Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
BMC Plant Biol. 2012 Aug 21;12:148. doi: 10.1186/1471-2229-12-148.
Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.
An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.
The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
遗传图谱构建和 QTL 检测是植物改良和育种的强大方法。构建高密度、高质量的遗传图谱将极大地有助于生产出满足人类需求的优质葡萄。最近开发的高通量、低成本的下一代测序（NGS）技术在基因组研究中得到了广泛应用。测序限制性位点相关 DNA（RAD）可能是一种简化基因分型的有效策略。将 NGS 与 RAD 相结合已被证明是开发单核苷酸多态性（SNP）标记的有力工具。
开发了一个由 100 个个体组成的 F1 群体。通过计算机模拟消化位点预测，选择了一种合适的限制酶用于构建 RAD 测序文库。将下一代 RAD 测序应用于 F1 群体及其亲本的基因型分析。通过 SNP 调制聚类策略，共开发了 1814 个高质量 SNP 标记：其中 1121 个标记映射到母本遗传图谱，759 个标记映射到父本图谱，1646 个标记映射到整合图谱。将遗传图谱与已发表的葡萄基因组进行比较，发现了两者的保守性和变异性。
证明了下一代 RAD 测序在葡萄 F1 群体基因分型中的适用性，成功地利用我们设计的 SNP 标记开发了高密度、高质量的遗传图谱。详细分析表明，该新开发的遗传图谱可用于多种基因组研究，如 QTL 检测、序列组装和基因组比较。
