J Integr Plant Biol ›› 2024, Vol. 66 ›› Issue (4): 645-659.DOI: 10.1111/jipb.13637  cstr: 32098.14.jipb.13637

所属专题： Biotechnology； SDGs 目标3: 良好健康与福祉

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  • 收稿日期:2023-11-21 接受日期:2024-02-20 出版日期:2024-04-01 发布日期:2024-04-13

Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

Lei Liang1, Yuancong Wang2, Yanbin Han1, Yicong Chen1, Mengfei Li1, Yibo Wu2, Zeyang Ma1,3,4, Han Zhao2* and Rentao Song1,3,4*   

  1. 1. 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;
    2. Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
    3. Sanya Institute of China Agricultural University, Sanya 572025, China;
    4. Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
    *Correspondences:Han Zhao(zhaohan@jaas.ac.cn);Rentao Song(rentaosong@cau.edu.cn, Prof. Song is responsible for the distribution of the materials associated with this article)
  • Received:2023-11-21 Accepted:2024-02-20 Online:2024-04-01 Published:2024-04-13

Abstract: 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 F1 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.

Key words: ChinaMu, Mutator, MuT-seq, PPR gene, Zea mays

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