Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria\u2009\xd7\u2009ananassa)

Soichiro Nagano,Fumi Maeda,Hideki Hirakawa,Kenta Shirasawa,Sachiko N Isobe,Masami Ishikawa

doi:10.1186/s12864-017-3762-y

Abstract

BackgroundThe strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S1 mapping population of the cultivar ‘Reikou’ with an IStraw90 Axiom® SNP array and previously published SSR markers.ResultsThe ‘Reikou’ linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes.ConclusionsOur results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Highlights

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species
single nucleotide polymorphism (SNP) genotyping with the IStraw 90 Axiom® array SNP genotyping of the S1 population was performed with the IStraw90 Axiom® SNP array (Affymetrix Inc., CA, USA) using the Affymetrix GeneTitan® system according to the manufacturer’s protocol
The polymorphic locus derived from subgenome-specific sequences of an S1 population (ABOOOOOO) exhibits disomic segregation patterns of AA:AB:BB = 1:2:1

Summary

Introduction

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. It is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. Sargent et al [10] proposed the model A-A, b-b, X-X, X-X by construction of the SNP linkage map and discrimination of the ancestral chromosomes, where the A genome donor is an ancestral diploid F. vesca-like species, and the b and X subgenomes are from a hypothetical hexaploid derived from an F. iinumae-like and one or more unknown ancestral diploids, respectively. Though the discussion around the genome structure has continued, most researchers agree that the strawberry subgenome was derived from two or more ancestor species

Methods

Results

Conclusion