Thesis
DETECTION OF FRUIT CRACKING AND FIRMNESS QTLS AND SUBSEQUENT CREATION OF DNA TESTS FOR USE IN SWEET CHERRY BREEDING
Washington State University
Master of Science (MS), Washington State University
01/2021
DOI:
https://doi.org/10.7273/000002395
Handle:
https://hdl.handle.net/2376/120572
Abstract
Cracked sweet cherry (Prunus avium L.) fruit are unmarketable and lead to higher labor costs, and sub-optimal fruit firmness decreases storability and consumer satisfaction. Trait improvement through breeding for increased cracking tolerance and fruit firmness is an attractive alternative to the variable results from management practices. DNA-informed breeding increases effectiveness, yet upstream and translational research, such as quantitative trait locus (QTL) discovery and characterization and DNA test development, respectively, are needed. The objectives of this work were to identify and characterize QTLs associated with fruit cracking or firmness, and develop DNA-based tests from these QTLs for use in DNA-informed breeding. Fruit cracking incidence and firmness were evaluated for two years in 2012 (half of seedlings; firmness only) or 2019 and 2020 for 259 unselected seedlings representing 22 important breeding parents. Phenotypic data, in conjunction with single nucleotide polymorphism (SNP) genotypic data from the RosBREED cherry 6K SNP array, were used in QTL analyses performed via Pedigree-Based Analysis using FlexQTL™ software, supplemented by a genome-wide association study using BLINK software. Haplotype analysis was conducted at QTLs to characterize SNP haplotypes and estimate phenotypic effects, and DNA-based tests were developed and/or evaluated. Four QTLs (two per trait) were consistent across years and/or analysis methods. The two fruit cracking QTLs combined explained 19–27% of the overall cracking phenotypic variance, while the two fruit firmness QTLs combined explained 21–31% of the overall firmness phenotypic variance. SNP haplotypes at these QTLs were successfully tracked to ancestral origins. For each QTL, pairwise SNP haplotype comparisons revealed different (p = 0.05) associated phenotypic levels between at least two haplotypes, which were considered functional SNP haplotypes. Primary SNPs successfully distinguished at least one of the contrasting functional SNP haplotypes at each QTL, and were successfully converted (array SNPs) into DNA tests. A previously developed SSR-based DNA-test was successfully evaluated and distinguished seven unique SSR haplotypes. The four stable QTLs detected here were in genomic regions aligned with previously reported QTLs, although two were reported as only transient. The DNA tests reported here can be implemented in breeding operations to genetically improve fruit cracking tolerance and firmness.
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Details
- Title
- DETECTION OF FRUIT CRACKING AND FIRMNESS QTLS AND SUBSEQUENT CREATION OF DNA TESTS FOR USE IN SWEET CHERRY BREEDING
- Creators
- William Wesley Crump
- Contributors
- Per McCord (Advisor)Cameron Peace (Committee Member)Zhiwu Zhang (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Horticulture, Department of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University
- Number of pages
- 139
- Identifiers
- 99900606652901842
- Language
- English
- Resource Type
- Thesis