数字农科院2.0

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

文献类型： 外文期刊

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

作者机构：

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

期刊名称： GENOME BIOLOGY

ISSN： 1474-7596

年卷期： 2021 年 22.0 卷 1.0 期

页码：

收录情况： JCR（2021版）

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. © 2021, The Author(s).

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