Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Plant and Environmental Science

Committee Chair/Advisor

Ksenija Gasic

Committee Member

Gregory Reighard

Committee Member

Christopher Saski

Committee Member

Guido Schnabel


DNA-informed breeding is becoming conventional for Rosaceae crops. The advancement of genomic tools and their application in breeding has potential to accelerate the breeding cycle and increase breeding efficiency. The objective of this dissertation was to explore the application of whole genome markers to identify marker-trait associations and potential candidate genes associated with peach disease resistance traits and evaluate the feasibility of applying genomic prediction models in breeding for disease resistance in peach. Two economically important diseases, brown rot and bacterial spot, were explored.

Genome wide association studies (GWAS) were first applied in detecting regions in the peach genome associated with fruit brown rot and bacterial spot leaf tolerance in peach. The results of the GWAS analyses revealed the polygenic nature for both fruit brown rot and foliar bacterial spot resistance in peach. The low phenotypic variance explained by the detected significant markers suggested genomic prediction might be the best approach in breeding for resistance of these diseases. In addition, candidate genes annotated with pathogen infection response/resistance were identified. Three genomic regions on chromosome 5 (1) and 6 (2) were found associated with resistance to both diseases, suggesting the pleiotropic effect on disease resistance traits of these region.

Genomic prediction (GP) for brown rot tolerance in peach revealed low to medium accuracy under five-fold cross validation. An alternative cross validation approach using a disease severity index recorded in the lab to predict field disease incidence (FDI) in non-phenotyped accessions revealed a moderate correlation (0.548 – 0.553). The genomic predicted breeding value distinguished accessions with low FDI from those with high FDI, which further supported using GP in early selection for brown rot resistance.

Overall, results presented here facilitate an understanding of the genetics underlying disease resistance in peach and support genomic selection as an appropriate method in selecting for fruit brown rot and foliar bacterial spot resistance in peach. Altogether, this work sets an important foundation for DNA-informed breeding of fruit brown rot and foliar bacterial spot resistance in peach.



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