Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

BMC Genomics

Research Article

Fumi Maeda¹  Masami Ishikawa²  Kenta Shirasawa³  Hideki Hirakawa³  Sachiko N. Isobe³  Soichiro Nagano³ 

[1] Chiba Prefectural Agriculture and Forestry Research Center, Chousei, Daizenno-Cyou 808, 299-4335, Midori, Chiba, Japan;Chiba Prefectural Agriculture and Forestry Research Center, Chousei, Daizenno-Cyou 808, 299-4335, Midori, Chiba, Japan;Institute for Horticultural Plant Breeding, Kamishiki 2-5-1, 270-2221, Matsudo, Chiba, Japan;Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, 292-0818, Kisarazu, Chiba, Japan;

关键词: Cultivated strawberry;    Fragaria;    Genotyping array;    Linkage map;    Subgenome;    Polyploidy;    Single nucleotide polymorphism;    Simple sequence repeat polymorphism;   

DOI  :  10.1186/s12864-017-3762-y

 received in 2016-12-22, accepted in 2017-05-03,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017