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

文献类型： 外文期刊

作者： Huang, Jingfen 1 ; Zhang, Yilin 2 ; Li, Yapeng 5 ; Xing, Meng 1 ; Lei, Cailin 1 ; Wang, Shizhuang 1 ; Nie, Yamin 1 ; Wang, Yanyan 1 ; Zhao, Mingchao 5 ; Han, Zhenyun 1 ; Sun, Xianjun 1 ; Zhou, Han 2 ; Wang, Yan 4 ; Zheng, Xiaoming 1 ; Xiao, Xiaorong 5 ; Fan, Weiya 1 ; Liu, Ziran 1 ; Guo, Wenlong 1 ; Zhang, Lifang 1 ; Cheng, Yunlian 1 ; Qian, Qian 1 ; He, Hang 2 ; Yang, Qingwen 1 ; Qiao, Weihua 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Crop Sci, State Key Lab Crop Gene Resources & Breeding, Beijing, Peoples R China

2.Peking Univ, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

3.Peking Univ, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

4.Peking Univ, Shandong Lab Adv Agr Sci Weifang, Inst Adv Agr Sci, Weifang, Shandong, Peoples R China

5.Chinese Acad Agr Sci, Natl Nanfan Res Inst Sanya, Sanya, Hainan, Peoples R China

6.Hainan Acad Agr Sci, Haikou, Hainan, Peoples R China

期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.7； 五年影响因子：16.1 ）

ISSN：

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： 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. Genetic variation present in wild rice is a reservoir of useful genes for rice breeding. Here, the authors report the haplotype-resolved gapless genome assembly of wild rice, the development of two sets of chromosome segment substitution lines, and the cloning of a blast resistance gene originated from wild rice.

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