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，Weihua Qiao

Nature Communications; 2024; IF 16.60

DOI: 10.1038/s41467-024-48845-6

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.