State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100091, China.
Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
J Integr Plant Biol. 2024 Apr;66(4):645-659. doi: 10.1111/jipb.13637. Epub 2024 Mar 7.
ChinaMu is the largest sequence-indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu-tag isolation method Mu-Tn5-seq (MuT-seq). Compared to the previous method used by ChinaMu, MuT-seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT-seq, we identified 113,879 germinal insertions from 3,168 Mu-active F families. We also assembled a high-quality genome for the Mu-active line Mu-starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu-starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu-starter line. The Mu-starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions. These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.
中国 Mu 是最大的序列索引突变异位（Mu）转座子插入库在玉米（Zea mays）中。在这项研究中，我们对中国 Mu 库的大小和质量进行了重大改进。我们开发了一种新的 Mu 标签分离方法 Mu-Tn5-seq（MuT-seq）。与中国 Mu 使用的先前方法相比，MuT-seq 回收了 1/3 更多的生殖插入，而仅需要大约 1/14 的测序体积和 1/5 的实验时间。使用 MuT-seq，我们从 3168 个 Mu 活性 F 家族中鉴定出 113879 个生殖插入。我们还组装了 Mu 活性系 Mu-starter 的高质量基因组，该基因组包含最初活跃的 MuDR 元素，用作突变群体的花粉供体。使用 Mu-starter 基因组，我们在 Mu-starter 系的 3244 个（7.4%）基因中恢复了 33662 个（15.6%）额外的生殖插入。Mu-starter 基因组还改进了 117689 个（54.5%）生殖插入的分配。新升级的中国 Mu 数据集目前包含 215889 个高质量的生殖插入。这些插入覆盖了 Mu-starter 和 B73Ref5 基因组中的 32224 个泛基因，包括这两个基因组共享的 23006 个（80.4%）核心基因。作为测试模型，我们研究了 Mu 插入在五肽重复（PPR）超家族中的情况，发现中国 Mu 中 92%（449/487）的 PPR 基因有插入，这表明中国 Mu 作为玉米功能基因组学资源的有用性。
