Date of Award

Spring 2016

Project Type


Program or Major

Plant Biology

Degree Name

Doctor of Philosophy

First Advisor

Thomas M Davis

Second Advisor

William K Thomas

Third Advisor

Janet R Sullivan


The cultivated octoploid strawberry Fragaria ×ananassa is one of the economically important fruit with market value of more than 2.8 billion dollars in the U.S. Molecular breeding of strawberry is becoming reliant on sufficient information of its genome composition. However, the diploid ancestry of the octoploid strawberry species has not been fully defined. This caused great challenges in developing high throughput genotyping tools such as SNP arrays. My overall research goal has been to help illuminate the origins and subgenome composition(s) of the cultivated strawberry and its immediate octoploid ancestors. For this purpose I have used three different approaches, each reported in a separate chapter of this thesis. In the long term, the knowledge I gained will help me to make contributions in strawberry breeding and investigation of other polyploid crops.

Chapter 1 describes a genome-scale phylogenetic approach. With the purpose of clarifying phylogenetic relationships among Fragaria species, an examination of phylogeny of genus Fragaria was conducted based on DNA sequence data from 24 nuclear genes from an extensive sampling of Fragaria species which include 96 DNA samples. The results revealed the complex phylogenetic relationships among diploid species and confirmed the identities of two diploids, F. vesca and F. iinumae as progenitors of the octoploids. In addition, strong phylogenetic signals provided by multiple phylogenetic trees suggested the presence of more than two types of subgenomes, and the possible contribution of diploid F. viridis and/or F. bucharica to the octoploid alleles.

In order to have a broader view of the subgenomic structure of the octoploid genomes, SNP-SNP markers which offer homoeologue specificities were utilized to construct the Fragaria ×ananassa linkage map. A segregating F1 population was developed from a cross between two F. ×ananassa cultivars, ‘Darselect’ and ‘Monterey’. 86 progeny and parental lines were genotyped using the Affymetrix Axiom®IStraw90®array. A linkage map containing 8,407 SNP markers were constructed, which included 575 subgenome affinities assigned SNP-SNP markers. Subgenomes originated from F. vesca, F. iinumae or unknown source(s) were identified. The resulting linkage map provided further support to findings using the phylogenetic approach, and provided valuable insights into the subgenome structure and integrity.

The third approach integrated both subgenome classified markers and linkage mapping. A pentaploid population was generated from the cross between diploid species F. vesca subsp. vesca accession H4 and the octoploid species F. virginiana accession ‘LB48’. 38 F1progeny was genotyped using Affymetrix Axiom®IStraw90®array. The resulting linkage map included 4,153 SNP markers spanning 2,218.52 cM on 26 linkage groups. Due to the lacking of SNP-SNP markers being mapped, 2,748 markers were classified into subgenome identity categories based on the phylogenetic analysis of marker flanking sequence and a set of diploid Fragaria homolog sequences. Linkage groups that were predominated by F. vesca-like and F. iinumae- like markers were identified. Markers in the unknown category were also identified, but their distribution pattern among linkage groups were unclear. For the ultimate goal of building a reference genome assembly of octoploid strawberry, linkage map constructed in this study could help to anchor scaffolds and assist in homoeolog chromosome sorting.

Three approaches employed in my PhD projects provided a multidimensional view of the subgenome composition of octoploid species. By including an extensive sampling of Fragaria species, the first approach reveled phylogenetic relationships between octoploids and other Fragaria species at diploids, tetraploid, hexaploid, and decaploid levels, as well as possible distinctions between two ancestral octoploid species F. virginiana and F. chiloensis. The next two approaches not only confirmed the existence of subgenomes contributed by three or more diploid ancestors, but also shed light on the identification of discrete subgenomes originated from F. vesca and F. iinumae.

Available for download on Wednesday, April 01, 2116