College of plant science and technology; National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University, Wuhan, China, 430070.
Department of Biochemistry, School of Dental Medicine; University of Pennsylvania, Philadelphia, USA 19104-6303.
G3 (Bethesda). 2021 Sep 27;11(10). doi: 10.1093/g3journal/jkab241.
Rapeseed is a globally cultivated commercial crop, primarily grown for its oil. High-density single nucleotide polymorphism (SNP) arrays are widely used as a standard genotyping tool for rapeseed research, including for gene mapping, genome-wide association studies, germplasm resource analysis, and cluster analysis. Although considerable rapeseed genome sequencing data have been released, DNA arrays are still an attractive choice for providing additional genetic data in an era of high-throughput whole-genome sequencing. Here, we integrated re-sequencing DNA array data (32,216, 304 SNPs) from 505 inbred rapeseed lines, allowing us to develop a sensitive and efficient genotyping DNA array, Bnapus50K, with a more consistent genetic and physical distribution of probes. A total of 42,090 high-quality probes were filtered and synthesized, with an average distance between adjacent SNPs of 8 kb. To improve the practical application potential of this array in rapeseed breeding, we also added 1,618 functional probes related to important agronomic traits such as oil content, disease resistance, male sterility, and flowering time. The additional probes also included those specifically for detecting genetically modified material. These probes show a good detection efficiency and are therefore useful for gene mapping, along with crop variety improvement and identification. The novel Bnapus50K DNA array developed in this study could prove to be a quick and versatile genotyping tool for B. napus genomic breeding and research.
油菜是一种全球广泛种植的商业作物，主要用于生产其油脂。高密度单核苷酸多态性（SNP）芯片被广泛用作油菜研究的标准基因分型工具，包括基因定位、全基因组关联研究、种质资源分析和聚类分析。尽管已经发布了大量油菜基因组测序数据，但在高通量全基因组测序时代，DNA 芯片仍然是提供额外遗传数据的有吸引力的选择。在这里，我们整合了来自 505 个自交油菜品系的重测序 DNA 芯片数据（32216 个 304 个 SNP），使我们能够开发出一种敏感且高效的基因分型 DNA 芯片 Bnapus50K，其探针具有更一致的遗传和物理分布。共筛选和合成了 42090 个高质量探针，相邻 SNP 之间的平均距离为 8kb。为了提高该阵列在油菜育种中的实际应用潜力，我们还添加了 1618 个与重要农艺性状（如含油量、抗病性、雄性不育和开花时间）相关的功能探针。此外，这些探针还包括那些专门用于检测转基因材料的探针。这些探针具有良好的检测效率，因此可用于基因定位以及作物品种改良和鉴定。本研究开发的新型 Bnapus50K DNA 芯片有望成为油菜基因组育种和研究的快速多功能基因分型工具。
