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A telomere-to-telomere genome assembly of zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

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The Crop Journal 2024年第1期12卷 142-153页

作者： Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu Tianfu Han Yadong Wang Center for Bioinformatics School of Computer Science and TechnologyHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Ministry of Agriculture Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary ***,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into ***,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong *** employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly *** assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference *** annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are ***13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier ***,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic *** summary,we deliver the first complete Chinese soybean cultivar T2T *** comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

关键词： Soybean Telomere-to-Telomere assembly zhonghuang 13 Structure variations

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QNE1 is a key flowering regulator determining the length of the vegetative period in soybean cultivars

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Science China(Life Sciences) 2022年第12期65卷 2472-2490页

作者： Zhengjun Xia Hong Zhai Yanfeng Zhang Yaying Wang Lu Wang Kun Xu Hongyan Wu Jinglong Zhu Shuang Jiao Zhao Wan Xiaobin Zhu Yi Gao Yingxiang Liu Rong Fan Shihao Wu Xin Chen Jinyu Liu Jiayin Yang Qijian Song Zhixi Tian Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyInnovation Academy for Seed DesignChinese Academy of SciencesHarbin 150081China Hybrid Rapeseed Research Center of Shaanxi Province Yangling 712100China College of Life Science Northeast Agricultural UniversityHarbin 150030China Institute of Industrial Crops Jiangsu Academy of Agricultural SciencesNanjing 210014China Huaiyin Institute of Agricultural Science of Xuhuai Region Jiangsu Academy of Agricultural SciencesHuai’an 223001China USDA ARS Soybean Genome&Improvement LabBeltsville 20705USA State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China

The soybean E1 gene is a major regulator that plays an important role in flowering time and ***,it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern *** mapped the novel quantitative trait locus QNE1(QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping *** cloning revealed Glyma.06G204300,encoding a TCP-type transcription factor,as a strong candidate gene for *** analysis further confirmed that functional single nucleotide polymorphisms(SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering *** protein encoded by the candidate gene is localized primarily to the ***,soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early *** conclude that despite their similar effects on flowering time,QNE1 and E4 may control flowering time through different regulatory mechanisms,based on expression studies and weighted gene co-expression network analysis of flowering time-related *** the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation.

关键词： QNE1 soybean TCP flowering time vegetative period maturity zhonghuang 13

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