Plant Science into Practice: the Pre-Breeding Revolution

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1 Plant Science into Practice: the Pre-Breeding Revolution Alison Bentley, Ian Mackay, Richard Horsnell, Phil Howell & Emma

2 NIAB is active at every point of the crop improvement pipeline Pre-breeding Plant characterisation Crop genetics Physiology Crop transformation Bioinformatics Seed certification Pathology NIAB Plant breeder s rights Sustainable systems Soil management A unique independent research organisation capable of transferring innovations in plant science into practical agriculture Precision farming Analytical services Farming systems Crop waste reduction Data analytics Crop evaluation Varieties Field trials Agronomy Consultancy Training

3 Genetics & Breeding Work on all aspects of crop genetic improvement: Pre-breeding Trait discovery GM & gene editing Breeding methods Teaching

4 Pre-breeding the art of identifying the desired traits, and starting to incorporate them into modern breeding materials Global Crop Diversity Trust Sits in the gap between more fundamental science and commercial plant breeding Unlikely to directly lead to finished varieties, much more likely to give rise to the parents of future varieties

5 Why do we need pre-breeding? Total UK royalty income to plant breeders, across all agricultural crops, approx 35m pa Large wheat breeding programme costs approx 1.5m pa, and take 7-12 years from first cross to commercial launch To maintain a competitive edge, and deliver profits to shareholders, commercial breeders must concentrate on market-driven innovation This gap between basic research and commercial programmes = market failure? Governments are now starting to recognise the importance of prebreeding in long-term food security

6 Adapted germplasm Related species Wild relatives Landraces Variety collections Segregating pops Precise stocks Advanced lines QTLs/markers Trait dissection

7 Today s talk Pre-breeding to develop/exploit: Wild relatives Segregating populations

8 Wild relatives Integrated public-sector pre-breeding New germplasm Landraces Synthetics Ancestral introgressions Genotyping Re-sequencing, SNP discovery, polymorphism screening across donors Bespoke genotyping of segregating populations using tailored markers Phenotyping Yield, components, biomass, under high/low N Resistances to take-all and aphids Elite wheats Gateway by which genetic improvements will reach growers Novel germplasm + trait & marker information

9 NIAB WISP pre-breeding 1. Tetraploid diversity T. dicoccoides T. dicoccum T. durum 2. Novel diversity Ae. tauschii

10 Tetraploid pre-breeding Robigus, Paragon Triticum aestivum (AA, BB, DD) X Wild Emmer Triticum dicoccoides (AA, BB) pentaploid F1 (AA, BB, D) X Robigus, Paragon Cultivated emmer, durum (AA, BB) Segregating backcross generation (AA, BB, D); (AA, BB, DD) Inbred BC1F5 generation (AA, BB); (AA, BB, DD)

11 Tetraploid pre-breeding

12 NIAB WISP pre-breeding 1. Tetraploid diversity T. dicoccoides T. dicoccum T. durum 2. Novel diversity Ae. tauschii

13 Synthetic pre-breeding Synthetic wheat Durum Ae. tauschii (AA, BB) x (DD) F 1 (ABD) Chromosome doubling Synthetic (AA, BB, DD)

14 Synthetic pre-breeding

15

16 Synthetic pre-breeding

17 820K Axiom array for hexaploid wheat and its secondary and tertiary gene pool Winfield et al. (2016) Plant Biotechnology Journal in press.

18 Synthetic pre-breeding Can we just grow synthetics? Basic faults - no inherent value as varieties Cross with elites & select for recombination between beneficial and deleterious SHW alleles Elite x SHW simple cross unrealistic Breeders screen ~1000 F 2 even for elite x elite F 2 for wider crosses Maximise recombination backcross to elite parent

19 0. Create primary SHW 54 created 1. Create F1 2. Backcross 54 SHW x Paragon as F1 40 SHW x Paragon as BC1 54 SHW x Robigus as F1 40 SHW x Robigus as BC1 4. SSD no selection BC1F2 BC1F5 3. Self BC1 BC1F2 5. Field observation : 2358 lines sown 2017: ~1000 lines in field 6. Archive Unselected BC1F6 7. Field selection To 2016: 1328 selections made

20 True F2 BC1F5

21 Increase in yield components Higher biomass Staygreen Elite types

22 Synthetic pre-breeding Disease susceptibility

23 Synthetic pre-breeding Disease susceptibility (& resistance?)

24 Integrated pre-breeding WISP genotyping has delivered (via A. KASP probes and sequences B. 820K and 35K probes and sequences C. Genotyping data Site accessed >30,000 per month and data sets downloaded several thousand times since launch With the WISP partners 1.1billion (and rising) genotyping data points across all platforms

25 Elite wheat cultivars SHW

26 NIAB Breeders Toolkit Currently: 53 primary synthetics /16 selections

27 NIAB Breeders Toolkit 35K array data (

28

29 5-10 years development Adapted germplasm Wild relatives (50) 10,000 lines (IP unrestricted)

30 Segregating populations Bi-parental approach: short term expediency Multi-founder approach: long term durability e.g MAGIC (Multiparent Advanced Generation Intercross) NAM (Nested Association Mapping) Association mapping panels

31 3. Segregating populations 90 4B 4D 80 Plant height 2010 Plant height 2011 Sclerotia size 2010 Sclerotia size _4B_0.0 2_4B_2.0 3_4B_30.1 4_4B_50.5 5_4B_51.1 6_4B_58.2 7_4B_58.9 8_4B_60.2 9_4B_ _4B_ _4B_ _4B_ _4B_ _4B_ _4B_ _4B_ _4B_ _4B_115.0 Plant height 2010 Plant height 2011 Sclerotia size 2010 Sclerotia size _4D_0.0 2_4D_5.5 4_4D_19.7 5_4D_24.7 6_4D_33.5 7_4D_34.1 8_4D_40.3 9_4D_43.6 Plant height / cm Ergot Sclerotia Size Anna Gordon, NIAB

32 3. Genetic modification What effect does removing all GA from ovule tissue have on the size of ergot sclerotia and grain? GA2Ox enzymes rapidly deactivate GA within cells. We will look at the effect of targeted GA depletion on ergot growth in the ovule. Anna Gordon, NIAB

33 3. Genetic modification 40 Mean Sclerotia weight / mg (error bars=se) _NULL _GM _NULL 9.4.6_GM _NULL 9.9.8_GM Anna Gordon, NIAB

34 3. Segregating populations NIAB Elite Multi-parent Advanced Generation Inter-Cross population (Mackay et al (2014) G3 4: ) Ladejobi et al. (2016) Applied and Translational Genomics

35 3. Segregating populations Camargo et al. (2016) Frontiers in Plant Science

36 3. Segregating populations Camargo et al. (2016) Frontiers in Plant Science

37 3. Segregating populations Camargo et al. (in preparation)

38 Current elite varieties Leaf angle Branching Remobilization Increased biomass Matt Milner, NIAB

39 Acknowledgements NIAB pre-breeding team Richard Horsnell Ahmad Shekhmous Tobias Barber Phil Howell Fiona Leigh NIAB Trait Genetics Ian Mackay Keith Gardner Funmi Ladejobi Anna Gordon Matt Milner Emma Wallington Re-synthesis University of Hohenheim WISP partners Phenology JIC (Dave Laurie, Adrian Turner) National Plant Phenomics Centre Anyela Camargo-Rodriguez John Doonan

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