Date of Award

Winter 2015

Project Type

Dissertation

Program or Major

Genetics

Degree Name

Doctor of Philosophy

First Advisor

Thomas M Davis

Second Advisor

Estelle M Hrabak

Third Advisor

Iago L Hale

Abstract

The wild strawberry Fragaria vesca (L. Rosaceae) is an important diploid model plant system for the study of processes associated with crop production, plant physiology, and cultivar development of the octoploid cultivated strawberry (F. ×ananassa), an economically important crop plant. A fosmid clone library developed from F. vesca ssp. americana ‘Pawtuckaway’, and a mapping population of 96 F2 progeny (YPF2) resulting from a cross of F. vesca ssp. semperflorens “Yellow Wonder’ with F. vesca ssp. americana ‘Pawtuckaway’, were employed to further develop genetic and genomic resources and advance the search for the molecular identity of the classically defined fruit color (c) locus, in Fragaria vesca.

The F. vesca ssp. americana 'Pawtuckaway’ fosmid clone library provided an early genomics-level resource for the improvement of the cultivated strawberry. The sequence from twenty gene-targeted fosmid inserts allowed characterization of 0.71 Mb of gene space for F. vesca. The study identified a total of 120 protein-encoding genes or pseudogenes, indicating that the strawberry genome is gene-dense, with an average of one gene per 5.9 Kb. This report provides a high-resolution depiction of the structure and content of the targeted gene neighborhoods.

Utilizing both the YPF2 mapping population and two of the clones from the fosmid library, the continuing search for the molecular identity of the fruit color locus was pursued. In this population, recombination was found between the previously suggested candidate gene, Flavanone 3-hydroxylase (F3H), and the c locus on linkage group I (LG1), eliminating F3H as a viable candidate for identity to the fruit color locus. As a part of this investigation, the gene space for the F3H neighborhood was elucidated and annotated. Additionally, a genetic linkage map was constructed with 53 loci representing 61 PCR-based markers distributed across the seven. vesca linkage groups, with a total length of 403.6 cM. Linkage group I was fine mapped, and in the process of searching for alternate candidate genes for the fruit color locus, mapping of a Myb-like gene on the YPF2 population and on an independent, YPF2A, mapping population supported it as a strong candidate, based on both position and likely function. Thus, an avenue is defined for future research aimed at defining the molecular identity of the c locus.

Finally, using the YPF2 mapping population and the Affymetrix IStraw90® Axiom® array, a reasonably high-density linkage map (3.77 cM/locus) was defined by 167 loci representing 987 SNP-based markers across seven linkage groups, with a total length of 623.2 cM. Thus, the IStraw90 SNP array was shown for the first time to be a viable genotyping tool in a strawberry species other than those upon which its design was based. Significant segregation distortion in the YPF2 population was found to strongly and systematically favor the maternally derived alleles. A high degree of synteny (87.2%) was seen between this F. vesca YPF2 map’s linkage groups and the F. vesca ssp. vesca ‘Hawaii’ v.1.1 pseudochromosomes. This new map is the first SNP-based linkage map for the F. vesca model system, thereby facilitating informative, trans-specific comparisons with other SNP-based maps in Fragaria.

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