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Biparental graph strategy to represent and analyze hybrid plant genomes

文献类型： 外文期刊

作者： Kong, Qianqian 1 ; Jiang, Yi 1 ; Sun, Mingfei 2 ; Wang, Yunpeng 3 ; Zhang, Lin 4 ; Zeng, Xing 4 ; Wang, Zhiheng 1 ; Wang, Zijie 1 ; Liu, Yuting 1 ; Gan, Yuanxian 1 ; Liu, Han 5 ; Gao, Xiang 1 ; Yang, Xuerong 2 ; Song, Xinyuan 3 ; Liu, Hongjun 2 ; Shi, Junpeng 1 ;

作者机构： 1.Sun Yat Sen Univ, Sch Agr & Biotechnol, Shenzhen Campus, Shenzhen 518107, Peoples R China

2.Shandong Agr Univ, Coll Life Sci, Modern Crop Biotechnol Res & Applicat Lab, Tai An 271018, Peoples R China

3.Jilin Acad Agr Sci, Inst Agr Biotechnol, Jilin Prov Crop Transgen Sci & Technol Innovat Ctr, Changchun 130033, Peoples R China

4.Northeast Agr Univ, Coll Agr, Changjiang Rd, Harbin 150030, Peoples R China

5.Beijing Univ Agr, Coll Plant Sci & Technol, Beijing 102206, Peoples R China

期刊名称：PLANT PHYSIOLOGY （ 影响因子：6.5； 五年影响因子：7.6 ）

ISSN： 0032-0889

年卷期： 2024 年

页码：

收录情况： SCI

摘要： 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. The assembly and phasing of 2 hybrid plant genomes enable the development of a biparental graph strategy to represent and analyze these hybrid genomes.

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