The BOY NAMED SUE quantitative trait locus confers increased meiotic stability to an adapted natural allopolyploid of Arabidopsis

Abstract

Whole-genome duplication resulting from polyploidy is ubiquitous in the evolutionary history of plant species. Yet, polyploids must overcome the meiotic challenge of pairing, recombining, and segregating more than two sets of chromosomes. Using genomic sequencing of synthetic and natural allopolyploids of Arabidopsis thaliana and Arabidopsis arenosa, we determined that dosage variation and chromosomal translocations consistent with homoeologous pairing were more frequent in the synthetic allopolyploids. To test the role of structural chromosomal differentiation versus genetic regulation of meiotic pairing, we performed sequenced-based, high-density genetic mapping in F2 hybrids between synthetic and natural lines. This F2 population displayed frequent dosage variation and deleterious homoeologous recombination. The genetic map derived from this population provided no indication of structural evolution of the genome of the natural allopolyploid Arabidopsis suecica, compared with its predicted parents. The F2 population displayed variation in meiotic regularity and pollen viability that correlated with a single quantitative trait locus, which we named BOY NAMED SUE, and whose beneficial allele was contributed by A. suecica. This demonstrates that an additive, gain-of-function allele contributes to meiotic stability and fertility in a recently established allopolyploid and provides an Arabidopsis system to decipher evolutionary and molecular mechanisms of meiotic regularity in polyploids.

Figure 1.

Pollen Viability in the Synthetic × Natural Allopolyploid Pedigree. (A) Pedigree of allopolyploids used in this study. Each bar represents a genomic copy whose fill indicates the species of origin and whose contour indicates recent or prehistoric origin. The pedigree assumes that A. suecica was produced by hybridization of autotetraploids. Alternative modes, such as involving 2N gametes or a diploid hybrid that doubled its chromosomes, are possible but not shown. (B) Mean pollen viability was measured for each plant, and the mean of the means was calculated for each genotype. Standard errors are indicated.

Figure 2.

Evidence of Meiotic Irregularities and Homoeologous Exchange in the Synthetic Allopolyploid. Examples of individual dosage plots. Sequencing reads were aligned to the reference genome and sorted into consecutive bins along the 13 chromosomes of the allopolyploid genome. For ease of visualization, relative read coverage is normalized such that dosage plots of fragments present in two copies fluctuated around 2.0. Changes up or down in relative coverage of consecutive bins indicates variation in dosage and correspond to the addition or deletion of a particular chromosome or chromosomal fragment, respectively. Relative coverage around the centromeric repeats consistently appears noisy most likely because of mis-mapping, quality of reference sequence, and changes in repeated elements. Gray arrows indicate aneuploidy of a whole or segment of a chromosome. The black arrow indicates an example of a complex dosage variation (part of a chromosome is present in one copy and another part is present in three copies). Compensating dosage variants, in which one chromosome fragment is missing and the corresponding homoeologous fragment from the other genome is present in three copies, are indicated by circles.

Figure 3.

Formation of a Homoeologous Exchange. A hypothetical allopolyploid with four chromosomes is illustrated. Thin or thick lines depict chromosomes from one ancestral or the other ancestral genome. Hatched lines represent the spindle apparatus. (A) Regular meiosis showing properly paired replicated chromosomes undergoing recombination and disjunction and the resulting meiotic products. (B) Intergenomic pairing and recombination between homoeologous chromosomes leading to the formation of two unbalanced gametes. (C) One unbalanced gamete fertilizes an egg leading to a zygote containing extra DNA from the thick-marked genome and missing the corresponding segment of the thin-marked genome. The outcome illustrated results from syntenic chromosomes. If the paired regions leading to exchanges are located on chromosomes that are structurally diverged (e.g., have inverted segments), the result can be catastrophic, leading to such aberrations as dicentric or acentric chromosomes, chromosomal breakage, and large deficiencies or duplication in the affected meiotic products. These, in turn, can lead to lethality in the gamete or in the zygote. [See online article for color version of this figure.]

Figure 4.

Meiotic Irregularities in the Syn × Nat F2 Plants. (A) to (C) FISH observations of meiotic spreads of developing microspores from F2 individuals. From left to right: Overlay, 4′,6-diamidino-2-phenylindole staining in blue, At-cen labeled FISH in red, Aa-cen labeled FISH in green. (A) Anaphase I, example of a regular meiosis. (B) Anaphase I, one potential laggard from an arenosa chromosome is observed. (C) Anaphase I, an arenosa chromosomal bridge is observed. (D) Correlation between departure from expected chromosome number and the percentage of viable pollen in the F2 population. The regression P value and R² value are indicated.

Figure 5.

Transmission Ratio Distortion in the F2. The mean percentage of allele derived from natural A. suecica in the F2 population was calculated for each marker bin. Different colors represent different chromosomes. Arrows indicate significant distortion from the expected 50% of A. suecica natural allele. [See online article for color version of this figure.]

Figure 6.

Dosage Variation in the Syn × Nat F2 Plants. Examples of individual F2 dosage plots obtained through whole-genome sequencing. Sequencing reads were aligned to the reference genome and sorted into consecutive bins along the 13 chromosomes of the allopolyploid genome. For ease of visualization, relative read coverage is normalized such that fragments present in two copies fluctuated around 2.0. Changes up or down in relative coverage of consecutive bins (arrows) indicates variation in dosage and correspond to the addition or deletion of a particular chromosome or chromosomal fragment, respectively. Relative coverage around the centromeric repeats consistently appears noisy most likely because of mis-mapping, quality of reference sequence, and changes in repeat copy number.

Figure 7.

Comparison of the Genetic and Physical Maps. (A) Marker bin order in the physical maps (published reference genomes of A. thaliana and A. lyrata) was compared with the marker order obtained from our F2 population. Two inversions (black circles) were identified. A few markers located on chromosome one of the A. lyrata genomic reference appeared reversed and translocated in the middle of chromosome two in our genetic map (gray circle). (B) and (C) The translocation between chromosome one of the A. lyrata reference genome and chromosome 2 of A. arenosa is confirmed by the karyotypes of F2 individuals carrying altered number of copies of A. arenosa chromosomes 1 or 2.

Figure 8.

Identification of a QTL Associated with Pollen Viability and Meiotic Irregularity. (A) Results of QTL detection using standard interval mapping in R/qtl (see Methods for a detailed description of the phenotypes and the QTL mapping parameters used). LOD scores are plotted along the five A. thaliana and the eight A. arenosa chromosomes. Significance thresholds of 3.74 (deviation from expected chromosome number) and 3.73 (pollen viability) were determined based on 1000 permutations and correspond to P values < 0.05. The locus corresponding to the peak exhibiting significant LOD scores for both phenotypes was named BYS. (B) and (C) Individual (cloud) and mean pollen viability (blue) (B) and individual (cloud) and mean deviation from expected chromosome number (meiotic irregularity in green) (C) for F2 plants that were homozygous for Syn (synthetic allopolyploid allele, left), heterozygous (middle), or homozygous for Nat (natural allopolyploid allele, right) at the BYS locus (indicated on [A] and located approximately at 16.9 Mb on scaffold 4 of the A. lyrata genomic reference). Standard errors are represented. Imputed genotypes are plotted in red.