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

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 KaepplerShawn M. Kaeppler, Yunjun Liu, Nathan Springer, Patrick S. Schnable, Guoying Wang, Frank F. White, Sanzhen Liu

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number175
JournalGenome biology
Volume22
Issue number1
DOIs
StatePublished - Dec 2021

Bibliographical note

Funding Information:
We thank Drs. Candice A.C. Gardner and Mark J. Millard at the North Central Regional Plant Introduction Station for distributing A188 seeds, Dr. Candice Hirsch from the University of Minnesota to provide guidance of tissue collection for RNA-Seq, Dr. Kathleen J. Newton from the University of Missouri for the discussion of NUMT and NUPT in maize genomes, Dr. Bill Tracy for the information about the A188 origin, and Drs. Christopher Toomajian and Guihua Bai for comments on the manuscript before publication. We thank the Doubled Haploid Facility at Iowa State University for producing DH lines and computational support from the Beocat High-Performance Computing Facility at Kansas State University. We thank funding support from the US National Science Foundation (awards No. 1741090 and 1656006), the USDA’s National Institute of Food and Agriculture (award no. 2018-67013-28511), and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences. This is the contribution number 21-040-J from the Kansas Agricultural Experiment Station.

Funding Information:
We thank Drs. Candice A.C. Gardner and Mark J. Millard at the North Central Regional Plant Introduction Station for distributing A188 seeds, Dr. Candice Hirsch from the University of Minnesota to provide guidance of tissue collection for RNA-Seq, Dr. Kathleen J. Newton from the University of Missouri for the discussion of NUMT and NUPT in maize genomes, Dr. Bill Tracy for the information about the A188 origin, and Drs. Christopher Toomajian and Guihua Bai for comments on the manuscript before publication. We thank the Doubled Haploid Facility at Iowa State University for producing DH lines and computational support from the Beocat High-Performance Computing Facility at Kansas State University. We thank funding support from the US National Science Foundation (awards No. 1741090 and 1656006), the USDA?s National Institute of Food and Agriculture (award no. 2018-67013-28511), and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences. This is the contribution number 21-040-J from the Kansas Agricultural Experiment Station. Kevin Pang was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The review history is available as Additional file 12.

Publisher Copyright:
© 2021, The Author(s).

Keywords

  • Genome assembly
  • Kernel color
  • Long reads
  • Maize
  • Structural variation

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