1. Hexaploid wheat- Triticum aestivum 2n= 6x= 42 1234567 A B D abcdabcd abcdabcd abcdabcd Similar gene orders but different content of similar repeats 7A abcdabcd 7D 7A Homoeologues pair in hybrids between wheat diploid progenitors Homoeologues abcdabcd 7B abcdabcd 7D The Ph1 locus restricts pairing to homologues.

2. Breeding Wheat hybrids In hybrids, no homologues-related chromosomes Wheat hybrid Ph1+ Ph1- Wild species of wheat carry important traits for disease resistance, salt, cold and drought tolerance Unfortunately Ph1 locus prevents the wheat and its wild relative chromosomes from pairing /recombining - and thus from transferring of these traits Single deletion of Ph1 locus (ph1b- 70Mb in size) used in breeding Can we regulate this locus? Can the process be improved? What is Ph1 doing? Can Ph1 be switched on and off?

3. telomeres centromeres subterminal heterochromatin “telomere regions” Interphase configuration Interstitial segments Meiocyte in premeiosis telomeres Meiocytes in early meiosis Dissect pairing process

4. Telomere regions of homologues pair in all the meiocytes examined in the absence of Ph1 Telomere pairing of homologues in hexaploid wheat does not require Ph1 Marked telomere regions of two homologues Telomere regions- Hexaploid wheat Ph1-

5. Kihara and Lilienfeld (1934) showed that wheat hybrids were prone to premature condensation- Implication- newly synthesized polyploids are prone to premature condensation Premature/asynchronous condensation is a hallmark of cells that have an inadequate replication checkpoint and have begun condensation before completing replication Overexpression of Cdc2 (checkpoint) gene activity caused premature asynchronous condensation Implication- newly synthesized polyploids need to control Cdc2 activity- so what is Ph1 affecting? Summary of related issues

6. Telomeres Ph1- Ph1+ Interstitial segments- 15% of the wheat chromosome (same size as a maize chromosome, entire drosophila or Arabidopsis genome, 10 yeast genomes) Interstitial segments- Hexaploid wheat Ph1- Ph1+

7. Telomere bouquet Summary of Ph1 effect- Hexaploid wheat Add Ph1 Homologues same conformation Homologues different conformation

8. Problem, on polyploidisation homologous sites are not synchronised in their condensation Solution -Ph1 synchronises condensation of homologous sites Ph1+ Ph1- Synchronisation- Hexaploid wheat One consequence of Ph1 is that pairing will occur when the chromosomes are more condensed

9. In hybrids, no homologues-related chromosomes Wheat hybrids Ph1’s effect? Heterochromatin (B chromosomes) can compensate for the absence of Ph1 in wheat hybrids- ie suppress pairing and recombination between wheat and wild relative chromosomes Heterochromatin (B chromosomes) delay S phase and cause greater compaction of chromosome regions

10. Hexaploid wheat- rye hybrid Ph1- Rye telomeric knobs premeiosis Ph1+ meiosis Sub-telomere regions Condensation Hexaploid wheat hybrids Telomere cluster when condensation has not begun Telomere cluster (pairing) when condensation has begun In hybrids, no homologues-related chromosomes

11. No natural variation in Ph1 phenotype- Can’t create a segregating populations, the starting point of all previous positional cloning projects- Can’t score thousands of plants for this phenotype, 5000 plants would be 150,000 metaphase spreads Variation only occurs with dosage EMS treatments don’t yield mutants But X-Ray and fast neutron irradiation do -A single deletion (ph1b) of the locus 70Mb in size- “Ph1 locus” arose on polyploidisation not present in diploids- it is specific to 5B Heterochromatin compensates for Ph1 Ph1 could be a multigene family or heterochromatin or both But wheat is 5 times larger than the human genome What is the Ph1 ? Cloning the issues

12. Identify further deletions of the Ph1 locus (30,000 fast neutron treated wheat plants PCR screened) Use the deletions to delimit a “small” region in wheat still defining the Ph1 locus Reveal gene content of delimited region using synteny with small genomed cereals (140kb in rice and 180kb in Brachypodium). Build hexaploid wheat BAC library (1,200,000 clones) Then gets really serious……. Strategy Moore, Gale, Kurata, and Flavell (1993) Nature Biotech Cereal Synteny and Rice/Brachypodium to reveal gene content of wheat

13. Brachypodium/ Rice regions 2.5Mb Contig Ph1 5B region

14. a segment of subtelomeric heterochromatin inserted into this cdc2 locus There is a single multigene family of cdc2 related genes Content of the Ph1 region Known function/ Known Tissue expression profile Not Ph1 Known function /Known Tissue expression profile Not Ph1

15. Subtelomeric repeat Chromosome 3AL Chromosome 5BL pre Ph1 1 23 Chromosome 3AL cdc2 gene cluster Chromosome 5BL with Ph1 123 Subtelomeric repeat 4 Following polyploidisation, the some telomere regions rearrange in wheat 1234567 A B D Ph1 arose on polyploidisation

16. Association with Ph1 activity in wheat and relatives Region contains markers consistently associated with Ph1 activity in tetraploid and hexaploid wheat and wild polyploid relatives

17. T. timopheevi AAGG- Ph1+ Ae. speltoides SS T. uratu AA Ae. tauschii DD T. turgidum AABB- Ph1+ T.aestivum AABBDD- Ph1+ Association with Ph1 activity

18. We know the cell biological basis of Ph1 activity We know the structure of the Ph1 “locus” We know that there is 5B specific expression from within the locus But we don’t yet know precisely how the locus is working We need to be able to dissect the components of the locus using small deletions (which may or may be not technically feasible using X-Ray treatment) Ph1 story Summary

19. Identification of a Ph1 mutant which does not have a large deletion Can we use drugs (orange sponge) which affect cdc2 activity to modulate pairing in hybrids? Is the future bright- is it orange? Can we improve the exploitation the introgression process? Application?

20. Cell Biology Luis Aragon Alcaide Enrique (Fadri) Martinez-Perez Pilar Prieto Aranda Mike Wanous Thomas Haizel Physical mapping etc Tracie Foote Michael Roberts Terry Miller Steve Reader Simon Griffiths Sebastien Allouis Rebecca Sharp Kath Mortimer Isabelle Bertin Collaborators Mike Gale -Markers Peter Shaw-Cell biology RGP-Japan - Rice INRA- Evry-BACs Dupont-Sequencing Syngenta-Rush work David Baulcombe siRNA Species used Wheat (meiosis and genomics) Rice (meiosis and sequence data) Brachypodium (centromeres and sequence data) Luzula, a rush (meiosis and centromeres) Rye (meiosis) Acknowledgements