An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines
An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines
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DOI：
10.1007/s00122-009-1071-9
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发表时间：
2009-08-01
影响因子：
5.4
通讯作者：
Takeda, Kazuyoshi
中科院分区：
文献类型：
--
作者：
Sato, Kazuhiro;Takeda, Kazuyoshi
利用寡核苷酸混合分析法（OPA）对大麦进行高通量单核苷酸多态性（SNP）基因分型，构建大麦遗传图谱。本研究以大麦栽培品种“Haruna Nijo”（Hordeum vulgare ssp. vulgare）和野生大麦菌株“H602”（H. vulgare ssp. spontaneum）用1，448个单基因衍生的OPA-SNP进行基因分型。其中，732个标记表现出多态性，384个标记与EST标记在我们的高密度转录图谱上交叉引用。OPA-SNP标记在大麦染色体上分布较好，分别为1H（93）、2 H（131）、3 H（123）、4 H（97）、5 H（108）、6 H（92）和7 H（88）。使用cMAP平台，可以在高密度EST图谱中整合EST标记位置。使用OPA-SNP对来自同一杂交（Haruna Nijo/H602）的99个BC（3）F（5）重组染色体置换系（RCSL）进行基因分型。这些数据被用来创建每个线的图形基因型，从而估计的位置，程度，和总数量的基因渗入野生大麦亲本。RCSL对大部分野生大麦基因组进行了采样，只有少数缺失片段。随着我们开发的资源，所有的QTL等位基因分离在这份种质资源，现在是潜在的目标，基于图位克隆。
An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar "Haruna Nijo" (Hordeum vulgare ssp. vulgare) and wild barley strain "H602" (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC(3)F(5) recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.