The role of genomic structural variation in the genetic improvement of polyploid crops

Schiessl, Sarah; Katche, Elvis; Ihien, Elizabeth; Chawla, Harmeet Singh; Mason, Annaliese S.

doi:10.1016/j.cj.2018.07.006

Cited by 76 publications

(58 citation statements)

References 119 publications

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“…Many complex cellular mechanisms that determine plant fertility are governed by genes requiring specific dosage balance and simultaneous expression (Lloyd et al ., ), and whose loss is therefore expected to reduce fertility. A multitude of gene dosage/copy number‐dependent traits have been identified in B. napus , some influencing plant reproductive systems such as flowering time (Schiessl et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids

et al. 2019

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Summary Synthetic allohexaploid Brassica hybrids (2n = AABBCC) do not exist naturally, but can be synthesized by crosses between diploid and/or allotetraploid Brassica species. Using these hybrids, we aimed to identify how novel allohexaploids restore fertility and normal meiosis after formation. Chromosome inheritance, genome structure, fertility and meiotic behaviour were assessed in three segregating allohexaploid populations derived from the cross (B. napus × B. carinata) × B. juncea using a combination of molecular marker genotyping, phenotyping and cytogenetics. Plants with unbalanced A–C translocations in one direction (where a C‐genome chromosome fragment replaces an A‐genome fragment) but not the other (where an A‐genome fragment replaces a C‐genome fragment) showed significantly reduced fertility across all populations. Genomic regions associated with fertility contained several meiosis genes with putatively causal mutations inherited from the parents (copies of SCC2 in the A genome, PAIR1/PRD3, PRD1 and ATK1/KATA/KIN14a in the B genome, and MSH2 and SMC1/TITAN8 in the C genome). Reduced seed fertility associated with the loss of chromosome fragments from only one subgenome following homoeologous exchanges could comprise a mechanism for biased genome fractionation in allopolyploids. Pre‐existing meiosis gene variants present in allotetraploid parents may help to stabilize meiosis in novel allohexaploids.

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Section: Discussionmentioning

confidence: 97%

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids

et al. 2019

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“…Homoeologous exchanges, as well as presence-absence variants and other karyotypic changes, have now been conclusively linked to phenotypic changes in many species, including polyploid crops (reviewed by Schiessl et al, 2019). In fact, a number of homoeologous exchanges (almost all examples involve duplication-deletion events, as reciprocal translocations are harder to detect) have now been demonstrated to have been selected for in crops: in Brassica napus (rapeseed), winter and spring crop types are differentiated by homoeologous exchanges involving major flowering time regulators such as FLC (Schiessl et al, 2017), and effects of homoeologous exchanges on disease resistance and glucosinolate metabolism have also been observed (Stein et al, 2017;Hurgobin et al, 2018).…”

Section: Homoeologous Recombination Events Can Generate Novel Variatimentioning

confidence: 99%

Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution

2020

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Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication-deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.

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“…Structural variants (SVs) include differences in copy number (copy number variation; CNV) of genes and repeats, presence-absence variation (PAV), various forms of chromosomal change such as inversions (Huang and Rieseberg, 2020) and translocations, and homoeologous exchanges (HEs; see Mason and Wendel, this issue). In fact, the two or more co-resident genomes of allopolyploids almost certainly contain structural variations, which have been shown to accumulate in all plant genomes studied (Saxena et al, 2014;Fuentes et al, 2019;Gabur et al, 2019;Schiessl et al, 2019). Thus, divergence of two diploids is accompanied by the natural accumulation of structural differences, which then become combined in a common nucleus during allopolyploidization.…”

Section: Structural Diversitymentioning

confidence: 99%

Genomics of Evolutionary Novelty in Hybrids and Polyploids

2020

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It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.

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The role of genomic structural variation in the genetic improvement of polyploid crops

Cited by 76 publications

References 119 publications

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids

Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution

Genomics of Evolutionary Novelty in Hybrids and Polyploids

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