wheat pre-breeding at niab: from germplasm to...
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Wheat pre-breeding at NIAB: from germplasm to genomics
Alison Bentley
NIAB wheat pre-breeding
1. Flowering time 2. Re-synthesis
3. MAGIC 4. Mapping/GS
@AlisonRBentley @NIABTAG
NIAB wheat pre-breeding
1. Flowering time 2. Re-synthesis
3. MAGIC 4. Mapping/GS
@AlisonRBentley @NIABTAG
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
-1.8%
+7.7%
+33.0%
Long Growing Season
Short Growing Season
% Yield Change
Photoperiod-1 kb 1 2 3 4 5 6 7 8 9 10 11 12 13 14
coding region
Transposon
Genome
D
A
A
Ppd allele
Ppd - D1.e1
Ppd - A1.e1
Ppd - A1.e2 Transposon
B Ppd - B1.e1
B Ppd - B1.e2
D ppd
A ppd - A1.e1
B Ppd - B1.e3 Transposon
D ppd - D1
Transposon
D ppd - D1
Allele donor
Ciano67/Soissons
Durum wheat
Durum wheat
Recital
Chinese Spring
Timstein
Cappelle - Desprez
Mercia
Norstar
Synthetic wheat
Characteristic
Early flowering
Early flowering
Early flowering
Early flowering
Early flowering
Early flowering
Null allele?
Neutral allele?
Null allele?
True wild - type allele
Key: Deletion SNP
kb 1 2 3 4 5 6 7 8 9 10 11 12 13 14
coding region
Transposon
Genome
D
A
A
Ppd allele
Ppd - D1.e1
Ppd - A1.e1
Ppd - A1.e2 Transposon
B Ppd - B1.e1
B Ppd - B1.e2
D ppd-D1.1
A ppd - A1.e1
B Ppd - B1.e3 Transposon
D ppd - D1.4
Transposon
D ppd - D1.5
Allele donor
Ciano67/Soissons
Durum wheat
Durum wheat
Recital
Chinese Spring
Timstein
Cappelle - Desprez
Mercia
Norstar
Synthetic wheat
Characteristic
Early flowering
Early flowering
Early flowering
Early flowering
Early flowering
Early flowering
Null allele?
Neutral allele?
Null allele?
True wild - type allele
Key: Deletion SNP Key: Deletion SNP
Bentley et al. (2011) Plant Breeding 130: 10-15 Bentley et al. (2013) Journal of Experimental Botany 64: 1783-1793
Understanding photoperiod response
Understanding photoperiod response
Treatment Temp (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
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)
Understanding photoperiod response
activate
repress
Pearce et al. BM
C P
lan
t Bio
log
y 20
14
, 14
:36
8
New understanding of photoperiod response?
Ppd-D1a vs Ppd-D1b
NIAB wheat pre-breeding
1. Flowering time 2. Re-synthesis
3. MAGIC 4. Mapping/GS
@AlisonRBentley @NIABTAG
Pre-breeding with CIMMYT synthetics 50 CIMMYT SHWs from ~440 crossed to Xi-19 and Paragon
1. Tetraploid diversity T. dicoccoides T. dicoccum T. durum
2. Novel diversity Ae. tauschii
NIAB re-synthesis and pre-breeding - WISP
F1 (ABD)
Durum Ae. tauschii (AA, BB) x (DD)
Chromosome doubling
Synthetic wheat (AA, BB, DD)
NIAB Breeder’s Toolkit http://www.niab.com/pages/id/419/Breeders__Toolkit
Axiom (Affymetrix) ~820,000 SNPs
iSelect (Illumina) ~81,000 SNPs
KASP (LGC Genomics) ~7,000 SNPs
www.cerealsdb.uk.net Winfield et al. (in press) Plant Biotechnology Journal
411 427 450
50
60
70
80
90
10
01
10
Ppd-D1 allele
Da
ys to
GS
55
Number of tillers
Fre
qu
en
cy
10 20 30 40 50 60 70
01
02
03
04
0
Characterising Ae. tauschii diversity
Pre-breeding with NIAB synthetics
• Systematic crossing to Robigus (winter) and Paragon (spring). • Development of 10,000 BC1F5 pre-breeding lines (unselected). • NAM analysis tools in development. • Early generation selections/bulks available via the NIAB Breeder’s Toolkit.
NIAB SHW-041 (Ent336) x Paragon
F1 x Paragon
27 BC1F1 x Paragon
192 BC2F1
34 BC2F1 x Paragon
192 BC3F1
44 BC3F1 x Paragon
BC4F1
192 BC1F1
BC4F3
Whole genome KASP; MAS 27 BC1F1
Whole genome KASP; MAS 34 BC2F1
Whole genome KASP; MAS 44 BC3F1
Genotyping; selfing
SUMMER 2016
WINTER 2012
1D
Developing Chromosome Segments Substitution Lines
NIAB wheat pre-breeding
1. Flowering time 2. Re-synthesis
3. MAGIC 4. Mapping/GS
@AlisonRBentley @NIABTAG
MAGIC Multi-parent Advanced Generation InterCross
28210315 complete pedigree
Mackay et al. (2014) G3 4:1603-1610 MAGIC line means
BLUP (log2)F
req
ue
ncy
0.0 0.5 1.0 1.5 2.0 2.5 3.0
05
01
00
15
02
00
25
03
00
Parent 1 Hereward
Parent 2 Robigus
Resistant progeny
Marker Estimated effect
2D 0.6476
3A 0.4223
1A 0.4069
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
Mapping Fusarium Head Blight (FHB) resistance
National Plant Phenomics Centre (Callum Scotson)
Variation in ear morphology: mapping in MAGIC
• Volume • Surface area • Internal density • Relative position
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.
• Stringent error control on 90K iSelect data, minimise amount of missing data • Variable markers in MAGIC - 20639 (MAGIC captures 81% of markers variable in UK wheat) • Markers available for mapping – 20586
Mapping 1. Recombination fractions calculated for co-dominant markers mpMap 2. Markers clustered into 300 groups using hierarchical clustering 3. 300 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 –log10 P >16, then added to map on chromosome by chromosome basis, followed by reordering
Generating the NIAB 8-way MAGIC map
3B physical vs genetic map distance
MAGIC QTL mapping - Awns
Marker_density
Segregation_distortion
0
200
400
600
800
0
25
50
75
1A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D
chis
quare
density p
er
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.
Marker_density
Segregation_distortion
0
200
400
600
800
0
25
50
75
1A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D
chi
squa
re
de
nsity
per
10c
M
• 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 (http://www.cerealsdb.uk.net) Winfield et al. (2015) PBJ in press
• 17 known Robigus pedigree lines, 69 non-Robigus pedigree lines • 678 perfect Robigus markers assignable to chromosome
Investigating interspecific introgressions
Perfect Robigus markers
blocks (>1 marker) ordered by length
blo
ck s
ize
(n
um
be
r o
f m
ark
ers
)
05
01
00
15
02
00
Perfect Robigus markers
blocks (>1 marker) ordered by length
blo
ck s
ize
(n
um
be
r o
f m
ark
ers
)
05
01
00
15
02
00
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”
Investigating interspecific introgressions
Oakley
Gatsby
@URSULA_Agri
NIAB wheat pre-breeding
1. Flowering time 2. Re-synthesis
3. MAGIC 4. Mapping/GS
@AlisonRBentley @NIABTAG
* * *
*
Callow, UK Cambridge, UK
Rosenthal, Germany
Arvalis, France
Traits scored include: • Yield • Flowering time (GS55) • Height • Awns • Ears/m2
• Tillering • Establishment • Winter kill • Lodging • Maturity • Specific weight • Thousand grain weight • Grain protein content
Association mapping – European winter wheat
Bentley et al. (2014) Theoretical and Applied Genetics 127: 2619-2631
DArT = 1,235 GbS = 108,871
Association mapping – European winter wheat
DArT Biogemma SNP
Ppd-D1a
FLOWERING TIME
Marco Scutari University of Oxford
Mackay et al. (2015) Food & Energy Security 4: 25-35
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)