Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes
Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes
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DOI：
10.1007/s00122-007-0591-4
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发表时间：
2007-09-01
影响因子：
5.4
通讯作者：
Ganal, Martin
中科院分区：
文献类型：
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作者：
Schneider, Katharina;Kulosa, Dagmar;Ganal, Martin
一组 13 个甜菜品系，以及红甜菜和瑞士甜菜以及甜菜亚种各一个基因型。 maritima 用于鉴定源自 315 个 EST 和 43 个非编码 RFLP 衍生基因座的基因组 DNA 序列比对中的多态性。在甜菜品系中，表达基因位点的平均 SNP 频率为 1/72 bp，非编码序列中 58 bp 中有 1 个，在添加剩余基因型后增加到 1/47 bp。在分析的 DNA 片段中，不同 SNP 位置的等位基因显示出指示单倍型结构的连锁不平衡。甜菜品系中平均发现 2.7 个单倍型，表达基因中的单倍型保守长度似乎超过 500 bp。采用七种不同的基因分型技术，包括通过 MALDI-TOF 质谱法检测 SNP、焦磷酸测序和标记核苷酸的荧光扫描，对三个 F-2 群体中的 538 个标记进行了 712 次分离分析。预测了 492 个映射序列的功能。遗传图谱分别包括群体 K1 中覆盖 599.8 cM 的 305 个基因座、群体 D2 中分布超过 636.6 cM 的 241 个基因座和群体 K2 中分布超过 507.1 cM 的 166 个基因座。基于多个群体共有的 156 个标记，构建了包含 524 个基因座、覆盖 664.3 cM 的综合图谱。对于 377 个基因座，确定了来自拟南芥的最相似序列的基因组位置，但几乎没有发现先前提出的祖先基因组结构的证据。
A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F-2 populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found.