Meiosis in allopolyploid Arabidopsis suecica

Improved synapsis dynamics accompany meiotic stability in Arabidopsis arenosa autotetraploids

During meiosis, the correct pairing, synapsis, and recombination of homologous chromosome pairs is critical for fertility of sexual eukaryotes. These processes are challenged in polyploids, which possess additional copies of each chromosome. Polyploidy thus provides a unique context to study how evolution can modify meiotic programs in response to challenges. We previously observed that in newly formed (neo-)polyploids of Arabidopsis arenosa, synapsis defects precede chromosomes associating in aberrant multivalent and univalent configurations. Here, we study synapsis dynamics in genotypes with varying levels of meiotic stability to ask whether efficient synaptic progression is a key component of evolving stable tetraploid meiosis. We develop a method to quantify synapsis dynamics using the progression of foci of the pro-crossover factor HEI10 as a reference. HEI10 initially appears at many small foci before accumulating only at crossover sites. In diploids, this transition begins while significant asynapsis is still present, though it quickly declines as HEI10 accumulates at fewer foci. In neo-tetraploids, suboptimal elongation of synaptic initiation sites and stalled synapsis, perhaps due to defective pairing, occurs before the onset of HEI10 accumulation. In established tetraploids, HEI10 accumulation begins only when synapsis is near complete, suggesting enhanced HEI10/synapsis codynamics (even compared to diploids). Hybrids generated by crossing neo- and established tetraploids exhibit intermediate phenotypes. We find the extent of asynapsis correlates positively with crossover numbers, and the frequency of multivalents and univalents, which can disturb chromosome segregation. Our work supports the hypothesis that improving the efficiency of synapsis is important for evolving polyploid meiotic stability.

The synaptonemal complex stabilizes meiosis in allotetraploid Brassica napus and autotetraploid Arabidopsis thaliana

Polyploidy plays a key role in genome evolution and crop improvement. The formation of bivalents rather than multivalents during meiosis of polyploids is essential to ensure meiotic stability and optimal fertility of the species. However, the mechanisms preventing multivalent recombination in polyploids remain obscure. We studied the role of the synaptonemal complex in polyploid meiosis by mutating the transverse filament component ZYP1 in allotetraploid Brassica napus and autotetraploid Arabidopsis. In B. napus, a mutation of all four ZYP1 copies results in multivalent pairing accompanied by pairing partner switches, nonhomologous recombination, and interlocks, leading to severe chromosome entanglement and fertility abortion. The presence of only one functional allele of ZYP1 compromises synapsis and multivalent associations occur at nonsynaptic regions. Moreover, the disruption of ZYP1 causes a complete shift from predominantly multivalent pairing to exclusively multivalent pairing in pachytene cells of synthetic autotetraploid Arabidopsis thaliana, resulting in a dramatic increase in the frequency of multivalents at metaphase I. We conclude that the ZYP1-mediated assembly of the synaptonemal complex facilitates the pairwise homologous pairing and recombination in both allopolyploid and autopolyploid species and plays a key role in ensuring a diploid-like bivalent formation in polyploid meiosis.

Homoeologous crossovers are distally biased and underlie genomic instability in first-generation neo-allopolyploid Arabidopsis suecica

First-generation polyploids often suffer from more meiotic errors and lower fertility than established wild polyploid populations. One such example is the allopolyploid model species Arabidopsis suecica which originated c. 16 000 generations ago. We present here a comparison of meiosis and its outcomes in naturally evolved and first-generation 'synthetic' A. suecica using a combination of cytological and genomic approaches. We show that while meiosis in natural lines is largely diploid-like, synthetic lines have high levels of meiotic errors including incomplete synapsis and nonhomologous crossover formation. Whole-genome re-sequencing of progeny revealed 20-fold higher levels of homoeologous exchange and eightfold higher aneuploidy originating from synthetic parents. Homoeologous exchanges showed a strong distal bias and occurred predominantly in genes, regularly generating novel protein variants. We also observed that homoeologous exchanges can generate megabase scale INDELs when occurring in regions of inverted synteny. Finally, we observed evidence of sex-specific differences in adaptation to polyploidy with higher success in reciprocal crosses to natural lines when synthetic plants were used as the female parent. Our results directly link cytological phenotypes in A. suecica with their genomic outcomes, demonstrating that homoeologous crossovers underlie genomic instability in neo-allopolyploids and are more distally biased than homologous crossovers.

Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Incorrect recombination partner associations contribute to meiotic instability of neo-allopolyploid Arabidopsis suecica

Combining two or more related homoeologous genomes in a single nucleus, newly formed allopolyploids must rapidly adapt meiosis to restore balanced chromosome segregation, production of euploid gametes and fertility. The poor fertility of such neo-allopolyploids thus strongly selects for the limitation or avoidance of genetic crossover formation between homoeologous chromosomes. In this study, we have reproduced the interspecific hybridization between Arabidopsis thaliana and Arabidopsis arenosa leading to the allotetraploid Arabidopsis suecica and have characterized the first allopolyploid meioses. First-generation neo-allopolyploid siblings vary considerably in fertility, meiotic behavior and levels of homoeologous recombination. We show that centromere dynamics at early meiosis is altered in synthetic neo-allopolyploids compared with evolved A. suecica, with a significant increase in homoeologous centromere interactions at zygotene. At metaphase I, the presence of multivalents involving homoeologous chromosomes confirms that homoeologous recombination occurs in the first-generation synthetic allopolyploid plants and this is associated with a significant reduction in homologous recombination, compared to evolved A. suecica. Together, these data strongly suggest that the fidelity of recombination partner choice, likely during the DNA invasion step, is strongly impaired during the first meiosis of neo-allopolyploids and requires subsequent adaptation.

Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis

Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.