European Cytogenetics Conference: Chromosomes, sequences, Mendel and humans

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The European Cytogenetics Conference, this year #ECA2015 in Strasbourg, is a terrific meeting to hear the latest on chromosome research, with a strong focus on human research but lots that is important for plant and animal cytogenetics. A key message this year is the ubiquity and importance of copy number variation – CNV – of sequences in genomes affecting numerous phenotypes, gene expression and genome modifications, as well as showing rapid evolution. Deep sequencing is important for understanding these variants, with molecular cytogenetics and array hybridization are critical to demonstrating their locations and nature.

The ECA programme starts with workshops where the need for data sharing (large databases array-CGH with Joris Vermeesch) and large databases on human disorders related to chromosomes – both congenital and in malignancies – such as ECARUCA (Nicole de Leeuw) were discussed. The effort required to implement and curate such databases is immense; at least in the plant and animal world we don’t have the ethical and patient issues on top of the complexity of data analysis (although we do miss the resolution of minor intellectual disabilities that can be caused by chromosomal aberrations of much less than 400kb; as shown by Marie Faoucher, Lyon). Another interesting session discussed extensive cross-laboratory trials to show where differences between labs arise in a quality control context. Harold Rieder from Dusseldorf showed in situ hybridization trials and all the differences between labs in protocols – he mentioned slide age, manufacturer and in-lab wiping/washing protocol of the glass slides used (things we emphasize in my own lab), as well as the huge influence on preparations from small variation in fixation protocols of living cells. In my experience, there are a number of plant research ‘schools’ which have a rather distinctive appearance to their chromosome preparations, no doubt arising from such minor treatment differences. Another workshop had a practical element: meiosis in action was shown in Maj Hulten and Trude Schwarzacher‘s workshop.

https://twitter.com/Pathh1/status/617356115962150912/photo/1

With Mariano Rocci, Leopoldo Ianuzzi and Valerie Fillon as co-organizers, our Animal and Plant Cytogenetics workshop included exciting presentations from five labs. Anna Zlotina opened the session showing microdissection of chicken lampbrush chromosomes. After amplification of the dissected DNA, she used the microdissected regions of a few million base pairs for in situ hybridization and this labelled small segments of the original chromosome segment; I expect that the dispersion of transposable elements over plant chromosomes would mean a similar strategy would not work. Interestingly, Anna was also able to use the amplified, dissected DNA for sequencing, and alignment to the chicken genomic sequence showed where the dissected segment lay within the sequence.

Two plant talks in the session had a common element of use of genomic in situ hybridization (a method first published in Annals of Botany in 1989) to elucidate relationships between species including polyploids within a genus. Qing Liu from the South China Botanic Garden use the chromosome painting method to sort out Sorghum genome relationships and repeat sequence evolution, while Paula Tomaszewska was investigating endosperm stability in hybrids between oat species at various ploidies. She could detect many aberrations, and understanding the nature and causes of these chromosomal instabilities will be critical to exploiting all the genetic variability within the genus for breeding with large productive endosperms, the source of most of the calories humans consume.

Plant Animal Workshop Group.
Plant Animal Workshop Group.

2015 marks the 150th anniversary of the presentation and publication of Mendel’s seminal paper presenting his Laws of Heredity. One expects that the unexciting and uninformative title Versuche über Pflanzenhybriden (Studies of plant hybrids) in his paper was one reason it was ignored – the importance of a paper title for finding work is something we have discussed here on AoBBlog and regularly among Annals of Botany Editors! In her talk, Trude Schwarzacher discussed research in Mendel’s time, when ‘blended inheritance’ was accepted, and then how Mendel came to carry out the work. Not least, he was taught by the physicist Christian Doppler at the University of Vienna, no doubt implanting the centrality of numeracy and what we now consider statistics, to understanding all phenomena, including those of biology.

Mendel's paper.
Mendel’s paper.

Trude also pointed out that of the seven characters Mendel worked with in pea, two are still very relevant to breeding of modern crops: the terminal flowering character, and dwarfism of the whole plant. The synthesis of the results in Mendel’s original paper, even today, is remarkable with considerable interpretation and presentation of a general model of inheritance: I do wonder how many modern referees would quibble about “unsubstantiated extensions”? Trude discussed Mendel’s interactions with another important botanist of the time, Karl Wilhelm Naegeli of Munich; in some ways, though, this was unfortunate in that firstly, it is not clear how much Naegeli understood the significance of Mendel’s genetical results and the laws of heredity, and also had the suggestion to work with the hawkweeds, genus Hieraceum, which includes many polyploids and apomicts. Hardly a model species to use to understand the principles of genetic inheritance, and no doubt disheartening for the Monk by then working in Brno! The final section of Trude’s talk put Mendel’s work into the context of chromosomes, as might be expected in a cytogenetics conference, although cell division and chromosomes were not described until later in the 19th century – the slideshare embedded above shows some images from these early work, with more recent results from her own lab.

Jaroslav Dolezel from the Czech Academy of Sciences, Oloumec, treated his audience to an insightful chromosome-centric view of plant genome evolution. Sequencing is telling us much, but is far from letting us know about the effects of chromosome rearrangements, genome and chromosomal organization, and repetitive DNA. In his talk, we were shown how polyploidy is a major driving force with recurrent cycles of polyploidiations and diploidization. He compared the multiple rounds seen in most plant species with the two rounds of whole genome duplication hypothesized by S Ohno in the genomes of the early vertebrate lineage. Both in plants and animals, genome duplications, allow relaxed selection of duplicated genes and accumulations of mutations, while genomic shock allows structural rearrangements, activations of transposons, modified gene expression and epigenetic modifications, leading to sub-functionalization, neo-functionalization and degeneration or gene loss. Nevertheless, Jaroslav pointed out that more work is needed on the impact of polyploidiation and wide hybridization, and we were shown many examples for his own work in wheat.

We saw how flow-sorting of chromosomes is allowing sequencing of the large wheat genome – at 17,000 Mbp, some six times the size of the human genome – and these data show the different ages of sub-genomes in polyploids and how new hybrids and polyploids can be created, obtaining useful information for wheat improvements in this important species only known from cultivation and human activity.

The whole ECA conference is showing the centrality of a chromosome-centric approach to understanding genome evolution and structure: reference genome sequences and the avalanche of sequence data is extraordinarily useful, but more is needed to get to the biology of the genome, the consequences for genetics and epigenetics, and the processes of evolution.

In this AoBBlog, I have focussed on the plant-related presentations at #ECA2015: I will include additional reviews of the talks and other sessions on molcyt.com from early next week.