Date of Graduation

5-2016

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Plant Science (PhD)

Degree Level

Graduate

Department

Plant Pathology

Advisor/Mentor

Clark, John R.

Committee Member

Bluhm, Burton H.

Second Committee Member

Garcia, Maria E.

Third Committee Member

Mason, Richard E.

Fourth Committee Member

Shi, Ainong

Keywords

Biological sciences; Breeding; Disease resistance breeding; Fruit; Horticulture; Marker-assisted breeding; Qtl

Abstract

For over two decades the incorporation of marker-assisted selection (MAS) has been discussed as an innovative approach to increase peach breeding efficiency. Although hundreds of quantitative trait loci (QTLs) have been identified, only a few have been converted into usable MAS tools. This highlights a disconnect between genomic discoveries and practical application in breeding programs, which has delayed use of MAS.

In this dissertation, three sequential steps were performed with the objective to bridge this gap and develop breeding-relevant DNA tests for MAS of fruit bacterial spot resistance (Xap1 and Xap6), fruit quality [blush (Rf), acidity (D), and acidity and soluble solid content (G7Flav)], and phenological traits [maturity date (G4mat), fruit type (G), and flesh color (Y)] across four RosBREED peach breeding programs. First, previously identified QTLs were further investigated and 32 SNPs were grouped into haplotypes and validated for association with breeding-relevant trait differences across RosBREED germplasm. The SNPs were divided into two mini-arrays and advanced breeding material from all programs were outsourced for design and testing. The validated SNP loci were used in marker-assisted parent selection (MAPS) in 2013-2015 at the University of Arkansas (UA) program to combine horizontal Xap resistance with high fruit quality spanning the season. Secondly, four of the SNP-based tests (Xap1, Xap6, G, and Y loci) were converted into sequence length polymorphism-based (SLP-based) tests (Ppe-XapF1-SSR, Ppe-XapF6-SSR, indelG, and PpCCD4b-SSR) and screened on the UA RosBREED germplasm and 22 additional F1 populations. Results were compared across both DNA tests to identify the most efficient genotyping approach for each trait. In 2015, two of the SLP-based DNA tests, the indelG (pubescent vs. glabrous) and PpCCD4b-SSR (white vs. yellow flesh) were advanced to test in marker-assisted seedling selection (MASS).

In the final step, QTL analysis was conducted for Xap fruit, Xap leaf, and Xap leaf-assay resistance along with seven fruit quality and phenological traits using the Pedigree-Based Analysis (PBA) approach and the UA RosBREED pedigree. Overall 20 QTLs were identified, 10 for Xap resistance and 10 for quality and phenological traits. These 20 QTLs are optimal targets for future DNA test development, validation, and use in MAS.

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