Presentation delivered by Dr. Ian King (University of Nottingham, UK) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
2. The Challenge: To produce high yielding superior wheat varieties that meet the
needs of an increasing global population – breeders need genetic variation to achieve this
3. The Challenge: To produce high yielding superior wheat varieties that meet the
needs of an increasing global population – breeders need genetic variation to achieve this
Relatively little genetic variation is available in
modern wheat varieties
The Problem
4. The Challenge: To produce high yielding superior wheat varieties that meet the
needs of an increasing global population – breeders need genetic variation to achieve this
How do we overcome this?
Relatively little genetic variation is available in
modern wheat varieties
The Problem
5. UK consortium to increase the
gene pool of wheat
PILLAR 1
Landraces
PILLAR 2
Synthetics
PILLAR 3
Wild
relatives
PILLAR 4
Elite
PHENOTYPING
GENOTYPING
BBSRC FUNDED PLANT
BREEDERS
9. X
Hybrid
Wheat Ancestral species/distant relatives
• Distant relatives provide a vast
reservoir for most if not all
agronomically important traits
• Interspecific hybrids provide the
starting point for introgressing genes
into wheat from its distant relatives
10. (Sears 1981)
How does introgression occur? Via homoeologous recombination
between the chromosomes of wheat and those of the distant
relative at meiosis in the gametes
The Ph1 locus has to be removed before homoeologous
recombination can occur. This is achieved by crossing to a line
in which the Ph1 locus has been deleted – ph1ph1
Screen lines cytologically and
for disease resistatance
11. (Sears 1981)
1) The identification of introgressions is difficult and time consuming
Why has introgression not been used more widely?
12. 2) Introgressions are frequently very large and
carry deleterious genes
Once a large alien chromosome segment had been introgressed into wheat it was very
difficult to reduce its size further by removal of the Ph1 locus - difficult to remove
deleterious genes
ph1/ph1 ph1/ph1
13. Identify plants with overlapping alien chromosome segments, in
which the target gene lies within the overlap and make a hybrid.
In the presence of Ph1 the alien and wheat chromosome segments will not recombine at
meiosis. However, the alien chromosome segments that overlap will giving rise to progeny
with small alien chromosome segments that carry the target gene but lack deleterious genes.
Wheat
Alien
Ph1/Ph1
X
T T
14. (Sears 1955 and 1981)
2) Introgressions were frequently very large
and carried deleterious genes
15. (Sears 1955 and 1981)
2) Introgressions were frequently very large
and carried deleterious genes
Need Genetic Markers
16. (Sears 1981)
Need for high throughput techniques to identify
and characterize introgressions
17. 1. Transfer of an entire ancestral genome to wheat in overlapping segments
Germplasm Development Programme – Start date 2011
Triticum urartu
Rye
Aegilops speltoides
Thinopyrum bessarabicum
Thinopyrum elongatum
Aegilops mutica
19. Identify plants with overlapping alien chromosome segments, in
which the target gene lies within the overlap and make a hybrid.
In the presence of Ph1 the alien and wheat chromosome segments will not recombine at
meiosis. However, the alien chromosome segments that overlap will giving rise to progeny
with small alien chromosome segments that carry the target gene but lack deleterious genes.
Wheat
Alien
Ph1/Ph1
X
T T
20. • Acid soil tolerance
• Drought
• Salinity
• High lysine
• Winter hardiness
• Disease resistance
• Powdery mildew
• Stem rust
• Stripe rust
• Leaf rust
• Boron tolerance
• High pollen load
• Out crossing
Utilize rye for improving wheat production
25. A
B
D
Wheat ph1/ph1
X
Wild relative (R)
ph1
X
A
B
D
Wheat Ph1/Ph1
High throughput screening of 1000’s of BC1 and
subsequent backcross progeny to identify
recombinants
Wheat/ancestral introgression
- Recombinants
Isolation of homozygous introgressions
Phenotyping
platform
26. A
B
D
Wheat ph1/ph1
X
Wild relative (R)
ph1
X
A
B
D
Wheat Ph1/Ph1
High throughput screening of 1000’s of BC1 and
subsequent backcross progeny to identify
recombinants
Wheat/ancestral introgression
- Recombinants
Isolation of homozygous introgressions
17,000 + crosses
in under 3 years!
Phenotyping
platform
28. Shrivelled grain culture – dry grains
Thynopyrum bessarabicum
x Chinese Spring Mutant 84
Triticum urartu x
Chinese Spring Mutant
84
Secale cereale x
Chinese Spring Mutant
84
(Summer season 2011)
35. • Mean exome sequence coverage per variety = 48X
• ~100,000 SNPs between 10 elite cultivars
• ~290,000 SNPs between elite hexaploid cultivars
and 9 landraces.
• ~650,000 SNPs between hexaploid wheat and wheat
relatives including Rye, Thinopyrum sp., Aegilops sp. and
Triticum urartu.
SNP discovery results:
37. Recombination in
Aegilops speltoides BC1s
Marker analysis of 22 BC1
recombinant plants –
Sacha Allen and Keith Edwards, Bristol
Introgressed Ae. speltoides
segments (blue) in 5
chromosomes
Introgressed Ae. speltoides
segments (blue) in 12
chromosomes
Size and position of
introgressed segments
will be characterised in
detail.
KASP
38. BC1 Aegilops speltoides – 22 genotypes sent to Bristol for primer
validation and genotyping.
All 22 genotypes had segments of Ae. speltoides present.
Least number of segments = 5
Highest number of segments = 12
• Need to make more backcrosses to isolate lines with single
introgressions
• Far more introgressions than expected
KASP
Isolate genotypes with a
single introgression
39. BC1 Aegilops speltoides – 22 genotypes sent to Bristol for primer
validation and genotyping.
All 22 genotypes had segments of Ae. speltoides present.
Least number of segments = 5
Highest number of segments = 12
• Need to make more backcrosses to isolate lines with single
introgressions
• Far more introgressions than expected
Ambylopyrum muticum, Triticum urartu, Ae. caudata, Secale cereale, Thinopyrum
Intermedium, Thinopyrum ponticum, Thinopyrum elongatum
KASP
Isolate genotypes with a
single introgression
41. • KASP can be used to screen several 1000’s of plants with circa 56
quickly and relatively cheaply
How can you screen with higher resolution and use more of the SNP’s
that have been developed?
KASP
Isolate genotypes with a
single introgression
42. WISP Axiom®
820k array
• 96 format 2 PEG design
• Includes SNPs among
elite lines
• Plus SNPs between elites
and landraces, and non-
wheat relatives
43. WISP Axiom®
820k array
• 96 format 2 PEG design
• Includes SNPs among
elite lines
• Plus SNPs between elites
and landraces, and non-
wheat relatives
Ex. 38, ooo Aegilops
speltoides SNPs
45. 820K Array ~ 593,755 validated SNPs
Axiom 384HT
Breeders chip
~35K SNPs
Mapped,
Codominant
Even coverage
Good PIC score
Axiom 384HT
Progenitors
~35K SNPs
Axiom 384HT
Others…
~35K SNPs
Being manufactured now.
Available to breeders
For spring 2014
Public and IP free!
Spring 2014
High Resolution Identification
of introgressions
46. A
B
D
Wheat ph1/ph1
X
Wild relative (R)
ph1
X
A
B
D
Wheat Ph1/Ph1
High throughput screening of 1000’s of BC1 and
subsequent backcross progeny to identify
recombinants
The technology is now available
to exploit the distant relatives of
wheat
Axiom®
35K array
Identify introgressions etc
+ KASP- used in later generations
47. A
B
D
Wheat ph1/ph1
X
Wild relative (R)
ph1
X
A
B
D
Wheat Ph1/Ph1
High throughput screening of 1000’s of BC1 and
subsequent backcross progeny to identify
recombinants
The technology is now available
to exploit the distant relatives of
wheat
Axiom®
35K array
Identify introgressions etc
+ KASP- used in later generations
Step change in
identification
and characterization of
Introgressions
48. Thinopyrum intermedium
440016 X Chinese Spring
Mutant P208/533
Thinopyrum elongatum
401007 X Chinese Spring
Mutant 84
Aegilops mutica 2130004
X Chinese Spring Euploid
94
Secale cereale 428373 X
Chinese Spring Mutant 84
Thinopyrum bessarabicum
531712 X Chinese Spring
Mutant 84
2. Wheat/ancestral introgression - Amphidiploids
49. - Develop a series of wheat/ancestral amphiploids from different species and accessions
(retaining the ancestral parents).
Wheat
X
Wild relative
Amphidiploids in a Paragon background
(Trait analysis – heat, salt, disease resistance etc)
Chromosome double
Season 1
Self
Season 2
Multiplication
Season 3/4
Trait analysis,
Phenotyping
platform
Ph1/Ph1
Ph1/Ph1
Ph1/Ph1 Ph1/Ph1
2. Wheat/ancestral introgression - Amphidiploids
50. – Colchicine – (Colchicum autumnale – autumn crocus)
inhibits microtubule polymerization
by binding to tubulin - spindle poison
= inhibiting chromosome segregation during meiosis
– Caffeine - (Coffea arabica – coffee)
inhibits plant cell cytokinesis
after nuclear division transverse cell walls fail to form – binucleate cells
- sister nuclei fuse or enter mitosis together and become polyploid
• Wheat/distant relative F1 hybrids at 4 tiller stage
• Split plants in half, trim roots and shoots
• Treatment overnight with a solution of 0.1% Colchicine, 2% DMSO, Tween-20;
or 3 g/L caffeine
• Washing off traces, potting, cool temperature at start (15˚C)
• Tag ears that shed pollen – fertility still low, sometimes only later tillers affected
(8th or later)
• Very careful threshing
Chromosome doubling
51. Colchicine treated F1 hybrid plants.
F1 hybrid
shedding
pollen.
Aegilops speltoides x
Chinese Spring Eup
F1 hybrid
setting
seed.
Aegilops mutica x
Chinese Spring Eup
54. Secale anatolicum
x Chinese Spring
Euploid 94
(Amp 1/6)
56 chromosomes
Multicolour GISH
A genome – yellow; 14 chromosomes
B genome – purple; 14 chromosomes
D genome – red; 14 chromosomes
Rye genome –green; 14 chromosomes
55. Multicolour GISH
A genome – yellow-blue; 14 chromosomes
B genome – purple; 14 chromosomes
D genome – red; 12 chromosomes
Ae. mutica genome –green; 13 chromosomes
Aegilops mutica x
Chinese Spring
Euploid 94
(Amp 28/1)
53 chromosomes
56. Multicolour GISH
A genome – green; 11 chromosomes
B genome + Ae. speltoides genome – purple; 28 (14 + 14) chromosomes
D genome – red; 12 chromosomes
Aegilops speltoides
x Pavon 76
(Amp 43/1)
51 chromosomes
57. In order to obtain the maximum value from
the introgression material developed they
need to be screened for a wide range of traits
58. • Salt – India
• Heat/drought tolerance – Sydney, India, CIMMYT
• Water and nutrient use efficiency – Nottingham, Sydney, CIMMYT
• Mineral content (Boron/Aluminium) - Nottingham
• Roots – Nottingham, RRES
• Photosynthetic capacity/chloroplast cell structure/biomass – Nottingham, RRES,
CIMMYT
• Disease/Insect Resistance – RRES, Sydney, India, CIMMYT
• Biofuel (ethanol) – Nottingham
Phenotyping
Development of an international phenotyping platform -
to determine the potential of the introgressions being generated
59. Phenotyping
Photosynthesis
Found increased photosynthesis in some BC1 plants of Triticum urartu,
Aegilops speltoides and Thinopyrum bessarabicum – actually all
the species he looked at.
The Triticum urartu and Thinopyrum bessarabicum BC1 plants of interest
have been included in the genotypes sent to Bristol for genotyping.
SCPRID PhD student – Cannan - has continued the work. Found plants of
interest among the BC3 Aegilops speltoides.
Disease resistance
Fusarium head blight, JIC; Take – all, RRES
Biofuels
62. New collaboration: The University of Nottingham
£2.2M The University of Sydney
Directorate of Wheat Research, India
Agharkar Research Institute, India
CIMMYT
New amphidiploids to be screened on numerous sites in UK,
Australia and India for wide range of phenotypic characteristics:
Water use efficiency
Nitrogen use efficiency
Mineral uptake
Photosynthetic capacity
Rust resistance
India and Australia
SCPRID Programme
63. Screening novel wheat germplasm in SCPRID (UoN/DWR/ARI)
Four Indian students recruited to start in academic year 2013-14
• Urmila Devi (introgression work)
• Jaswant Singh (tolerance to hostile soils / root phenotyping)
• Ajit Nehe (nitrogen-use efficiency)
• Kannan Chinnathambi (photosynthetic efficiency)
The three‘physiology’ students based in India until June 2014 (DWR/ARI)
Jaswant will start work immediately with DWR supervisors to establish field-trial plots:
- 6 sites of poor quality soils
- 1 standard site with 2x N-levels
Ajit and Kannan return to India in Oct./Nov. 2013 following initial training
2013/14: Indian genotypes (n=40, 4 replicate plots), root and shoot traits measured
2014/15: Amphidiploid material and Indian genotypes (n=40)
2015/16: Amphidiploid material (n=40)
2016/17: Amphidiploid material (n=40)
Jaswant, Ajit and Kannan will spend periods of 2014 and 2015 in UK to develop high-
throughput assays for root and shoot phenotyping of all ancestral lines, amphidiploids
and introgression series. This will inform choice of material for bulking and field-trials.
68. Root phenotyping (very high throughput)
Item unit cost (£ excl. VAT) Unit per tank Cost per tank (£ excl. VAT)
Frames and panels 152.55 152.55
Water reservoirs (custom drip trays) 32.80 9 295.20
19" X 24" Anchor paper (inc. cutting) 0.212 192 40.70
240 mm x 300 mm black polythene 0.0114 192 2.19
Q Connect foldback clip 19 mm 0.0072 192 1.38
Hoagland’s solution (16.3 g) 17.20 2.88 g 2.72
CAPITAL COSTS: £447.75 per tank
+camera and stand
RECURRING ITEMS: £0.25 /individual
STAFF: £0.70 /individual
GROWTH-ROOM: £0.50 /individual
Sowing: <5 person hours per tank, <£0.50 per individual at £18 h-1
Imaging: <2 person hours per tank, <£0.20 per individual at £18 h-1
Growth room costs: £100 per tank per run = £0.50 per individual, assume £8k per year at £200 per week for 40 weeks
Current cost = ~£1.45 per individual, excl. capital depreciation
69. 5214 kb 949 kb
Very high throughput, 20k plants per year feasible for one person….
Root phenotyping (very high throughput)
72. Glasgow Ae. buncialis Ae. uniaristata T. dicocchodies Ae. variablis
Ae. genticulata Ae. markgafii Ae. columnaris T. urartu Ae. peregrina
Glasgow Ae. biuncialis Ae. uniaristata T. dicoccoidies Ae. variablis
Ae. genticulata Ae. markgafii Ae. columnaris T. urartu Ae. peregrina
73. Hounsfield CT Facility
An X-ray Computed Tomography Facility for Rhizosphere Research
Key Features
• 3 CT Scanners working from 0.5 µm to 5 mm resolution
• Accommodating samples up to 25 cm diameter & 1 m length
• Rapid scanning within 10 minutes
• Automated sampling system enabling 4-D visualisation
• Automated root imaging via RooTrak
• New Building opening Feb 2014
Malcolm Bennett
78. http://wheatisp.org/
“In the next 50 years, we will need to harvest as much wheat as has been produced
since the beginning of agriculture, some 10,000 years ago."
The BBSRC wheat breeding programme is divided into 4 pillars (Landraces, Synthetics, Alien Introgression, Elite Wheats) and 2 themes (Phenotyping
and Genotyping). These are represented by the 6 circles below; each is clickable and takes you to the website of the respective area).
Free of IP
79. Ian & Julie King
Csilla Nemeth
Surbhi Mehra
Caiyun Yang
Paul Kasprzak
Duncan Scholefield
Stella Edwards
Stephen Ashling
PhD Students:
Jonathan Atkinson
Urmila Dogra
Paul Waldron
Jason Raynor
Lauren Baker
Jack Heath
New Postdoctoral Researchers
Andras Cseh - Hungary
Glacy Silva - Brazil
Research Fellow BBSRC/Nottingham
Research Fellow BBSRC/Nottingham
Postdoc position ERC
King’s Group
http://www.wheatisp.org/