SummaryHigh‐throughput genotyping arrays have provided a cost‐effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384‐well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the ‘Triticum aestivum Next Generation’ array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins ‘Core Collection’. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype‐optimized novel SNPs and legacy cross‐platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome‐wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.

中文翻译：

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开发下一代小麦 SNP 基因分型芯片

摘要高通量基因分型芯片为六倍体小麦及其近缘种的基因分型提供了一种经济有效、可靠且可互操作的系统。现有的、被高度引用的芯片（包括我们的 35K Wheat Breeder's 芯片和 Illumina 90K 芯片）是基于有限的品种序列多样性以及对 SNP 位置的不完全了解而设计的。小麦测序的最新进展使我们能够获得大量的 SNP 多样性，同时技术进步使我们能够在 384 孔格式 Axiom 阵列上安装比以前更多的探针。在这里，我们描述了一种新颖的 Axiom 基因分型阵列，即“小麦下一代阵列 (TaNG)，主要源自沃特金斯“核心收藏”中 204 个优良小麦品系和 111 个小麦地方品种的全基因组脱脂测序。我们使用一种新颖的单倍型优化方法来选择具有最高组合品种辨别力的 SNP，并使用设计迭代步骤来测试和替换未能转换为可靠标记的 SNP。最终设计包含 43 372 个 SNP，包含单倍型优化的新型 SNP 和传统跨平台标记的组合。我们表明，与以前的阵列相比，该设计具有改进的 SNP 分布，并且可用于生成具有比我们以前的阵列明显更多数量的不同箱的遗传图谱。我们还展示了 TaNGv1.1 在全基因组关联研究 (GWAS) 中的性能改进及其在拷贝数变异 (CNV) 分析中的实用性。该阵列可在市场上购买，并可免费获得支持标记注释和初始基因分型结果。