Potato Mapping / QTLs

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Potato Mapping / QTLs Powered By Docstoc
					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

∙   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

• 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
Determining Association of
 Quantitative Characters

Used a 600 potato cultivar representing
  genetic diversity of over 100 years
      Approach for determining

     Five markers selected based on linkage to QTL for
resistance to late blight or plant maturity were used through

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
• There should have been no marker trait
      • 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 race-
  nonspecific 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
• 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
• 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

• 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

16 potato defense
signaling genes mapped
to 10 of the 12
5 of these genes were
located in the same
genome fragment as
known QRLs
These genes were
sequenced and studied in
more detail
• 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

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