Vezzulli Silvia, Micheletti Diego, Riaz Summaira, Pindo Massimo, Viola Roberto, This Patrice, Walker M Andrew, Troggio Michela, Velasco Riccardo
IASMA Research Centre, Via E, Mach 1, 38010 San Michele all'Adige (TN), Italy.
BMC Plant Biol. 2008 Dec 16;8:128. doi: 10.1186/1471-2229-8-128.
Efforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus.
This study was performed by genotyping 137 SNPs through the SNPlex Genotyping System (Applied Biosystems Inc.) and by comparing the SNPlex sequencing results across 35 (of the 137) regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers.
Using SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms), but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera.
对不同生物体进行基因组测序的工作仍在不断增加。DNA序列通常是针对一个个体进行解码，其应用则针对整个物种。最近对高度杂合的葡萄品种黑比诺（克隆ENTAV 115）进行的基因组测序产生了数千个多态性位点，并为研究其多态性程度向同一物种的其他个体以及该属内其他个体的可转移性提供了一个良好的模型。
本研究通过SNPlex基因分型系统（应用生物系统公司）对137个单核苷酸多态性（SNP）进行基因分型，并比较了来自69个葡萄种质的137个区域中的35个区域的SNPlex测序结果。发现黑比诺在酿酒葡萄的不相关品种间的杂合状态可转移性为31.5%，在酿酒葡萄的野生类型间为18.8%，在非酿酒葡萄的葡萄物种间为2.3%，与圆叶葡萄间为0%。此外，平均等位基因频率被用于评估SNP的信息性并开发有用的标记子集。
通过SNPlex应用以及测序分析的佐证，来自杂合葡萄品种黑比诺的SNP标记的信息性在酿酒葡萄（包括品种和野生类型）中得到了验证，但在非酿酒葡萄的葡萄物种中的应用有限，在这些物种中，鉴于引物位点的同源性足够，重新测序策略可能更受青睐。这项工作将为未来的应用提供便利，如酿酒葡萄内的图谱绘制和多样性研究、种质鉴定以及基因组研究辅助育种。
