POTATO GENOME ANALYSIS
Christiane Gebhardt
MPI for Plant Breeding Research
Köln, Germany
Potatoes are like humans:
Self-incompatible outbreeders.
(A x B) x (C x D) crosses.
All wild types.
Large biodiversity.
Differences:
Ploidy level: 4n and 2n.
Large experimental F1 families
possible
Vegetative propagation.
Genome size 1/3 of human
genome: ~ 1000 Mbp.
Long term goals
• to elucidate the genetic basis of complex agronomic
characters of potato at the molecular level;
• to contribute to the understanding of structure, function
and natural diversity of crop plant genomes;
• to contribute to the genetic improvement of the
cultivated potato by developing molecular diagnostic
tools to assist the breeding of new cultivars.
Basic science
Genome structure
and evolution
Molecular basis of QTL
for agronomic traits
Association
studies
Selective
genomic
sequencing
Comparative maps
Biodiversity,
haplotypes
Candidate genes
Function maps for
pathogen resistance
and tuber traits
Molecular maps
Applied science
Haplotype-based
plant breeding
Markers for
population-based
MAS
Engineering
agronomic traits
R-gene cloning
Markers for
pedigree-based
MAS
Comparing the crop genome (genetic map) with the model
genome (physical map)
A
a
B
b
c
C
A. thaliana, 121 Mbp
mb
S. tuberosum, ca. 1000 Mbp
cM
Ch. Gebhardt
MPIZ
COMPARATIVE MAPPING WITH ESTs and STS MARKERS
CONSERVED BETWEEN POTATO AND ARABIDOPSIS
(EuDicotMap):
1. Linkage maps of 12 potato chromosomes were constructed based
on 445 RFLP loci.
2. Marker sequences were compared to the Arabidopsis genomic
sequence (BLASTN: P < exp -10, BLASTX: P < exp - 15)
RESULTS
1. 321 RFLP loci in potato have multiple sequence similarity with
the Arabidopsis genome sequence (1500 „hits“).
2. Ca. 41 % of the potato genetic map have syntenic relationships
with ca. 50 % of the Arabidopsis physical map.
Some potato
chromosomes have
more syntenic
relationships with
the Arabidopsis
genome than
others.
Syntenic blocks are redundant.
Potato map segments detect ancient duplications
in the Arabidopsis genome.
Gebhardt et al. 2003, TPJ 34: 529
Synteny between different potato
map segments and the same
Arabidopsis genome segment
reveals ‚hidden‘ intra- and
interchromosomal duplications in
the potato genome.
Similar experiments, comparing
sugar beet (Beta vulgaris),
sunflower (Helianthus annuus) and
Prunus spp with
Arabidopsis thaliana,
based on different sets of EST
markers, give similar results.
A.tha. 2
rDNA
I-II B
mb
1
2
Sugar
beet
Sun
flower
Prunus
Potato
3
4
5
6
7
8
II-IV A
9
10
11
12
I-II A
13
14
I-II C
15
16
II-III A
17
18
19
20
Dominguez et al. 2003, PBJ 1: 91
Genome
Archeology
Comparing the genomes of
contemporary, distantly
related plant species
‚excavates‘ the remains of
an ancestral plant genome.
Ch. Gebhardt
MPIZ
Basic science
Genome structure
and evolution
Molecular basis of QTL
for agronomic traits
Association
studies
Selective
genomic
sequencing
Comparative maps
Biodiversity,
haplotypes
Candidate genes
Function maps for
pathogen resistance
and tuber traits
Molecular maps
Applied science
Haplotype-based
plant breeding
Markers for
population-based
MAS
Engineering
agronomic traits
R-gene cloning
Markers for
pedigree-based
MAS
Potato function map for tuber traits
I
GP264
II
Icdh-1
GP1(c)
GP23
SK2
CP100
III
rbcS-c
GluA
GP180(a)
Pk
AGPaseB-c
GMPase
rbcS-1
GP303
Me-a
Pain-1
GluB
CP11
PC116
Cis
GP293(a)
GP255(i)
CP18
Fbp-cy
AGPaseS-c
CP6
SssI
Pha1-b
Tk
GP88
GP504
GP276
Pha1-a
Ppe-a
Aldolase-pl
Prk
G6pdh
GP35(d)
Sut4
GP82
GP35(t)
CP113
Fk
CP104(d)
Starch QTL
GP76
SbeI
GP295
VII
VIII
GbssI/wx
Ppa1-b
Pgk-cp
Pme
Aco
Glo-a
AGPaseB-a
GP40(a)
GP92
Ldh2-a
prp1
CP20(a)
GP167(b)
AGPaseS-b
Mdh
Glo-b
Ppc-a
Fbp-cp
Ucp
Ppa2
FBA
Inv-ap-b
SbeII
XI
GP122
UGPase
GP125
ShkB
Dbe
GP218
Sut1
Rca FBA
Ndpk
StpH
XII
CP49(a)
CP280
Tal1
Ant
pat(a)
Ppa1-a
GP183
Fum1-b
Sus4
GP129
Pha2
Sugar QTL
GP308(b)
GP215(a)
Inv-ap-a
Ppe-c
GP171
Fum1-a
X
GP35(e)
GP27
GP181
Hxk
IX
CP137(b)
CP43
Gb-R1
Ppe(b)
Pfp-a
CP132
CP134(b)
GP211
Me-b
GP194
GP127
Yield QTL
Sut2
Pdh-E1
GapC-cy
Gpt
GP179
GP234
rbcS-2
GP79
Stp1
UPTG
Dpe-P
GP35(p)
SssIII
Pfp-b
PSTR(f)
GP186
VI
Agl
GP261
GP1(a)
GP26
V
IV
Pt2
Ldh2-b
Ppa1-c
GP185
GP254
Sus3
Sps
GP34
Pt1
PSTR(i)
Starch metabolism
Sugar metabolism
Transport, energy
Ppc-b
AGPaseB-b
All genes functional in carbohydrate metabolism,
regulation and transport are candidate genes.
RESPIRATION
GLYCOLYSIS
GapC
DEGRADATION
AMY
STP
Ppa
Starch
PPi Hexose-P
Sbe
Sucrose-P
SPS
S6P
PPi
Sucrose
SUS
UGP
AGP
UDP-Glc
ADP-Glc
SYNTHESIS
INV
Glucose
Fructose
SS
Amyloplast
After Sowokinos 2001, Am. J. Pot. Res. 78
Cytoplasm
Fructose
Vacuole
Cell wall
IX
prp1
CP137(b)
CP20(a)
GP167(b)
Fbp-cp
Ucp
Ppa2
FBA
Inv-ap-b
SbeII
Ndpk
StpH
GP35(e)
Fum1-b
GP129
GP254
PSTR(i)
Pt1
Co-localization of a
functional candidate gene
(invertase) with QTL for
tuber sugar content
(Menendez et al. 2002,
Genetics 162).
The example of candidate gene
association mapping of:
CHIP COLOR
The color of potato chips
and French fries
depends on the glucose
and fructose content of
raw tubers.
High sugars, Low sugars
Bad chips
Li Li et al. (2005) Genetics 170: 813
Good chips
Single strand conformation polymorphism (SSCP) of
Invap in tetraploid breeding pools
Chips quality depends on fructose and
glucose content of tubers.
Invertase allele d is associated with chips quality (P < 0.001)
in a breeding pool of 179 tetraploid genotypes.
Thanks
for your
attention
Funding: European Union (EuDicotMap)
BMBF (German Federal Ministry for Education and Research), GABI-CHIPS.
MPG (Max-Planck society).