Introduc)on
to
plant
gene)cs
and
resources
Graham
Teakle
Warwick Crop Centre, School of Life
Sciences
Crop Improvement in VeGIN
Increase
range
and
accessibility
of
allelic
varia)on
•  Natural
gene%c
varia%on
‐
Diversity
sets
•  Induced
gene%c
varia%on
–
TILLING
mutant
popula%on
Understand
the
gene)c
basis
of
traits
•  Iden%fy
new
sources
of
desirable
traits
•  Map
trait
varia%on
‐ monogenic
traits
polygenic
traits
(Quan%ta%ve
Trait
Loci,
QTLs)
•  Map
candidate
genes
for
selected
traits
Technology
development
•  Whole
genome
and
transcriptome
sequencing
•  Marker
development
and
high
throughput
genotyping
(SNPs)
•  Improved
gene%c
maps
and
integra%on
with
genome
sequence
Definitions:
Chromosome
Pair
1
Linkage
Group
1
Chromosome
Pair
2
Linkage
Group
2
F
M
F
M
Marker
1
Marker
2
Marker
7
Locus
Marker
9
Marker
3
Linked
markers
cM
Marker
8
Polymorphic
or
Heterozygous
Alleles
Marker
4
Marker
10
Marker
5
Marker
11
Marker
6
Marker
12
Unlinked
markers
Monomorphic
or
Homozygous
Mapping populations & Quantitative Trait Loci (QTL)
Female
parent
Homozygous
Doubled
haploid
(DH)
line
produc)on
or
Inbreeding
Male
parent
X
Bi‐parental
segrega)ng
mapping
popula)on
M1
Meisosis
QTL
M2
M3
M4
Gametes
(Eggs/Pollen)
M5
Trait
screening
12
Heterozygous
F1
10
8
6
4
2
Meisosis
(Recombina.on)
0
1
2
3
4
5
6
Low
values
7
8
9
10
11
12
13
14
15
16
High
values
QTLs for Water use efficiency
A12
x
GD33
DH
popula%on:
δ13C
and
δ18O
QTL
Andrew Thompson, University of Warwick
C1
C2
C3
C4
C5
C6
C7
C8
0
50
100
c
M
150
δ18O
Gleadthorpe
δ18O
Kirton
δ13C
Gleadthorpe
δ13C
Kirton
Mean
Drought
Control
C9
QTLs
for
other
Brassica
traits
at
Warwick
•  Post
harvest
senescence
•  Virus
resistance
•  Germina%on/seedling
vigour
•  Root
growth
•  Nitrogen
assimila%on
•  Juvenility
•  Mineral
use
efficiency
•  Resistance
to
other
pathogens
•  Leaf
morphology
•  Transforma%on
•  Circadian
rhythms
•  Seed
oil
content/quality
•  Glucosinolate
content
The breeding genepool of crops generally has a narrow
genetic base compared to the wider species genepool
Species
Genepool
Selec)on
during
Domes)ca)on
Crop
Genepools
B
F
F
F
G
D
A
D
E
C
B
F
E
B
G
B
E
B
C
F
Crop
type
1
(e.g.
Winter
OSR)
C
A
F
D
F
A
C
F
A
C
Crop
type
2
(e.g.
Spring
OSR)
C
F
G
C
E
E
C
D
D
C
Crop
type
3
(e.g.
Swede)
Diversity sets at Warwick
Genebanks
Warwick HRIGRU
e.g. >6000 Brassica
accessions
Much genetic
redundancy
Diversity Foundation
Sets (DFS)
Diversity Fixed
Foundation Sets
(DFFS)
Reference sample
representing available
diversity
Species
No.
founder
lines
Brassica
oleracea
(C
genome)
Wild
species
(C
genome)
Brassica
napus
(AC
genome)
Leeuce
Carrot
Onion
376
88
189
96
64
+
30
cvs
96
Genetically homozygous
(fixed) immortal lines
No.
Fixed
Popula)on
type
lines
140
148
71
96
n/a
n/a
DH
DH
DH/Inbreeding
Inbreeding
Half
sib
families
Half
sib
families
BolDFFS founder composition
C genome species: BCgDFFS
89 Founder accessions from 14 species
Founder
plant
x
Selfed
seed
&
DNA
Microspore‐
responsive,
self
compa)ble,
rapid
cycling
DH
line
F1
Microspore
culture
F2
DH
line
Bulk
up
Marker
analysis
to
compare
DH
line
with
founder
Founder
Accessions
Total
DH
accessions
with
DH
lines
lines
B. alboglabra
1
1
20
B. atlantica
2
1
3
B. balearica
1
0
0
B. bourgaei
1
1
3
B. cretica
8
6
29
B. hilarionis
3
1
4
B. incana
10
5
22
B. insularis
2
1
2
B. macrocarpa
16
2
4
B. maurorum
1
0
0
B. montana
3
4
25
B. oleracea
24
12
32
B. rupestris
4
1
2
B. villosa
13
1
2
DH lines from 36 Founder
accessions, 12 species
PCO Analysis of 100 SSRs on 94 BolDFS lines
1006
alleles
in
total
503
alleles
at
>=5
abundance
used
for
diversity
analysis
0.2
Coordinate 2
0.1
0
Broccoli
Brussels sprout
Cabbage
Cauliflower
Chinese white kale
Kale
Kohl rabi
Tronchuda kales
Wild species &
C genome
-0.1
-0.2
-0.3
-0.4
-0.2
-0.1
0
0.1
0.2
0.3
Coordinate 1
0.4
0.5
0.6
PCO analysis of >500 SNPs on the Wild C genome DFFS
Oleracea
(21)
0.3
Montana(4)
Macrocarpa
(17)
0.2
Coordinate 2
Cre%ca
(8)
Bourgaei
(1)
0.1
Insularis
(2)
0
Atlan%ca
(2)
Incana
(10)
-0.1
Alboglabra
(1)
-0.2
Hilarionis
(2)
Rupestris
(4)
-0.2
-0.1
0
0.1
0.2
Coordinate 1
0.3
0.4
0.5
Villosa
WUE and biomass in the BolDFFS
Andrew Thompson, University of Warwick
Decreasing
Transpiration
Lines
that
grow
well
in
dry
and
control
irriga)on
treatments
Increasing WUE
Antioxidant content diversity in Brassicas
Guy Barker, University of Warwick
Total
an)oxidants
in
field
trial
(nmol)
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
Diversity of TuMV and TuYV resistance in
the BolDFFS and BnaDFFS
John Walsh, University of Warwick
Ongoing
research
to
31st
March
2012.
Recent
progress:
Turnip
Yellows
Virus
(TuYV)
Turnip
Mosaic
Virus
(TuMV)
No.
lines
screened
Result
No.
lines
screened
Result
BnaDFFS
BolDFFS
27
76
Sources
of
par)al
Sources
of
complete
resistance
iden)fied
resistance
iden)fied
15
44
Sources
of
pathotype
Sources
of
par)al
resistance
iden)fied
resistance
iden)fied
Diversity of seed omega fatty acid content
%
total
faey
acid
Guy Barker, University of Warwick
B.napus
Alpha
linolenic
acid
(18:3n3)
B.oleracea
B.rapa
Seed availability
  Brassica
and
leeuce
‐
Graham
Teakle
(graham.teakle@warwick.ac.uk)
  Onion
–
Andrew
Taylor
(andrew.taylor@warwick.ac.uk)
  Carrot
–
Charloee
Allender
(charloee.allender@warwick.ac.uk)
  Seed
availability
is
dependent
on
stock
levels
  Charges
–
covers
handling
a
distribu%on
and
cost
of
replacement
  It
should
be
noted
that
for
larger
requests,
the
requester
may
wish
to
include
these
costs
in
grant
applica%ons
  A
materials
transfer
agreement
may
also
need
to
be
signed,
depending
on
the
resource
required