- Population genomics
- Evolution of meiosis
- Gene network evolution
- Mechanisms of habitat adaptation and morphological evolution
Evolution of meiosis in Arabidopsis arenosa
Whole genome duplication can provide an evolutionary opportunity, but also brings with it significant challenges to numerous basic biological processes. A major one, and the one we are focusing on, is sorting the extra chromosome copies during meiosis. Numerous studies of newly formed polyploids have shown that this is a big problem, and we have shown that the same is true in A. arenosa. Yet stable polyploids are abundant in nature, showing that evolution can find solutions. Plants are particularly adept at doubling their genome content and subsequently stabilizing - what the genetic basis of that is remains largely mysterious.
Understanding naturally evolved solutions to chromosome segregation challenges in the face of genome duplication promises new insights into basic aspects of chromosome pairing and recombination. It will help us understand an important evolutionary process. Polyploidy is an important tool in agriculture, where the fertility problems caused by meiotic chromosome mis-segregation presents a serious bariier. And finally, whole genome duplications are implicated in spontaneous abortions in humans, and polyploidy-associated instabilities in chromosome segregation are implicated in cancer progression following somatic genome duplications. Indeed, one of the genes we identified as a target of selection in A. arenosa is a biomarker of aggressive cancers and has been a successful therapeutic target.
Why does doubling a genome impair chromosome segregation? Consider meiosis - this fine-tuned machinery has been perfected over eons to separate pairs of homologous chromosomes. So what happens when suddenly four homologs are present? Often, it turns out, sorting all these extra copies is challenging. Chromosome copies can partner with more than one additional homolog, forming complex multivalents at meiosis that can lead to meiotic abnormalities, aneuploid gamete formation and low fertility. We now know A. arenosa is no exception - here too doubled diploid genotypes show meiotic abnormalities not observed in the evolved tetraploid (Yant et al. 2013).
The figure above shows metaphase I chromosome spreads from (A) diploid A. arenosa, (B) the natural autotetraploid with arrowhead indicating one unpaired univalent, and (C) a newly generated confirmed tetraploid made by treating diploid A. arenosa with colchicine. The colchicine doubled line has messy chromosome organization at metaphase I with some multivalent associations evident (bottom of panel). This suggests that the diploids are not "pre-adapted" to well organized meiosis as tetraploids. (These images were taken by James Higgins at the University of Birmingham, UK).
Established autopolyploids are abundant in nature and are usually meiotically stable. In general these species have cytologically diploid-like chromosome behavior at meiosis, but the chromosomes may still associate randomly (so there are four alleles segregating at each locus instead of two). This is also true of A. arenosa, which shows regular, diploid-like chromosome pairing in meiotic metaphase I, albeit with fewer chiasmata than diploids. How does this work? How do chromosomes with no partner preferences "know" to only pair with one other partner? What changes occured at the molecular level to cytologically diploidize meiosis and prevent multivalent formation in established A. arenosa? Based on decades of literature, it seems a major factor for autopolyploids is a reduction in crossing-over, which can prevent single chromosomes from associating with more than one partner; consistent with this, autotetraploid A. arenosa has fewer crossovers per bivalent (usually only 1) than the diploids (average 1.4).
To begin addressing how polyploid meiosis might stabilize, we undertook a genome scan for selection in tetraploid A. arenosa, and for divergence between diploid and tetraploid A. arenosa. We sequenced 16 tetraploid and 8 diploid individuals to ask whether there are signatures in the genome indicative of adaptation to whole genome duplication. Comparing the genomes of diploids and tetraploids, has been a fruitful collaboration with Levi Yant and understanding cytological aspects has been a result of a very fruitful collaboration with Chris Franklin and James Higgins.
The image above shows the output from one of our genome scans (see Yant et al 2013). It shows divergence between diploid and tetraploid A. arenosa for 100 SNP windows. Peaks of divergence are evident, and one of them, noted here, is ASY3, a meiosis gene with one of the strongest peaks genome-wide.
The image above shows two examples of the very strong peaks we've found in our genome scan (soon to be published; Yant et al 2013). The dots are single SNPs - both of these genes are strongly differentiated between diploids and tetraploids, and both are important for events in early meiosis. For ASY3 at least, it is clear the peak itself lies in the coding region and not the promoter.
Our initial genome scans have revealed interesting candidate genes that may have been involved in either the initial formation of the tetraploids or in their subsequent meiotic stabilization (Hollister et al 2012; Yant et al 2013). We are following these up with molecular studies using genetic and cytogenetic approaches to gain molecular insight into autotetraploid meiosis. This is primarily the work of Kevin Wright, an NRSA postdoctoral fellow in the lab, Andrew Lloyd, a Marie Curie Fellow in the Lab, Jeremy O'Connell, a postdoc in the lab, Franchesco Molina-Henoa, a Fulbright PhD student in the lab, and Holly Elmore, a PhD student in the lab. Currently we are focusing mostly on early events in prophase I of meiosis.
In one case, we already know that a genetic variant common in tetraploids but very rare in diploids is critical for successful meiosis: tetraploids homozygous for the diploid-like allele show extensive meiotic abnormalities that appear similar to those we see in colchicine-doubled diploids. The tetraploid alleles seems to reduce crossover number, via reduced interference. This is a hypothesis we are exploring togather with Nancy Kleckner (Harvard), James Higgins (U. Leicester, UK) and Chris Franklin (U. Birmingham).
We are also investigating the molecular evolution and population genetics of several candidate genes that we know are differentiated between diploid and tetraploid A. arenosa. These have confirmed that the selective sweeps we have seen evidence of are very strong, and very discrete (they accompany just single genes, and sometimes even just part of a gene).
Relevant Publications from our lab (or collaborators):
- Bomblies, K., Madlung, A. (2014) Polyploidy in the Arabidopsis genus. Invited review. Chromosome Research. 22: 117-134 (Link).
- Higgins, J. D., Wright, K. M., Bomblies, K., Franklin, C. H. F. (2013) Cytological techniques to analyze meiosis in Arabidopsis arenosa for investigating adaptation to polyploidy. Frontiers in Plant Science. doi: 10.3389/fpls.2013.00546. (Link).
- Yant, L.*, Hollister, J. D.*, Wright, K. M., Arnold, B. J., Higgins, J. D., Franklin, F. C. H. and Bomblies, K. (2013) Meiotic adaptation to genome duplication in Arabidopsis arenosa. Current Biology. Vol 23, pp. 2151-2156. * = contributed equally (Link).
- Hunter, B.*, Wright, K. M.* and Bomblies, K. (2013) Short read sequencing in studies of natural variation and adaptation. Curr Op Plant Biol. Vol 16, pp. 85-91. * = contributed equally. (Link).
- Hollister, J., Arnold, B., Svedin, E., Xue, K., Dilkes, B. and Bomblies, K. (2012) Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genetics, 8(12): e1003093 (Open Access - Link).