Chromosome-level genome assembly of a regenerable maize inbred line A188

文献类型： 外文期刊

第一作者： Lin, Guifang

作者： Lin, Guifang;He, Cheng;Koo, Dal-Hoe;Le, Ha;Zheng, Huakun;Lin, Jinguang;Zhao, Mingxia;Hao, Yangfan;Liu, Sanzhen;Zheng, Jun;Liu, Yan;Qin, Yang;Liu, Yunjun;Wang, Guoying;Tamang, Tej Man;Park, Sunghun;McFraland, Frank;Kaeppler, Heidi;Kaeppler, Shawn M.;Wang, Bo;Tang, Haibao;Tang, Haibao;McCarty, Donald R.;Wei, Hairong;Cho, Myeong-Je;Springer, Nathan;Schnable, Patrick S.;White, Frank F.

作者机构：

关键词： Maize; Genome assembly; Long reads; Structural variation; Kernel color

期刊名称：GENOME BIOLOGY （ 影响因子：13.583； 五年影响因子：17.433 ）

ISSN： 1474-760X

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

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