Use of a single reference genome for genome‐wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence–absence variations (PAVs). In this study, we present the draft de novo genome assembly of ‘PHJ89’, an ‘Oh43’‐type inbred line of maize (Zea mays L.). From three separate reference genome assemblies (‘B73’, ‘PH207’, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole‐seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome‐wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map Sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43‐type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.

中文翻译：

---

多个玉米参考基因组通过基因组全关联研究在不同近交系中影响变异的鉴定。

将单个参考基因组用于全基因组关联研究（GWAS），将代表的基因空间限制为单个登录的基因空间。这种局限性可能会使存在与缺失变异（PAV）内的基因的鉴定和表征复杂化。在这项研究中，我们提出草案从头基因组装配“PHJ89”，玉米的“Oh43'型自交系（玉蜀黍L.）。从代表玉米主要种质组的三个独立的参考基因组组件（“ B73”，“ PH207”和PHJ89）中，我们从942个专家组中生成了三个独立的全苗基因表达谱和单核苷酸多态性（SNP）矩阵近交系。我们确定了34447（B73），39672（PH207）和37436（PHJ89）转录本，它们在相应的参考基因组程序集中不存在。在942个近交组中进行了全基因组关联研究，使用SNP和表达数据值绘制了甘蔗花叶病毒的图谱（SCMV）抵抗力。GWAS的结果突出显示了其他参考基因组在基因发现中的影响，当使用含有该基因的B73参考基因时，GWAS结果以表达值作为PAV的替代量度，可以可靠地检测已知抗性基因的物理位置，但不是PH207参考。这项研究提供了Oh43型PHJ89基因组装配的宝贵资源，以及从三个不同参考基因组生成的942个人的SNP和表达数据。