Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Plant Commun. 2022 Jul 11;3(4):100331. doi: 10.1016/j.xplc.2022.100331. Epub 2022 May 5.
Along with rapid advances in high-throughput-sequencing technology, the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research. Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers. In this study, we developed a multiplex molecular marker, the haplotype-tag polymorphism (HTP), that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map. After applying strict filtering criteria, we obtained 6,163 highly polymorphic HTPs, which were evenly distributed in the genome. Furthermore, we developed a genome-wide HTP analysis toolkit, HTPtools, which we used to establish an HTP database (HTPdb) covering the whole genomes of 3,587 maize inbred lines commonly used in breeding. A total of 172,921 non-redundant HTP allelic variations were obtained. Three major HTPtools modules combine seven algorithms (e.g., chain Bayes probability and the heterotic-pattern prediction algorithm) and a new plotting engine named "BCplot" that enables rapid visualization of the background information of multiple backcross groups. HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction. The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping, germplasm resource analyses, and genomics-informed breeding in maize.
随着高通量测序技术的快速发展，分子标记的开发和应用对于作物育种和遗传研究的进展至关重要。理想的分子标记应该能够快速对成千上万的育种材料进行基因型分析，每个材料使用数十到数百个标记。在本研究中，我们开发了一种多重分子标记，即单倍型标记多态性（haplotype-tag polymorphism，HTP），它整合了来自 3587 个玉米自交系的 Maize6H-60K 数组数据和重组块图谱的 6375 个块。应用严格的过滤标准后，我们获得了 6163 个高度多态性的 HTP，它们均匀分布在基因组中。此外，我们开发了一个全基因组 HTP 分析工具包 HTPtools，用于建立一个包含 3587 个常用育种自交系全基因组的 HTP 数据库（HTPdb）。共获得了 172921 个非冗余的 HTP 等位基因变异。HTPtools 的三个主要模块结合了七种算法（如链贝叶斯概率和杂种优势模式预测算法）和一个名为“BCplot”的新绘图引擎，能够快速可视化多个回交群体的背景信息。HTPtools 是为复杂系谱重建和玉米杂种优势模式预测等大数据分析而设计的。本研究中开发的基于 HTP 的分析策略和工具包适用于高通量基因型分析和遗传作图、种质资源分析以及基于基因组的玉米育种。
