wheat pre-breeding at niab: from germplasm to...

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

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


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)


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

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

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

http://www.cerealsdb.uk.net/

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



Genotyping; selfing

SUMMER 2016

WINTER 2012

1D

Developing Chromosome Segments Substitution Lines

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

http://www.cerealsdb.uk.net/

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

* * *

*

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)

wheat pre-breeding at niab: from germplasm to...

Documents