Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

Jingfen Huang, Yilin Zhang, Yapeng Li, Meng Xing, Cailin Lei, Shizhuang Wang, Yamin Nie, Yanyan Wang, Mingchao Zhao, Zhenyun Han, Xianjun Sun, Han Zhou, Yan Wang, Xiaoming Zheng, Xiaorong Xiao, Weiya Fan, Ziran Liu, Wenlong Guo, Lifang Zhang, Yunlian Cheng, Qian Qian, Hang He (), Qingwen Yang () and Weihua Qiao ()
Additional contact information
Jingfen Huang: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Yilin Zhang: State Key Laboratory of Protein and Plant Gene Research, Peking University
Yapeng Li: Chinese Academy of Agricultural Sciences
Meng Xing: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Cailin Lei: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Shizhuang Wang: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Yamin Nie: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Yanyan Wang: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Mingchao Zhao: Chinese Academy of Agricultural Sciences
Zhenyun Han: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Xianjun Sun: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Han Zhou: State Key Laboratory of Protein and Plant Gene Research, Peking University
Yan Wang: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Xiaoming Zheng: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Xiaorong Xiao: Chinese Academy of Agricultural Sciences
Weiya Fan: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Ziran Liu: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Wenlong Guo: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Lifang Zhang: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Yunlian Cheng: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Qian Qian: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Hang He: State Key Laboratory of Protein and Plant Gene Research, Peking University
Qingwen Yang: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Weihua Qiao: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Date: 2024
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DOI: 10.1038/s41467-024-48845-6

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