National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, Zhengzhou, China.
Plant Biotechnol J. 2020 Jun;18(6):1354-1360. doi: 10.1111/pbi.13361. Epub 2020 Mar 10.
The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.
分子标记分析的快速发展和应用促进了小麦育种中的基因组选择以及全基因组连锁和关联研究。虽然基于 PCR 的标记（如简单序列重复和功能标记）和测序基因型分析极大地促进了基因发现和标记辅助选择，但更准确和完整的普通小麦参考基因组的发布导致了基于不同密度或应用目标的单核苷酸多态性（SNP）芯片的设计。在这里，我们从 SNP 数量、分布、密度、相关基因、杂合性和应用等方面评估了 7 种小麦 SNP 芯片。结果表明，小麦 660K SNP 芯片包含了最高比例（99.05%）的具有可靠物理位置的基因组特异性 SNP。SNP 密度分析表明，SNP 在整个基因组中几乎均匀分布。此外，小麦 660K SNP 芯片中的 229266 个 SNP 位于 66834 个注释基因或启动子间隔内。小麦 660K SNP 芯片揭示的注释基因几乎涵盖了小麦 35K（97.44%）、55K（99.73%）、90K（86.9%）和 820K（85.3%）SNP 芯片揭示的所有基因。因此，小麦 660K SNP 芯片可以替代其他 6 个芯片，并且在广泛的应用中具有广阔的前景。总之，小麦 660K SNP 芯片是可靠且具有成本效益的，可能是小麦遗传改良中目标基因型分析和标记辅助选择的最佳选择。
