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

文献类型： 外文期刊

作者： Liang, Lei 1 ; Wang, Yuancong 2 ; Han, Yanbin 1 ; Chen, Yicong 1 ; Li, Mengfei 1 ; Wu, Yibo 2 ; Ma, Zeyang 1 ; Zhao, Han 2 ; Song, Rentao 1 ;

作者机构： 1.China Agr Univ, Coll Agron & Biotechnol, Natl Maize Improvement Ctr,Joint Int Res Lab Crop, State Key Lab Maize Biobreeding,Frontiers Sci Ctr, Beijing 100091, Peoples R China

2.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Jiangsu Prov Key Lab Agrobiol, Nanjing 210014, Peoples R China

3.Sanya Inst China Agr Univ, Sanya 572025, Peoples R China

4.Hainan Yazhou Bay Seed Lab, Sanya 572025, Peoples R China

关键词： ChinaMu; Mutator; MuT-seq; PPR gene; Zea mays

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：11.4； 五年影响因子：10.1 ）

ISSN： 1672-9072

年卷期： 2024 年 66 卷 4 期

页码：

收录情况： SCI

摘要： 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.

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