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.

中文翻译：

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小麦660K SNP阵列显示了在多倍体小麦中进行标记辅助选择的巨大潜力。

分子标记测定法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。尽管基于PCR的标记（例如简单的序列重复和功能标记）和通过测序进行的基因分型对基因发现和标记辅助选择做出了巨大贡献，但更准确和完整的面包小麦参考基因组的发布导致了单基因设计基于不同密度或应用目标的核苷酸多态性（SNP）阵列。在这里，我们根据其SNP数量，分布，密度，相关基因，杂合性和应用评估了7种类型的小麦SNP阵列。结果表明，小麦660K SNP阵列包含具有可靠物理位置的基因组特异性SNP的百分比最高（99.05％）。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阵列中的229 266个SNP位于66 834个带注释的基因或启动子间隔中。Wheat 660K SNP阵列揭示的带注释基因几乎覆盖了Wheat 35K（97.44％），55K（99.73％），90K（86.9％）和820K（85.3％）SNP阵列揭示的所有基因。因此，Wheat 660K SNP阵列可以替代其他6个阵列，并显示出广泛的可能应用前景。总之，Wheat 660K SNP阵列可靠且具有成本效益，可能是小麦遗传改良中靶向基因分型和标记辅助选择的最佳选择。小麦660K SNP阵列中的229266个SNP位于66834个带注释的基因或启动子间隔中。Wheat 660K SNP阵列揭示的带注释基因几乎覆盖了Wheat 35K（97.44％），55K（99.73％），90K（86.9％）和820K（85.3％）SNP阵列揭示的所有基因。因此，Wheat 660K SNP阵列可以替代其他6个阵列，并显示出广泛的可能应用前景。总之，Wheat 660K SNP阵列可靠且具有成本效益，可能是小麦遗传改良中靶向基因分型和标记辅助选择的最佳选择。小麦660K SNP阵列中的229266个SNP位于66834个带注释的基因或启动子间隔中。Wheat 660K SNP阵列揭示的带注释基因几乎覆盖了Wheat 35K（97.44％），55K（99.73％），90K（86.9％）和820K（85.3％）SNP阵列揭示的所有基因。因此，Wheat 660K SNP阵列可以替代其他6个阵列，并显示出广泛的可能应用前景。总之，Wheat 660K SNP阵列可靠且具有成本效益，可能是小麦遗传改良中靶向基因分型和标记辅助选择的最佳选择。Wheat 660K SNP阵列可以替代其他6种阵列，并显示出广泛应用前景。总之，Wheat 660K SNP阵列可靠且具有成本效益，可能是小麦遗传改良中靶向基因分型和标记辅助选择的最佳选择。Wheat 660K SNP阵列可以替代其他6种阵列，并显示出广泛应用前景。总之，Wheat 660K SNP阵列可靠且具有成本效益，可能是小麦遗传改良中靶向基因分型和标记辅助选择的最佳选择。