Environmental Regulation of Heterosis in the Allopolyploid Arabidopsis suecica.

Allopolyploids are organisms possessing more than two complete sets of chromosomes from two or more species and are frequently more vigorous than their progenitors. To address the question why allopolyploids display hybrid vigor, we compared the natural allopolyploid Arabidopsis suecica to its progenitor species Arabidopsis thaliana and Arabidopsis arenosa. We measured chlorophyll content, CO2 assimilation, and carbohydrate production under varying light conditions and found that the allopolyploid assimilates more CO2 per unit chlorophyll than either of the two progenitor species in high intensity light. The increased carbon assimilation corresponds with greater starch accumulation, but only in strong light, suggesting that the strength of hybrid vigor is dependent on environmental conditions. In weaker light A. suecica tends to produce as much primary metabolites as the better progenitor. We found that gene expression of LIMIT DEXTRINASE1, a debranching enzyme that cleaves branch points within starch molecules, is at the same level in the allopolyploid as in the maternal progenitor A. thaliana and significantly more expressed than in the paternal progenitor A. arenosa. However, expression differences of ß-amylases and GLUCAN-WATER DIKINASE1 were not statistically significantly elevated in the allopolyploid over progenitor expression levels. In contrast to allopolyploids, autopolyploid A. thaliana showed the same photosynthetic rate as diploids, indicating that polyploidization alone is likely not the reason for enhanced vigor in the allopolyploid. Taken together, our data suggest that the magnitude of heterosis in A. suecica is environmentally regulated, arises from more efficient photosynthesis, and, under specific conditions, leads to greater starch accumulation than in its progenitor species.

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

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.

Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids.

Polyploidization is an important mechanism for introducing diversity into a population and promoting evolutionary change. It is believed that most, if not all, angiosperms have undergone whole genome duplication events in their evolutionary history, which has led to changes in genome structure, gene regulation, and chromosome maintenance. Previous studies have shown that polyploidy can coincide with meiotic abnormalities and somatic cytogenetic mosaics in Arabidopsis allotetraploids, but it is unclear whether this phenomenon can contribute to novel diversity or act as a mechanism for speciation. In this study we tested the hypothesis that mosaic aneuploidy contributes to the formation of incipient diversity in neoallopolyploids. We generated a population of synthesized Arabidopsis allohexaploids and monitored karyotypic and phenotypic variation in this population over the first seven generations. We found evidence of sibling line-specific chromosome number variations and rapidly diverging phenotypes between lines, including flowering time, leaf shape, and pollen viability. Karyotypes varied between sibling lines and between cells within the same tissues. Cytotypic variation correlates with phenotypic novelty, and, unlike in allotetraploids, remains a major genomic destabilizing factor for at least the first seven generations. While it is still unclear whether new stable aneuploid lines will arise from these populations, our data are consistent with the notion that somatic aneuploidy, especially in higher level allopolyploids, can act as an evolutionary relevant mechanism to induce rapid variation not only during the initial allopolyploidization process but also for several subsequent generations. This process may lay the genetic foundation for multiple, rather than just a single, new species.

Genomic changes in synthetic Arabidopsis polyploids.

Polyploids are common and arise frequently by genome duplication (autopolyploids) or interspecific hybridization (allopolyploids). Neoallopolyploids display sterility, lethality, phenotypic instability, gene silencing and epigenetic changes. Little is known about the molecular basis of these phenomena, and how much genomic remodeling happens upon allopolyploidization. Extensive genomic remodeling has been documented in wheat, but little remodeling occurs in cotton. Newly synthesized Arabidopsis allopolyploids, which display phenotypic instability and low fertility, displayed several, possibly related mechanisms that can remodel genomes. We detected transcriptional activity of several transposons although their transposition was limited. One represents a new family of conditionally active En-Spm-like transposons of Arabidopsis thaliana, which underwent remodeling of CG methylation upon allopolyploidization. A random amplified fragment length polymorphism survey suggested remodeling at few, specific loci. Meiotic analyses revealed the appearance of chromosomal fragments in a substantial fraction of anther meiocytes. In several individuals produced by hybrids between the synthetic and a natural allopolyploid pollen viability inversely correlated with meiotic instability. Activity of selected DNA transposons and the possibly related chromosomal breaks could cause changes by inducing translocations and rearrangements.

Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids?

Allopolyploidy, the joining of two parental genomes in a polyploid organism with diploid meiosis, is an important mechanism of reticulate evolution. While many successful long-established allopolyploids are known, those formed recently undergo an instability phase whose basis is now being characterized. We describe observations made with the Arabidopsis system that include phenotypic instability, gene silencing and activation, and methylation changes. We present a model based on the epigenetic destabilization of genomic repeats, which in the parents are heterochromatinized and suppressed. We hypothesize that loss of epigenetic suppression of these sequences, here defined as the heterome, results in genomic instability including silencing of single-copy genes.

FISH analysis of meiosis in Arabidopsis allopolyploids.

Although allopolyploids are common in nature and in agriculture, knowledge of their origin, evolution and genomic regulation is limited. We study synthetic allotetraploids of Arabidopsis thaliana and Arabidopsis arenosa as well as the natural allotetraploid Arabidopsis suecica. To elucidate the composition and behavior of the allotetraploid genome, we used chromosome painting with probes from contiguous regions of chromosome 4 of A. thaliana and fluorescent in-situ hybridization with centromeric (CEN) probes specific for each parental genome. We documented the presence of 16 A. arenosa and 10 A. thaliana chromosomes and demonstrate that two different A. arenosa chromosomes are homeologous to chromosome 4 of A. thaliana. Although chromosome pairing in pollen mother cells was predominantly homologous, CENs of different parental origin coalesced at early prophase I, but resolved into proper pairs by metaphase. In addition, CENs of homologous chromosomes were not paired in tapetum cells and endopolyploidy without strict polyteny was evident by the large number of independent CENs. Thus, the Arabidopsis synthetic allopolyploids were capable of homologous pairing as early as three generations after their formation. This indicates that diploid-like pairing is not the result of adaptive mutations in genes that regulate pairing nor the result of structural remodeling of the genomes: rather, it is likely that either the parents provided genes controlling pairing behavior or that features of the parental chromosomes hinder homeologous pairing.

Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant.

Centromeric H3-like histones, which replace histone H3 in the centromeric chromatin of animals and fungi, have not been reported in plants. We identified a histone H3 variant from Arabidopsis thaliana that encodes a centromere-identifying protein designated HTR12. By immunological detection, HTR12 localized at centromeres in both mitotic and meiotic cells. HTR12 signal revealed tissue- and stage-specific differences in centromere morphology, including a distended bead-like structure in interphase root tip cells. The anti-HTR12 antibody also detected spherical organelles in meiotic cells. Although the antibody does not label centromeres in the closely related species Arabidopsis arenosa, HTR12 signal was found on all centromeres in allopolyploids of these two species. Comparison of the HTR12 genes of A. thaliana and A. arenosa revealed striking adaptive evolution in the N-terminal tail of the protein, similar to the pattern seen in its counterpart in Drosophila. This finding suggests that the same evolutionary forces shape centromeric chromatin in both animals and plants.