High-throughput SNP genotyping to accelerate crop improvement.
High-throughput SNP genotyping to accelerate crop improvement.
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DOI：
10.9787/pbb.2014.2.3.195
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发表时间：
2014-01-01
影响因子：
--
通讯作者：
Thomson, M. J.
中科院分区：
文献类型：
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作者：
Thomson, M. J.
如果部署得当，下一代测序（NGS）和单核苷酸多态性（SNP）基因分型的最新进展有望大大加速作物改良。与以前的标记系统相比，高通量 SNP 基因分型具有许多优势，包括丰富的标记、快速处理大量群体、满足不同需求的各种基因分型系统，以及由于 SNP 标记的双等位基因性质而直接的等位基因调用和数据库存储。 NGS 技术实现了快速全基因组测序，提供广泛的 SNP 发现池，为不同的种质选择信息标记。高度多重的固定阵列平台已经实现了强大的方法，例如全基因组关联研究。另一方面，性状特异性 SNP 标记的常规部署需要灵活、低成本的系统，使用 Fluidigm 的 Dynamic ArraysTM、Douglas Scientific 的 Array TapeTM 和 LGC 的用于运行 KASPTM 标记的自动化系统等平台，对大型育种群体中少量的 SNP 进行基因分型。与此同时，通过多重测序进行低成本高密度全基因组扫描的测序基因分型 (GBS) 正在迅速流行。本综述将讨论现代育种者将 SNP 标记整合到其计划中的一系列选项，无论是外包给服务提供商还是建立内部基因分型设施，并将提供国际水稻研究所基因分型服务实验室所展示的水稻研究和育种中 SNP 部署的示例。
Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP genotyping offers a number of advantages over previous marker systems, including an abundance of markers, rapid processing of large populations, a variety of genotyping systems to meet different needs, and straightforward allele calling and database storage due to the bi-allelic nature of SNP markers. NGS technologies have enabled rapid whole genome sequencing, providing extensive SNP discovery pools to select informative markers for different sets of germplasm. Highly multiplexed fixed array platforms have enabled powerful approaches such as genome-wide association studies. On the other hand, routine deployment of trait-specific SNP markers requires flexible, low-cost systems for genotyping smaller numbers of SNPs across large breeding populations, using platforms such as Fluidigm's Dynamic ArraysTM, Douglas Scientific's Array TapeTM, and LGC's automated systems for running KASPTM markers. At the same time, genotyping by sequencing (GBS) is rapidly becoming popular for low-cost high-density genome-wide scans through multiplexed sequencing. This review will discuss the range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities, and will provide an example of SNP deployment for rice research and breeding as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.