Wheat pre-breeding at NIAB: from germplasm to genomics. Alison Bentley

Transcription

1 Wheat pre-breeding at NIAB: from germplasm to genomics Alison Bentley

2 NIAB wheat pre-breeding 1. Flowering time 2. Re-synthesis 3. MAGIC

3 NIAB wheat pre-breeding 1. Flowering time 2. Re-synthesis 3. MAGIC

4 Flowering time Why flowering time? Central to adaptation Early flowering varieties yield higher in hot, dry environments Climate change likely to effect areas with late season heat/drought stress Late flowering varieties perform well in environments with long growing seasons % Yield Change -1.8% +7.7% +33.0% Long Growing Season Short Growing Season

5 Photoperiod kb Genome coding region Ppd allele Allele donor Characteristic D Ppd - D1.e1 Ciano67/Soissons Early flowering A Ppd - A1.e1 Durum wheat Early flowering A B B Transposon Transposon Ppd - A1.e2 Ppd - B1.e1 Ppd - B1.e2 Durum wheat Recital Chinese Spring Early flowering Early flowering Early flowering B Transposon Ppd - B1.e3 Timstein Early flowering A ppd - A1.e1 Transposon D ppd - D1.4 D ppd - D1.5 Cappelle - Desprez Mercia Norstar Null allele? Neutral allele? Null allele? D ppd-d1.1 Synthetic wheat True wild - type allele Key: Deletion SNP

6 Understanding photoperiod response Bentley et al. (2011) Plant Breeding 130: Bentley et al. (2013) Journal of Experimental Botany 64:

7 Understanding photoperiod response Temp Treatment (Day) Temp (Night) Water T1_D1 18 C 15 C Field capacity T1_D2 18 C 15 C 50% F capacity T2_D1 23 C 18 C Field capacity T2_D2 23 C 18 C 50% F capacity

8 Understanding photoperiod response FT Ppd-A1a>Ppd-D1a>Ppd-B1a YLD Ppd-A1(0.06)>Ppd-D1(-0.53)>Ppd-B1(-1.97) FT Ppd-D1a>Ppd-A1a>Ppd-B1a YLD Ppd-B1(0.42)>Ppd-D1(0.21)>Ppd-A1(0.08) FT Ppd-A1a>Ppd-D1a>Ppd-B1a YLD Ppd-D1(2.72)>Ppd-B1(0.02)>Ppd-A1(-0.42) FT Ppd-D1a>Ppd-A1a>Ppd-B1a YLD Ppd-D1(1.89)>Ppd-B1(0.52)>Ppd-A1(0.18)

9 New understanding of photoperiod response? Ppd-D1a vs Ppd-D1b activate repress Pearce et al. BMC Plant Biology 2014, 14:368

10 NIAB wheat pre-breeding 1. Flowering time 2. Re-synthesis 3. MAGIC

11 Pre-breeding with CIMMYT synthetics 50 CIMMYT SHWs from ~440 crossed to Xi-19 and Paragon

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

13 Durum Ae. tauschii (AA, BB) x (DD) F 1 (ABD) Synthetic wheat (AA, BB, DD) Chromosome doubling NIAB Breeder s Toolkit Toolkit

14 KASP (LGC Genomics) ~7,000 SNPs iselect (Illumina) ~81,000 SNPs Axiom (Affymetrix) ~820,000 SNPs Winfield et al. (in press) Plant Biotechnology Journal

15 Days to GS Frequency Characterising Ae. tauschii diversity Number of tillers Ppd-D1 allele

16 Pre-breeding with NIAB synthetics Systematic crossing to Robigus (winter) and Paragon (spring). Development of 10,000 BC 1 F 5 pre-breeding lines (unselected). NAM analysis tools in development. Early generation selections/bulks available via the NIAB Breeder s Toolkit.

17 Developing Chromosome Segments Substitution Lines NIAB SHW-041 (Ent336) x Paragon WINTER 2012 F 1 x Paragon 1D 192 BC 1 F 1 Whole genome KASP; MAS 27 BC 1 F 1 27 BC 1 F 1 x Paragon 192 BC 2 F 1 Whole genome KASP; MAS 34 BC 2 F 1 34 BC 2 F 1 x Paragon 192 BC 3 F 1 Whole genome KASP; MAS 44 BC 3 F 1 44 BC 3 F 1 x Paragon BC 4 F 1 Genotyping; selfing SUMMER 2016 BC 4 F 3

18 NIAB wheat pre-breeding 1. Flowering time 2. Re-synthesis 3. MAGIC

19 MAGIC Multi-parent Advanced Generation InterCross complete pedigree

20 Frequency Mackay et al. (2014) G3 4: MAGIC line means Parent 2 Robigus Parent 1 Hereward Line/SNP 2A_SNP 3A_SNP 1A_SNP Alchemy R S S Brompton S S S Claire R S S Hereward S S R Rialto S R S Robigus S S S Soissons S S R Xi19 S R S MEL_1 R R R MEL_2 R R R Resistant progeny Marker BLUP (log2) Estimated effect 2D A A

21 Mapping Fusarium Head Blight (FHB) resistance

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23 Variation in ear morphology: mapping in MAGIC Volume Surface area Internal density Relative position National Plant Phenomics Centre (Callum Scotson)

24 Generating the NIAB 8-way MAGIC map Gardner, Wittern and Mackay (submitted) A highly recombined, high-density, eight founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments.

25 Generating the NIAB 8-way MAGIC map Stringent error control on 90K iselect data, minimise amount of missing data Variable markers in MAGIC (MAGIC captures 81% of markers variable in UK wheat) Markers available for mapping Mapping 1. Recombination fractions calculated for co-dominant markers mpmap 2. Markers clustered into 300 groups using hierarchical clustering groups interactively combined to form 21 linkage groups 4. Linkage groups assigned to 21 chromosomes based on BLAST hits (IWGSC1), POPSEQ data(iwgsc2), 90k Consensus map (Wang et al 2014), MAGIC 9k map, Bristol deletion bins, Genome Zipper data 5. Chromosomes ordered interactively in mpmap 6. Unmapped dominant markers and markers previously dropped assigned to chromosomes by mapping them as traits. If mapped with log 10 P >16, then added to map on chromosome by chromosome basis, followed by reordering

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27 3B physical vs genetic map distance

28 MAGIC QTL mapping - Awns

29 chisquare density per 10cM New opportunity to examine aspects of underlying genetic structure of UK wheat gene pool: blocks of markers detect known and unknown introgressions. These make mapping hard but their subsequent phenotypic characterisation and tagging in UK germplasm is easy. 800 Marker_density Segregation_distortion A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D

30 chisquare density per 10cM 800 Marker_density Segregation_distortion A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D

31 Investigating interspecific introgressions Robigus Important component of pedigrees in NW Europe Used to improve yield, OBM*, Septoria*, mildew, brown rust Pedigree thought to contain Triticum dicoccoides (wild emmer) Locations of introgressed fragments in Robigus (and its descendents) unknown Investigate Bristol University 820K Axiom array database ( Winfield et al. (2015) PBJ in press 17 known Robigus pedigree lines, 69 non-robigus pedigree lines 678 perfect Robigus markers assignable to chromosome

32 block size (number of markers) block size (number of markers) Investigating interspecific introgressions Perfect Robigus markers blocks (>1 marker) ordered by length Perfect Robigus markers blocks (>1 marker) ordered by length MAGIC 4AL SD linkage block (SD against Robigus allele) 23% of perfect Robigus markers in 820K dataset Perfect fit to biggest perfect Robigus linkage block 3x bigger than next largest block Also in Glasgow (contains T. dicoccoides) Matches all predictions of interspecific introgression fragment Instant MAGIC NILs

33 Gatsby

34 NIAB wheat pre-breeding 1. Flowering time 2. Re-synthesis 3. MAGIC

35 Association mapping European winter wheat Traits scored include: Yield Flowering time (GS55) Height Awns Ears/m 2 Tillering Establishment Winter kill Lodging Maturity Specific weight Thousand grain weight Grain protein content Callow, UK * * Arvalis, France Cambridge, UK * * Rosenthal, Germany

36 Association mapping European winter wheat FLOWERING TIME Ppd-D1a DArT Biogemma SNP DArT = 1,235 GbS = 108,871 Bentley et al. (2014) Theoretical and Applied Genetics 127:

37 Marco Scutari University of Oxford

38 Mackay et al. (2015) Food & Energy Security 4: 25-35

39 NIAB pre-breeding team Richard Horsnell Ahmad Shekhmous Tobias Barber Gemma Rose Phil Howell Fiona Leigh NIAB Trait Genetics Ian Mackay Keith Gardner Lukas Wittern (BBSRC/Cambridge/Bayer CropScience) Flowering time JIC (Dave Laurie, Adrian Turner) National Plant Phenomics Centre Anyela Carmargo-Rodriguez Re-synthesis CIMMYT University of Hohenheim WISP partners MAGIC Franziska Fischer/Marie Gantet (FHB) Funmi Ladejobi (Yield components) CSIRO (Rohan Shah/Emma Huang) Association mapping/gs TriticeaeGenome consortium Marco Scutari (Oxford) John Hickey (Roslin) Gregor Gorjanic (Roslin)