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Title: A high density linkage map of the ancestral diploid strawberry F. iinumae using SNP markers from the ISTRAW90 array and GBS

item MAHONEY, LISE L. - University Of New Hampshire
item SARGENT, DANIEL J. - Fondazione Edmund Mach
item WOOD, DAVE, J. - University Of New Hampshire
item WARD, JUDSON A. - Driscoll'S
item Bassil, Nahla
item HANDCOCK, JAMES F. - Michigan State University
item FOLTA, KEVIN M. - University Of Florida
item DAVIS, THOMAS M. - University Of New Hampshire

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2016
Publication Date: 3/28/2016
Citation: Mahoney, L., Sargent, D., Wood, D., Ward, J., Bassil, N.V., Handcock, J., Folta, K., Davis, T. 2016. A high density linkage map of the ancestral diploid strawberry F. iinumae using SNP markers from the ISTRAW90 array and GBS. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.08.0071.

Interpretive Summary: An Asian strawberry species, Fragaria iinumae, is believed to be one of two known ancestors of the cultivated strawberry. Genomic resources such as a genetic linkage map and DNA sequences exist for a representative from the other known ancestor species, Fragaria vesca. In this study, we developed the first genetic map for a Fragaria iinumae population. Comparison of the resulting map to that of F. vesca revealed substantial conservation in DNA sequence and gene order in addition to possible regions of divergences. This map provides a basis for future studies whose objective is to understand the genomic structure of the cultivated strawberry.

Technical Abstract: Fragaria iinumae is recognized as an ancestor of the octoploid strawberry species, including the cultivated strawberry, Fragaria ×ananassa. Here we report the construction of the first high density linkage map for F. iinumae. The map is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the Affymetrix IStraw90® Axiom® SNP Array; and Genotyping by Sequencing (GBS). The F2 generation mapping population was derived from F. iinumae hybrid F1D; the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The map consists of seven linkage groups, and has an overall length of 451.7 cM as defined by 496 loci populated by 4,173 markers: 3,280 from the IStraw90® Array and 893 from GBS. Comparisons with two versions of the F. vesca ssp. vesca ‘Hawaii 4’ pseudo-chromosome assembly reveal substantial conservation of synteny and colinearity; yet identified differences point to possible genomic divergences and/or to genomic assembly errors. This map provides a basis for anchoring a F. iinumae genome assembly, as a prerequisite for constructing a second diploid reference genome for Fragaria.