Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement

Nie, Shujun, Wang, Bo, Ding, Haiping, Lin, Haijian, Zhang, Li, Li, Qigui, Wang, Yujiao, Zhang, Bin, Liang, Anping, Zheng, Qi, Wang, Hui, Lv, Huayang, Zhu, Kun, Jia, Minghui, Wang, Xiaotong, Du, Jiyuan, Zhao, Runtai, Jiang, Zhenzhen, Xia, Caina, Qiao, Zhenghao, Li, Xiaohu, Liu, Boyan, Zhu, Hongbo, An, Rong, Li, Yucui, Jiang, Qian, Chen, Benfang, Zhang, Hongkai, Wang, Dening, Tang, Changxiao, Yuan, Yang, Dai, Jie, Zhan, Jing, He, Weiqiang, Wang, Xuebo, Shi, Jian, Wang, Bin, Gong, Min, He, Xiujing, Li, Peng, Huang, Li, Li, Hui, Pan, Chao, Huang, Hong, Yuan, Guangsheng, Lan, Hai, Nie, Yongxin, Li, Xinzheng, Zhao, Xiangyu, Zhang, Xiansheng, Pan, Guangtang, Wu, Qingyu, Xu, Fang, Zhang, Zhiming (July 2021) Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement. The Plant journal : for cell and molecular biology. ISSN 1365-313X

Abstract

Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
organism description > plant behavior
organism description > plant behavior > crop yield improvement
organs, tissues, organelles, cell types and functions > tissues types and functions > endosperm
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations
organs, tissues, organelles, cell types and functions
organism description > plant
organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:
Depositing User: Sasha Luks-Morgan
Date: 12 July 2021
Date Deposited: 25 Aug 2021 14:38
Last Modified: 25 Jan 2024 15:45
Related URLs:
URI: https://repository.cshl.edu/id/eprint/40332

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