J Integr Plant Biol ›› 2026, Vol. 68 ›› Issue (2): 366-382.DOI: 10.1111/jipb.70099

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  • 收稿日期:2025-08-17 接受日期:2025-11-05 出版日期:2026-02-02 发布日期:2026-02-03

Near-complete genome assembly of a transformation-efficient elite inbred line LH244 and its comparison with B73

Kaiwen Tan1†, Xinxiang Liu2†, Zijian Wang1, Zhengquan Zhang1, Wei Huang1, Shengnan Liu1, Zhen Lin1, Haiming Zhao1, Hainan Zhao1,3, Yang Liu4, Fangpu Han4,5, Jinsheng Lai1,3,6,7*, Weibin Song1,7*, Jiuran Zhao2* and Jian Chen1,3*   

  1. 1. State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, China Agricultural University, Beijing 100193, China

    2. Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China

    3. Frontiers Science Center for Molecular Design Breeding (Ministry of Education), China Agricultural University, Beijing 100193, China

    4. State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

    5. University of Chinese Academy of Sciences, Beijing 100049, China

    6. Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China

    7. Sanya Institute of China Agricultural University, Sanya 572025, China

    †These authors contributed equally to this work.

    *Correspondences: Jinsheng Lai (jlai@cau.edu.cn); Weibin Song (songweibin@cau.edu.cn); Jiuran Zhao (maizezhao@126.com); Jian Chen (jianchen@cau.edu.cn, Dr. Chen is fully responsible for the distribution of all materials associated with this article)

  • Received:2025-08-17 Accepted:2025-11-05 Online:2026-02-02 Published:2026-02-03
  • Supported by:
    This work was supported by the Biological Breeding—Major Projects (2023ZD04074), the National Natural Science Foundation of China (32425041,32271541 and 32572347), Innovation Capabilities Construction Project of Beijing Academy of Agriculture and Forestry Sciences (KJCX20210410), the National Key Research and Development Program of China (2021YFD1200701), and Joint Research on Maize Improvement of Henan (2022010202).

Abstract: The highly transformable maize inbred line LH244 represents an attractive model for gene discovery and genome engineering. However, the lack of a high-quality genome assembly has limited its utility in functional genomics research. Here, we present a 2.29 Gb near-complete assembly of the LH244 maize genome, with an overall base accuracy of 99.998%. Except for five gaps associated with super-long thymine–adenine–guanine (TAG) repeat arrays, all the genome sequences were assembled from telomere to telomere (T2T). Comparative analysis revealed high genetic similarity between LH244 and B73, including 80.06% genome-wide synteny and 90.92% of genes nearly identical. The LH244 genome was also compared with the complete Mo17 genome and revealed extensive intraspecific genomic variations. A total of 14 megabase-scale structural variations (SVs) were identified, including a 3.15 Mb insertion, harboring 95 genes, within the 45S rDNA array of LH244 but not in the Mo17 genome. In addition, there were five knob arrays, with an average size of 21.76 Mb and the longest of 38.70 Mb, only existing in the LH244 genome. Despite the substantial variation in knob abundance, knob-6S and knob-8L were highly conserved between LH244 and Mo17, showing strong synteny and sequence identity, as well as consistent insertion patterns of genes and transposable elements (TEs). Overall, our study provides a near-complete reference genome of an important transformable maize germplasm, which will serve as a much-needed resource for functional genomics and genome editing of maize.

Key words: comparative genomics, knob, LH244, maize, near‐complete assembly

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