Potato Mapping / QTLs

1. Potato Mapping / QTLs Amir Moarefi VCR 221 04 19 06

3. 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

4. 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.

5. Determining Association of Quantitative Characters Used a 600 potato cultivar representing genetic diversity of over 100 years

6. 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

7. PCR patterns observed

8. 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

9. Frequency Distribution for R11400 Distribution of cultivars having (black) or not having (grey) the R1 fragment Higher number represents resistance and early maturity

10. 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.

12. 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

13. 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

14. 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

15. 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

16. PCR based Markers

17. Observed Segregation

18. After tons of analysis ….

19. Plant Maturity vs Resistance to Late Blight Factors for resistance to Late Blight exist that can be separated from maturity effect • Genes are physically linked but structurally and functionally unrelated • Many unrelated genes control both QTLs over the whole genome, which by chance linkage is observed • Controlled by a pleiotropic allele of the same/related gene of a common ancestor

20. 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

22. 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

23. 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)

24. Finding Arabidopsis Homologs

25. Corresponding Solanum Tuberosum Genes

26. 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

27. 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