Design your genome! How to exchange chromosomes and organelles between Arabidopsis ecotypes. (and why we d like to do so)

Transcription

1 Design your genome! How to exchange chromosomes and organelles between Arabidopsis ecotypes. (and why we d like to do so) Erik Wijnker International Conference on New Plant Breeding Molecular Technologies 9 &10 October, Jaipur, India

2 Content: Generating cybrids Exchanging cytoplasm Reverse breeding Exchanging chromosomes Applications

3 The GFP-tailswap haploid inducer GFP CENH3

4 The GFP-tailswap haploid inducer GFP CENH3

5 Generating cybrids with GFP-tailswap X Heterozygote Haploid

6 Generating cybrids with GFP-tailswap X Heterozygote Haploid Doubled Haploid

7 Cybrids show new phenotypes 0.8 Nuclear DNA Col-0 Ler-0 Ws-4 Bur-0 Ely Shah C Col-0 Ler-0 Ws-4 Bur-0 Ely Shah C24 Photosynthesis Mark Aarts 0.3 Jeremy Harbinson 0.2 Joost Keurentjes Accessions 300 chosen for high or low rates of photosynthesis % Plant size Padraic Flood Ely WT Plant age Ely with Col cytoplasm Plant age

8 Generating inducer lines with different cytoplasms X Heterozygote An inducer in a new cytoplasm!

9 A complete cybrid testpanel Col Ler WS-4 Bur Ely Sha C24 Col Ler WS-4 Bur Ely Sha C24

10 Generating cybrids: Cytoplasm in Arabidopsis inherits maternally Cybrids arise through maternal genome elimination The maternal nuclear genome eliminates The maternal organellar genome remains

11 Content: Generating cybrids Exchanging cytoplasm Reverse breeding Exchanging chromosomes Applications

12 About selection in breeding: X Be a breeder in the... selection quiz! This is a F1 (a hybrid) Can What you is the identify nicest its corncob? parents?

13 Two crucial observations: X 1) Offspring selection: easy! 2) Parent selection: very difficult!

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15 X Breeding with complex heterozygotes is very difficult

16 and thus plant breeders generate as much random variation as possible? no!

17 Classical vs reverse breeding X Classical breeding Selection Reverse Breeding

18 Crossover suppression RNAi:DMC1

19 Segregation of non-recombinant chromosomes

20 Doubled haploid production

21 Parent selection

22 Hybrid recreation x x x Erik Wijnker 2011

23 Reverse breeding = Exchanging chromosomes 1) Crossover suppression Non-recombinant chromosomes segregate 2) Regenerate balanced spores as doubled haploids These are chromosome substitution lines These are parental pairs Erik Wijnker 2011

24 Reverse breeding Kees van Dun Cilia Lelivelt Bastiaan de Snoo Rob Dirks Joost Keurentjes Shima Naharudin Hans de Jong Maruthachalam Ravi Simon Chan Dirks et al. (2009). Plant Biotechnology Journal 7(9): (review) Wijnker et al. (2012): Nature Genetics 44(4): Wijnker et al. (2014): Nature protocols 9: Erik Wijnker 2011

25 Content: Generating cybrids Exchanging cytoplasm Reverse breeding Exchanging chromosomes Applications Erik Wijnker 2011

26 The big questions in heterosis What are the contributions of: research: Cytoplasm effects Maternal and Paternal effects DNA Methylation, small RNA s and Gene Expression

27 A Chromosome Substitution Library

28 Isogenic hybrids x x x x x x x x x x x x x x x x

29 A CSL in Columbia cytoplasm

30 A CSL in Landsberg cytoplasm

31 A CSL in any cytoplasm

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37 Erik Wijnker Group of Arp Schnittger, University of Hamburg, Germany Papers on Reverse Breeding: Dirks et al. (2009). Plant Biotechnology Journal 7(9): (review) Wijnker et al. (2012): Nature Genetics 44(4): Wijnker et al. (2014): Nature protocols 9:

38 On residual crossovers: Meiotic aberrations (laggards, polyads) increase strongly when crossovers are completely absent. For efficient crossover suppression few crossovers may be allowed. Dirks et al., 2009: Plant biotechnology journal 7(9):

39 Reverse breeding generates transgene free offspring Transformants Possible DH s X Recruit parents without RNAi-construct

40 Columbia wt On what chromosome is the locus for early flowering?

41 Columbia wt Epistatic interactions:

42 Columbia wt Epistatic interactions:

43 Epistatic interactions: