major role in orchestrating the unique gene expression profile of a hybrid (Groszmann et al ., ; Shi et al ., ; Zhang et al ., ; Zhu et al ., ; Ding and Chen, ). We profiled transcriptomes in leaf and root of the reciprocal F 1 hybrids and their parent cultivars (NPB and 93‐11).…”

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

“…Early generations of allopolyploids are often associated with emergent genetic and epigenetic instabilities (Wendel, ; Comai, ; Salmon et al ., ; Adams, ; Chen, ; Otto, ; Doyle et al ., ; Leitch & Leitch, ; Ainouche & Jenczewski, ; Feldman & Levy, ; Madlung & Wendel, ; Diez et al ., ; Song & Chen, ; Wendel et al ., ; Dion‐Cote & Barbash, ; Ding & Chen, ). The most pervasive and immediate genetic consequence of nascent polyploidy is disruption of normal meiosis due to mismatches between the meiotic machinery of diploids that now must adapt to handle the abruptly doubled chromosome set (Hollister, ; Mercier et al ., ; Bomblies et al ., ).…”

Polyploidization‐driven differentiation of freezing tolerance in Solidago canadensis

“…Previous studies have reviewed reasons for gene expression divergence in polyploid plants, which mainly includes that (a) most homoeologous genes are co‐expressed, (b) a few genes are lost or mutated and (c) epigenetic modifications may reprogram gene expression (Chen, ). Polyploidization rearranges the genome and induces a large quantity of epigenetic modifications, leading to different DNA methylation levels compared to their diploid relatives (Ding & Chen, ; Liu, Vega, & Feldman, ; Song & Chen, ; Weiss‐Schneeweiss, Emadzade, Jang, & Schneeweiss, ). DNA methylation usually regulates gene expressions negatively in plants, such as A. thaliana , A. adenophora , Nicotiana tabaccum and Zea mays (Choi & Sano, ; Steward, Ito, Yamaguchi, Koizumi, & Sano, ; Xie et al, ; Xie et al, ).…”