A high density linkage map of the ancestral diploid strawberry, F. iinumae, using SNP markers from the IStraw90 Array and GBS

Publication Overview
TitleA high density linkage map of the ancestral diploid strawberry, F. iinumae, using SNP markers from the IStraw90 Array and GBS
AuthorsN/A
TypeJournal Article
Journal NameThe Plant Genome
Volume9
Issue2
Year2016
CitationLise L. Mahoney, Daniel J. Sargent, Judson A. Ward, Nahla V. Bassil, James F. Hancock, Kevin M. Folta, Thomas M. Davis. A high density linkage map of the ancestral diploid strawberry, F. iinumae, using SNP markers from the IStraw90 Array and GBS. The Plant Genome 2016 9(2)

Abstract

Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter “Array”), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. ‘Hawaii 4’ pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria.
Features
This publication contains information about 893 features:
Feature NameUniquenameType
TP9453TP9453genetic_marker
TP6383TP6383genetic_marker
TP6800TP6800genetic_marker
124_101623124_101623genetic_marker
TP848TP848genetic_marker
TP3803TP3803genetic_marker
TP8232TP8232genetic_marker
TP5939TP5939genetic_marker
TP6532TP6532genetic_marker
TP695TP695genetic_marker
TP534TP534genetic_marker
4_16435404_1643540genetic_marker
TP368TP368genetic_marker
TP434TP434genetic_marker
4_11954654_1195465genetic_marker
4_10821464_1082146genetic_marker
4_10710644_1071064genetic_marker
4_8723324_872332genetic_marker
4_8722864_872286genetic_marker
TP1453TP1453genetic_marker
4_2594224_259422genetic_marker
4_2050974_205097genetic_marker
4_2050544_205054genetic_marker
4_2050224_205022genetic_marker
4_1047214_104721genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Fragaria-Fii