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Research paper | Open Access

Genome assembly of KA105, a new resource for maize molecular breeding and genomic research

Ting Lia,b, Shutu Xua,b( ), Jiawen Zhaoa,c, Yapeng Wanga,b, Jun Zhanga,b, Xin Weia,b, Jianzhou Qua,b, Ruisu Yua,b, Xinghua Zhanga,b, Chuang Maa,c( ), Jiquan Xuea,b( )
The Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Northwest A&F University, Yangling 712100, Shaanxi, China
Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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Abstract

Superior inbred lines are central to maize breeding as sources of natural variation. Although many elite lines have been sequenced, less sequencing attention has been paid to newly developed lines. We constructed a genome assembly of the elite inbred line KA105, which has recently been developed by an artificial breeding population named Shaan A and has shown desirable characteristics for breeding. Its pedigree showed genetic divergence from B73 and other lines in its pedigree. Comparison with the B73 reference genome revealed extensive structural variation, 58 presence/absence variation (PAV) genes, and 1023 expanded gene families, some of which may be associated with disease resistance. A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes, of which eight were induced by at least one kind of stress, participating in gene modules responding to stress such as drought and southern leaf blight disease. More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development. The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

Keywords

Genome assemblyPedigree analysisStructural variationTranscriptome atlasDifferential network

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The Crop Journal
Volume 11 Issue 6,
December 2023
Pages 1793-1804
DOI: 10.1016/j.cj.2023.08.006
Cite this article:
Li T, Xu S, Zhao J, et al. Genome assembly of KA105, a new resource for maize molecular breeding and genomic research. The Crop Journal, 2023, 11(6): 1793-1804. https://doi.org/10.1016/j.cj.2023.08.006

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Received: 10 April 2023
Revised: 18 August 2023
Accepted: 31 August 2023
Published: 22 September 2023
© 2023 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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