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, Qianqian Kong School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Yi Jiang School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Mingfei Sun Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University , Tai'an 271018 , China Search for other works by this author on: Oxford Academic Yunpeng Wang Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences , Changchun, 130033 , China Search for other works by this author on: Oxford Academic Lin Zhang Northeast Agricultural University, Changjiang Road, Xiangfang District , Harbin, 150030 , China Search for other works by this author on: Oxford Academic Xing Zeng Northeast Agricultural University, Changjiang Road, Xiangfang District , Harbin, 150030 , China Search for other works by this author on: Oxford Academic Zhiheng Wang School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Zijie Wang School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Yuting Liu School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Yuanxian Gan School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic
, Han Liu College of Plant Science and Technology, Beijing University of Agriculture , Beijing, 102206 , China Search for other works by this author on: Oxford Academic Xiang Gao School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Search for other works by this author on: Oxford Academic Xuerong Yang Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University , Tai'an 271018 , China Search for other works by this author on: Oxford Academic Xinyuan Song Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences , Changchun, 130033 , China Corresponding authors: Junpeng Shi (shijp6@mail.sysu.edu.cn), Hongjun Liu (HongjunL@sdau.edu.cn) & Xinyuan Song (songxinyuan1980@163.com) Search for other works by this author on: Oxford Academic Hongjun Liu Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University , Tai'an 271018 , China Corresponding authors: Junpeng Shi (shijp6@mail.sysu.edu.cn), Hongjun Liu (HongjunL@sdau.edu.cn) & Xinyuan Song (songxinyuan1980@163.com) Search for other works by this author on: Oxford Academic Junpeng Shi School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, 518107 , China Corresponding authors: Junpeng Shi (shijp6@mail.sysu.edu.cn), Hongjun Liu (HongjunL@sdau.edu.cn) & Xinyuan Song (songxinyuan1980@163.com) Search for other works by this author on: Oxford Academic
Qianqian Kong and Yi Jiang contributed equally to this work
Author Notes
Plant Physiology, kiae375, https://doi.org/10.1093/plphys/kiae375
Published:
11 July 2024
Article history
Received:
14 May 2024
Revision received:
14 May 2024
Accepted:
20 June 2024
Published:
11 July 2024
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Qianqian Kong, Yi Jiang, Mingfei Sun, Yunpeng Wang, Lin Zhang, Xing Zeng, Zhiheng Wang, Zijie Wang, Yuting Liu, Yuanxian Gan, Han Liu, Xiang Gao, Xuerong Yang, Xinyuan Song, Hongjun Liu, Junpeng Shi, Bi-parental graph strategy to represent and analyze hybrid plant genomes, Plant Physiology, 2024;, kiae375, https://doi.org/10.1093/plphys/kiae375
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Abstract
Hybrid plants are found extensively in the wild, and they often demonstrate superior performance of complex traits over their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges associated with genome assembly and the lack of appropriate methodologies for their subsequent representation and analysis. Here, we present the assembly and analysis of two hybrids, an intraspecific hybrid between two maize (Zea may ssp. mays) inbred lines and an interspecific hybrid between maize and its wild relative teosinte (Zea may ssp. parviglumis), utilizing a combination of PacBio High Fidelity (HiFi) sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well-phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a bi-parental genome graph, the haplotypic assemblies can facilitate downstream short-reads-based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over a single linear genome. Our work offers a comprehensive workflow that aims to facilitate the decoding of numerous hybrid plant genomes, particularly those with unknown or inaccessible parentage, thereby enhancing our understanding of genome evolution and heterosis.
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Author notes
Qianqian Kong and Yi Jiang contributed equally to this work
© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
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