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

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

doi:10.1186/s13059-021-02396-x

Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionsThe 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.

Highlights

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
We identified 178 gene clusters in A188 each of which contains at least three paralogous genes, comprising in total 694 genes
We identified 2259 paralogous gene pairs of which one member was located in a high-recombination chromosomal compartment and the other in a low-recombination compartment (“Methods” section)

Summary

Introduction

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. A188 is amenable to somatic embryogenic culture and regeneration and was the first maize line used to. A popular maize transformation line, Hi-II, was isolated from offspring of a cross between A188 and B73, an elite maize reference inbred line [5, 6]. Highly valuable for plant regeneration and transformation, A188 is not agronomically desirable, having small ears and low grain yield. A188, in addition to traits related to transformability, can serve as a model inbred line for the genetic dissection of many important agronomic traits, heterosis, and plant-environment interactions

Methods

Results

Discussion

Conclusion