Assembly of a high-quality reference genome and characterization of a chemical-mutagenized library of an elite soybean cultivar Tianlong 1

Yinghua Sheng; Yicheng Huang; Zilun Jin; Xuyan Wang; Chenghui Liu; Jingwen Zhang; Zhipeng Zhou; Chuang Ma; Jianwei Zhang; Min Chen

doi:10.1016/j.jgg.2025.08.006

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Assembly of a high-quality reference genome and characterization of a chemical-mutagenized library of an elite soybean cultivar Tianlong 1

doi: 10.1016/j.jgg.2025.08.006

a. Sanya Institute of Henan University, Sanya, Hainan 572025, China;
b. State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China;
c. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China;
d. College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430074, China;
e. State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China

Funds:

This work was supported by the National Natural Science Foundation of China (grant number 31970344) and Joint Funds of the Natural Science Foundation of Hainan Province (grant number 2021JJLH0065).

Received Date: 2025-06-01
Accepted Date: 2025-08-13
Rev Recd Date: 2025-08-12

Available Online: 2025-08-26

Abstract

Abstract

Soybean (Glycine max L.) is a globally vital crop for oil production and food security. High-quality genomic resources are instrumental for both functional genomics and breeding. Here, we report a near-complete, high-quality genome assembly of the elite cultivar Tianlong 1 (TL1), featuring fully resolved telomeres and centromeres, as well as a gap-free assembly of 14 of its 20 chromosomes. On the basis of the genome assembly, we generate an ethyl methanesulfonate (EMS)-mutagenized population comprising 2,555 M₇ plants. Whole-genome re-sequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms (SNPs) and 542,709 insertions/deletions (InDels), achieving 91.89% coverage of predicted protein-coding genes. Phenotypic screening demonstrates robust genotype–phenotype associations, with two nonsynonymous mutants displaying pronounced defects in seed and leaf development. Collectively, the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.
- Soybean,
- EMS mutant library,
- Tianlong 1,
- SNP,
- InDels,
- High-quality genome

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