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

IF 6 1区 农林科学 Q1 AGRONOMY
Ting Li , Shutu Xu , Jiawen Zhao , Yapeng Wang , Jun Zhang , Xin Wei , Jianzhou Qu , Ruisu Yu , Xinghua Zhang , Chuang Ma , Jiquan Xue
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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.

KA105 的基因组组装--玉米分子育种和基因组研究的新资源
优良近交系是玉米育种的核心,是自然变异的来源。虽然许多优良品系已经测序,但对新开发品系的测序关注较少。我们构建了精英近交系 KA105 的基因组组装,该近交系是最近由一个名为 "陕A "的人工育种群体培育出来的,已显示出育种所需的理想特性。其血统显示与 B73 及其血统中的其他品系存在遗传差异。与 B73 参考基因组的比较发现了广泛的结构变异、58 个存在/不存在变异(PAV)基因和 1023 个扩展基因家族,其中一些可能与抗病性有关。通过对胁迫诱导转录组进行基于网络的整合分析,发现了13个KA105特异的PAV基因,其中8个基因至少被一种胁迫诱导,参与响应干旱和南方叶枯病等胁迫的基因模块。在果仁发育过程中,KA105 和 B73 之间有 20 多万个基因对存在差异相关。KA105 参考基因组和转录组图谱是进一步改良种质、调查玉米基因组变异和基因功能的资源。
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来源期刊
Crop Journal
Crop Journal Agricultural and Biological Sciences-Agronomy and Crop Science
CiteScore
9.90
自引率
3.00%
发文量
638
审稿时长
41 days
期刊介绍: The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics. The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.
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