GenePair Haplotypes: Novel Molecular Markers for Genetic Studies in Octoploid Strawberry

1
Gene-Pair Haplotypes Novel Molecular Markers for
Genetic Studies in Octoploid Strawberry

• Denise C. M. Tombolato, Philip J. Stewart, Thomas
  M. Davis, Kevin M. Folta

2
Challenges to Profitable Production
3
Challenges to Profitable Production
4
Challenges to Profitable Production
5
Challenges to Profitable Production
6
Challenges to Profitable Production
7
Possible Remedy Cultivar improvement

• Traditional strawberry breeding
• Linkage mapping in the octoploid background is
  difficult
• Molecular approaches

8
Strawberry Genomics at UF
Functional genomics
Structural genomics Molecular markers for MAS
Gene discovery and analysis of expression
Assessment of gene function in transgenic
strawberry
9
Strawberry Genomics at UF
Functional genomics
Structural genomics Molecular markers for MAS
Gene discovery and analysis of expression
Assessment of gene function in transgenic
strawberry
10
Gene-Pair Haplotype

• Complex Molecular Marker to
• study segregation of the diploid subgenomes in
  the octoploid background, thus permitting
  molecular mapping

11
Gene-Pair Haplotype

• Complex Molecular Marker to
• study segregation of the diploid subgenomes in
  the octoploid background, thus permitting
  molecular mapping

12
Gene-Pair Haplotype

• Complex Molecular Marker to
• study segregation of the diploid subgenomes in
  the octoploid background, thus permitting
  molecular mapping

13
Gene-Pair Haplotype

• Complex Molecular Marker to
• study segregation of the diploid subgenomes in
  the octoploid background, thus permitting
  molecular mapping
• delineate allele contribution by diploid genomes
  to the octoploid genome

14
Gene-Pair Haplotype

• Complex Molecular Marker to
• study segregation of the diploid subgenomes in
  the octoploid background, thus permitting
  molecular mapping
• delineate allele contribution by diploid genomes
  to the octoploid genome

15
Gene-Pair Haplotype

• Complex Molecular Marker to identify
  polymorphisms
• between subgenomes
• within subgenomes

16
Microcolinearity
octoploid strawberry
17
Microcolinearity
arabidopsis
octoploid strawberry
18
Microcolinearity
311bp
arabidopsis
octoploid strawberry
19
Microcolinearity
311bp
arabidopsis
octoploid strawberry
20
Microcolinearity
311bp
arabidopsis
octoploid strawberry
Primer F
Primer R
21
Microcolinearity
311bp
arabidopsis
octoploid strawberry
C
TATATA
BamHI
T
TATA
BamHI
T
EcoRI
TATATA
C
TATA
BamHI
InDel
SNP
SSR
RFLP
22
Microcolinearity
311bp
arabidopsis
octoploid strawberry
C
TATATA
BamHI
T
Within genomes
TATA
BamHI
T
EcoRI
TATATA
Between genomes
C
TATA
BamHI
InDel
SNP
SSR
RFLP
23
Locus GPH10

• PCR-amplified from octoploid cultivated
  strawberry Festival, as well as diploids Fragaria
  viridis, F. iinumae, F. nubicola, F.
  nilgerrensis, F. mandschurica, F. vesca
• Cloned
• Restriction-digested
• Sequenced
• Detected polymorphisms
• 6 in the octoploid
• 4 in the diploids

Clones from octoploid
20
2
18
19
28
29
1kb
500bp
300bp
200bp
100bp
24
Conclusions

• GPH are complex molecular markers that facilitate
  genetic mapping in the octoploid cultivated
  strawberry
• GPH markers will help define strawberry and the
  Rosaceae gene space and will provide information
  about the evolution of the Rosaceae family
• GPH concept may be applied to other polyploid
  species

25
Acknowledgements

• Dr. Thomas Davis at the University of New
  Hampshire
• Dr. Kevin Foltas lab at the University of
  Florida

Supported by