Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Abstract

SummaryPolyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized autoand allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution. Polyploidy and its formsPolyploidy occurs throughout the evolutionary history of all eukaryotes, (1,2) predominately in flowering plants (3,4) including many important agricultural crops. (5) Compared to plants, polyploidy occurs rarely in animals, but clearly exists in some invertebrates (e.g. insects) and vertebrates (e.g. fish, amphibians and reptiles). (4,6) The relative paucity of polyploidy in animals is attributed to the delicate schemes of sex determination and animal development, which are disrupted by polyploidization. (7,8) Therefore, polyploid animals rarely exist. (9) Moreover, aneuploid and polyploid cells in animals and human are often associated with malignant cell proliferation or carcinogenesis. (10) However, endopolyploidy (somatic polyploid cells within a diploid individual) appears to be a physiological response to developmental changes in plants and some animals, (11,12) indicating plasticity of plant and animal genomes. In the post-sequencing era, polyploidy is proving to be a fascinating and challenging field of plant biology, stimulating many research advances and insightful reviews. (2,13 -24) Here we attempt to update the views using genomic-scale results and provide new mechanistic insights.Historically, Winkler (1916) introduced the term polyploidy, (25) and Winge (1917) called attention to the general importance of polyploidy in the evolution of angiosperms. (26) At that time, research in polyploidy was somewhat limited by the plant and animal materials that were available in nature. In 1937, Blakeslee and Avery induced polyploidy in plants using colchicine, a chemical inhibitor of mitotic cell divisions. (27) The technique has been successfully used to induce chromosome doubling in meristemic cells of diploids and interspecific hybrids. Doubling a single 'diploid' genome results in an autotetraploid, while doubling c...

External factors accelerate expression divergence between duplicate genes

“…In development, duplicate genes diverge in expression relatively slowly and tend to be coregulated. A relatively slow rate of expression divergence between the duplicates might provide genetic robustness against null mutations [10] and selective advantage by dosage-dependent gene regulation [11,29] that enables organisms to fine-tune complex regulatory networks through genetic and epigenetic mechanisms [30]. Therefore, duplicate genes could promote an adaptive mechanism for environmental changes or provide genetic robustness and dosage-dependent regulation during organismal development, which might facilitate polyploid evolution.…”

Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp

“…Recent polyploids have been identified in fishes and amphibians (Choleva and Janko, 2013;Gui and Zhou, 2010;Otto, 2007;Song et al, 2012) and some diploidized tetraploid species have been demonstrated in some teleost fish lineages including cyprinids, catostomids, and salmonids (Allendorf and Thorgaard, 1984;Collares-Pereira et al, 2013;Gui and Zhou, 2010;Yang and Gui, 2004), but the two recent rounds of polyploidy have been documented only in the polyploid gibel carp. Recent genome-wide studies have confirmed that the problem of genetic incompatibility raised by polyploidy may be resolved by the accumulation of diverse mutational changes to form a stable chimerical and diploidized genome (Buggs et al, 2011;Chen and Ni, 2006;Louis et al, 2012;Tate et al, 2009). And, a lot of biogeographic and ecological investigations have revealed the close association between polyploidy occurrence and environmental change (Parisod et al, 2010;Wu et al, 2010).…”

Production of Autopolyploid Lowland Switchgrass Lines Through In Vitro Chromosome Doubling

“…It has also been reported that genome polyploidation can have potential selective advantages such as increased heterozygosity, as well as novel variation and allelic subfunctionalization [46][47][48][49].…”

“…However, the molecular mechanisms that contribute to the novel phenotypes of autopolyploidy plants remain largely unexplored [48][49][50][51]. Interestingly, one report has described the loss of selfincompatibility after polyploidation events [52].…”