Nagano Soichiro, Shirasawa Kenta, Hirakawa Hideki, Maeda Fumi, Ishikawa Masami, Isobe Sachiko N
Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan.
Chiba Prefectural Agriculture and Forestry Research Center, Chousei, Daizenno-Cyou 808, Midori, Chiba, 299-4335, Japan.
BMC Genomics. 2017 May 12;18(1):374. doi: 10.1186/s12864-017-3762-y.
The 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 S mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers.
The '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.
Our 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.
草莓（Fragaria × ananassa）是一种异源八倍体（2n = 8x = 56）的异交物种。尽管它是世界上消费最广泛的浆果作物，但其复杂的基因组结构阻碍了其遗传和基因组分析，因此需要区分同源染色体间的亚基因组特异性位点。在本研究中，我们鉴定了候选亚基因组特异性单核苷酸多态性（SNP）和简单序列重复（SSR）位点，并使用品种‘丽红’的S作图群体、IStraw90 Axiom® SNP芯片和先前发表的SSR标记构建了连锁图谱。
‘丽红’连锁图谱由11,574个位点（11,002个SNP和572个SSR位点）组成，跨越31个连锁群，总长2816.5 cM。这11,574个位点位于连锁图谱上4738个独特位置（bin）。在已定位的位点中，8999个（8588个SNP和411个SSR位点）呈现AA:AB:BB等位基因1:2:1的分离比例，这表明这些位点有可能源自候选亚基因组特异性序列。此外，2575个位点（2414个SNP和161个SSR位点）呈现AB:BB等位基因3:1的分离，表明它们源自同源基因组序列。同源连锁群的比较分析揭示了各亚基因组间基因组结构的差异。
我们的结果表明，候选亚基因组特异性位点随机分布于整个基因组中，且各亚基因组间存在小到大规模的结构变异。连锁图谱上已定位的SNP和SSR位点有望成为八倍体草莓构建假分子的种子点。
