Potato Mapping / QTLs
Amir Moarefi
VCR 221
04 19 06
General Overview
Association between DNA markers and agronomic
characteristics would allow:
∙
Genetic Assessment of specific genotypes prior to phenotypic
evaluation
∙
Identify superior trait alleles in germplasm
∙
High Resolution QTL mapping
∙
Validate the genes responsible for the quantitative characters
Background on Tuberosum
• The Potato (Solanum Tuberosum ssp tuberosum) is
a non-inbred tetraploid plant with tetrasomic
inheritance
• Genetic Basis was broadened over the last century
by introgression of genes with resistance to biotic
and abiotic stress from various Solanum species
• Including the first introgression, which occurred
with Solanum demissum, which show resistance in
late blight (Phytophthora Infestans) and late
maturity.
Determining Association of
Quantitative Characters
Used a 600 potato cultivar representing
genetic diversity of over 100 years
Approach for determining
Association:
Five markers selected based on linkage to QTL for
resistance to late blight or plant maturity were used through
PCR
All markers found on Chromosome V in a “Hotspot”, except
GP76 which maps to chromosome VI
PCR patterns observed
Association Tests
GP76500 does not show any association for any trait
BA47f2, R1 and CosA show association for blight resistance
R11400 and CosA210 show association to late maturity
Frequency Distribution for R11400
Distribution of cultivars having (black) or not having
(grey) the R1 fragment
Higher number represents resistance and early maturity
Conclusions
• There should have been no marker trait associations
• Cultivar Collections are heterogenous in terms of place and
time of origin
• Various other introgressions existed from other unknown
Solanum Species
• Late Blight resistance varied based in P. infestans strain
• However CosA210 R11400 and BA47f2650 all showed
late blight resistance and later plant maturity found
exclusively in accessions of S. demissum
• Suggesting that the marker trait association may
have resulted from a single introgression.
Taking a Different Approach
• The R gene in Solanum demissum is only a
temporary monogenic resistance to Late Blight
• Quantitative resistance to late blight is mostly racenonspecific and controlled by more than one gene
• The correlation between resistance and late
maturity must also be separated
• Same Gene with Pleiotropic effects
• Different Gene but Closely Linked
QTLs for Late Blight
• Many DNA based markers have been used
for mostly diploid and few tetraploid
populations to determine QTLs on the 12
potato chromosomes for Late Blight
• Recently R1 gene was shown to be in a plant
resistance gene family containing
nucleotide-binding (NP) and leucine-rich
repeats (LRR) regions
Approach
• Look at QTLs for late blight resistance and
plant maturity in two tetraploid S. tuberosum
populations using PCR based markers
• Markers must contain following criteria:
They must map to regions that were
previously shown to map quantitative /
qualitative to pathogens in diploid species.
• Late Blight Resistance was conducted in the
Fields to correct effects on Plant Maturity
Plant Material
• Two tetraploid S. tuberosum F1
families were analyzed with no
hypersensitive resistance phenotype
to P. infestans
• The Escort and Nikita families were
produced by crossing cv. Leyla pollen
which is a susceptible cultivar with
cvs seeds
PCR based Markers
Observed Segregation
After tons of analysis ….
Plant Maturity vs Resistance to
Late Blight
Factors for resistance to Late Blight
exist that can be separated from
maturity effect
1. Genes are physically linked but structurally
and functionally unrelated
2. Many unrelated genes control both QTLs
over the whole genome, which by chance
linkage is observed
3. Controlled by a pleiotropic allele of the
same/related gene of a common ancestor
Marker Assisted Selection for
Late Blight Resistance
• Want cultivars with high levels of resistance
to late blight that are not compromised by
late maturity
• Except for Marker GP179 markers alleles
that were chosen varied between the two
half-sib families
• Due to crossing over between the resistance
QTL and marker allele in both parent
genotypes
• Non-Identity of the 570bp fragment
General Overview
• Plant defense against pest and pathogens
involves recognition and activation of
appropriate defenses
• Many of the general mechanisms for this
defense should be conserved in all flowering
plants
• Therefore structural and functional analysis of
a Model Species (Arabidopsis thaliana) should
allow for the identification of orthologs
Qualitative vs Quantitative
• Qualitative Resistance is characterized by two
distinct phenotypes: resistant or susceptible.
• Quantitative Resistance is characterized by
continuous phenotypic variation.
• For Quantitative Resistance any gene involved in
pathogen recognition or defense can be involved
and can be identified as Quantitative Resistance
Loci (QRL)
Finding Arabidopsis Homologs
Corresponding Solanum
Tuberosum Genes
Mapping of
Linkage Groups
16 potato defense
signaling genes mapped
to 10 of the 12
chromosomes
5 of these genes were
located in the same
genome fragment as
known QRLs
These genes were
sequenced and studied in
more detail
Conclusions
• Thus of the 19 Arabidopsis genes related to
pathogen recognition and response
– 16 potato Defense Homologs were identified
• 5 were closely linked to known QRLs
• StSGT-1/StSGT-2 : involved in cell cycle progression
• StPAD4-1/StPAD4-2: lipase like gene involved in salicyclic
acid signalling
• StAOS2 – allele oxide synthase involved in the
cytochrome P450 superfamily
• StEDS1- interactor of StPAD4
• Further Studies will reveal the contributions
of these genes to variation in potato disease
resistance