Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

Abstract

Box 1 GlossaryAllopolyploidypolyploidy when the parents are either from different species (taxonomic allopolyploidy) or genetically diverse (genetic allopolyploidy). Amplified fragment length polymorphism (AFLP)a PCR-based tool that selectively amplifies a subset of restriction enzyme-digested DNA fragments and detects the presence/absence of unique polymorphisms in the genomes of interest. Aneuploid/unbalanced gameteshaving more or fewer chromosomes than a complete set. This is a deviation from the total chromosome number being a multiple of the haploid set. A haploid set refers to a single, unique set of chromosomes from an organism. Autopolyploidypolyploidy when the parents are either the same species (taxonomic autopolyploidy) or genetically very similar (genetic autopolyploidy). Biased fractionationthe asymmetric loss of duplicated genes following a whole genome duplication resulting in one subgenome having more retained genes than the other subgenome(s) in a polyploid genome. Bivalentwhen chromosome pairing involves alignment between a pair of homologous chromosomes. Chimeric gene/fusion genea combination of coding sequences from different homologous and homoeologous genes. Chromatina complex of DNA molecules and histone proteins that form chromosomes in eukaryotic cells. Chromosome pairingthe coming together of homologous chromosomes in a genome forming alignment along the length of the chromosome. Most often referenced in the prophase of meiosis. Chromosome segregationthe process of chromosomes being randomly sorted into daughter cells or gametes during mitosis and meiosis, respectively. Crossing overreciprocal exchange of large DNA sequences/segments between paired homologous chromosomes to repair DNA damage due to DSBs during meiosis. Diploidizationthe process in which a polyploidy genome returns to functioning as a diploid. The process includes changes in expression patterns, methylation, gene loss, and chromosome number reduction. Disomic inheritanceregular chromosome pairing and segregation of alleles from each homologous chromosome into the gamete. This often refers to the pairing of homologous chromosomes from the same parent in an allotetraploid and the segregation of one homologous chromosome from each parent into the gamete. DNA double-strand breaks (DSBs)programmed formation of cell's self-induced breaks in DNA catalyzed by highly conserved topoisomerase-like SPO11 and other associated proteins to initiate meiotic recombination. DNA methylationa biological process involving the addition of a methyl (CH 3 ) group, often onto the fifth carbon of the cytosine residue of a DNA molecule. Dosage-sensitive markersmolecular markers that can detect the variation due to loss or duplication of specific DNA fragments/copies compared with the expected total fragments in a specific genomic locus across the genomes of interest. Fusion transcripttranscript resulting from a chimeric/fusion gene. Gene conversiona nonreciprocal swap of smaller DNA segments between chromosomes. Genetic markers -DNA sequences with ...

Chromosome translocation affects multiple phenotypes, causes genome‐wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat

“…In contrast to many other neoallopolyploid crops in which homoeologous chromosome segment exchanges widely occur (Chen et al., 2018; Deb et al., 2023; Gaeta & Chris Pires, 2010; Hurgobin et al., 2018; Lloyd et al., 2018; Mason & Wendel, 2020), the three subgenomes of bread wheat are largely intact due to the presence of genetic loci (e.g., the Ph1 and Ph2 ) that simultaneously prompt homologous pairing and recombination and efficiently suppress non‐homologous pairing and/or recombination (Griffiths et al., 2006; Sears, 1976; Serra et al., 2021). Our results demonstrate that a single new RT event is sufficient to induce dysregulation of hundreds to thousands genes with variable extents between tissues in a synthetic hexaploid wheat.…”