Biparental graph strategy to represent and analyze hybrid plant genomes.
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
Author Information
Qianqian Kong: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Yi Jiang: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Mingfei Sun: Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China. ORCID
Yunpeng Wang: Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China. ORCID
Lin Zhang: College of Agriculture, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin 150030, China.
Xing Zeng: College of Agriculture, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin 150030, China.
Zhiheng Wang: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Zijie Wang: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China. ORCID
Yuting Liu: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Yuanxian Gan: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Han Liu: College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China. ORCID
Xiang Gao: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
Xuerong Yang: Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China. ORCID
Xinyuan Song: Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China.
Hongjun Liu: Modern Crop Biotechnology Research and Application Laboratory, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China. ORCID
Junpeng Shi: School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China. ORCID
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 2 hybrids, an intraspecific hybrid between 2 maize (Zea mays ssp. mays) inbred lines and an interspecific hybrid between maize and its wild relative teosinte (Z. mays ssp. parviglumis), utilizing a combination of PacBio High Fidelity 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 biparental genome graph, the haplotypic assemblies can facilitate downstream short-read-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.
