With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events. To evaluate the performance of 55 K array, we genotyped 593 inbred lines with diverse genetic backgrounds. Compared with the widely-used Illumina® MaizeSNP50 BeadChip, our 55 K array has lower missing and heterozygous rates and more SNPs with lower minor allele frequency (MAF) in tropical maize, facilitating in-depth dissection of rare but possibly valuable variation in tropical germplasm resources. Population structure and genetic diversity analysis revealed that this 55 K array is also quite efficient in resolving heterotic groups and performing fine fingerprinting of germplasm. Therefore, this maize 55 K SNP array is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) for both tropical and temperate maize.

中文翻译：

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开发了具有改善的基因组覆盖率的玉米55 K SNP阵列，用于分子育种。

随着基因分型成本的降低，单核苷酸多态性（SNP）由于其丰度高，在整个玉米（Zea mays L.）基因组中的分布均匀以及适用于高通量分析而得到了广泛的接受。在这项研究中，在Affymetrix®Axiom®平台上开发了具有改善的基因组覆盖率的玉米55 K SNP阵列，其中55,229个SNP均匀分布在基因组中，包括22,278个外显子和19,425个内含子SNP。该阵列包含451个与368个已知基因和两个重要农艺性状相关的标记（耐旱性和仁油生物合成），当前参考基因组未涵盖的4067个标记，734个在不同组之间有显着差异的标记，以及132个标记是重要转基因事件的标记。为了评估55 K阵列的性能，我们对具有不同遗传背景的593个自交系进行了基因分型。与广泛使用的Illumina®MaizeSNP50 BeadChip相比，我们的55 K阵列在热带玉米中具有较低的缺失和杂合率，以及更多的SNP，具有较低的次要等位基因频率（MAF），有利于深入剖析热带种质中罕见但可能有价值的变异资源。种群结构和遗传多样性分析表明，这种55 K阵列在分辨杂合基团和对种质进行精细指纹识别方面也非常有效。因此，该玉米55 K SNP阵列是进行种质评估（包括种质指纹，遗传多样性分析和杂种分组），标记辅助育种，