Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms
Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms
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DOI：
10.1007/s11032-004-0261-z
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发表时间：
2004-11-01
影响因子：
3.1
通讯作者：
Velasco, R
中科院分区：
文献类型：
--
作者：
Salmaso, M;Faes, G;Velasco, R
EST（表达序列标签）测序、SNP（单核苷酸多态性）开发和单倍型评估是支持标记辅助选择的有力工具。葡萄藤基因组目前正在我们的实验室使用EST-SNP方法进行清除。9个亲本基因型，用来创建5个种间或种内杂交品种，已经被测试来评估葡萄、葡萄和另一个种内杂交品种之间的多态性程度，测量它们的核苷酸多样性。通过与公共数据库中糖代谢、细胞信号、花青素代谢和防御相关基因的同源性，对4类功能基因的cDNA序列进行snp分析。推导引物对，用于扩增相应的基因组序列。对近12000 bp的DNA进行了扫描，发现基因型之间存在多达247个SNP的差异，当比较不同葡萄品种的克隆时，每78 bp出现一个SNP的比例最高。重新测序允许在研究的9个基因型中定义单倍型，并通过分析分离群体来证实这些定义。在相同的9个基因型的25个基因片段中，考虑SSCP与重测序的效率。
EST (expressed sequence tags) sequencing, SNP (single nucleotide polymorphisms) development and haplotype assessment are powerful tools for the support of marker-assisted selection. The grapevine genome is currently being scavenged in our laboratory using an EST-SNP approach. Nine parental genotypes, used to create five inter- or intra-specific hybrids, have been tested to evaluate the degree of polymorphism between Vitis vinifera, Vitis riparia and a further intraspecific hybrid, measuring their nucleotide diversity. The SNPs were analysed on cDNA sequences of 4 functional classes of genes based on homology with genes present in a public database: sugar metabolism, cell signalling, anthocyanin metabolism and defence related. Primer pairs were deduced and used to amplify corresponding genomic sequences. Almost 12,000 bp of DNA have been scanned revealing differences among genotypes of up to 247 SNPs, with the highest rate of one SNP occurring every 78 bp when clones of different Vitis species are compared. Re-sequencing allowed the definition of haplotypes in the nine genotypes studied and these were confirmed by analysing segregating populations. The efficiency of SSCP, in comparison with re-sequencing, was considered for 25 gene fragments of the same 9 genotypes.