Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm.

IF 6.2 1区 生物学 Q1 PLANT SCIENCES The Plant Journal Pub Date : 2024-10-25 DOI:10.1111/tpj.17088
Yan Naing Win, Tyll Stöcker, Xuelian Du, Alexa Brox, Marion Pitz, Alina Klaus, Hans-Peter Piepho, Heiko Schoof, Frank Hochholdinger, Caroline Marcon
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Abstract

The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) stock with dent (B73, Co125) and flint (DK105, EP1, and F7) germplasm, resulting in the generation of 8064 mutagenized BonnMu F2-families. Sequencing of these Mu-tagged families revealed 425 924 presumptive heritable Mu insertions affecting 36 612 (83%) of the 44 303 high-confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425 924 total insertions/36 612 affected genes) and 53 insertions per BonnMu F2-family (425 924 total insertions/8064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F2-families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the presumptive germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene-dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5' untranslated region of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163 843 of 425 924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies.

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扩充波恩姆(BonnMu)转座子诱导的玉米(Zea mays L.)齿状和燧状种质突变序列索引库。
BonnMu 资源是为玉米功能基因组学研究而设计的转座子标记突变体集合。为了扩大这一资源,我们将活性突变体(Mu)种群与凹痕(B73、Co125)和火石(DK105、EP1 和 F7)种质杂交,产生了 8064 个诱变的 BonnMu F2 家族。对这些带有 Mu 标记的家系进行测序,发现 425 924 个推定的可遗传 Mu 插入影响了 44 303 个高置信度玉米基因模型(B73v5)中的 36 612 个(83%)。我们平均观察到每个基因有 12 个 Mu 插入(425 924 个总插入/36 612 个受影响基因),每个 BonnMu F2 家系有 53 个插入(425 924 个总插入/8064 个家系)。可通过玉米遗传学和基因组学数据库(MaizeGDB)访问波恩穆 F2 家系的穆插入基因和幼苗表型照片。通过自动突变测序工作流实用程序(MuWU)进行的下游检查发现,94% 的推定胚芽插入位点位于基因区,只有 6% 的小部分插入基因组的非编码基因间序列。一致的是,Mu插入位点与基因密集的染色体臂一致。总共有 42% 的 BonnMu 插入位于基因的 5' 非翻译区,与可访问的染色质相对应。此外,38%的插入基因(425 924个插入基因中的163 843个)的Mu1、Mu8和MuDR被证实是致病的Mu元件。我们可公开访问的欧洲波恩Mu资源拥有涵盖两个主要种质群的插入归档,从而为正向和反向遗传学研究提供了便利。
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来源期刊
The Plant Journal
The Plant Journal 生物-植物科学
CiteScore
13.10
自引率
4.20%
发文量
415
审稿时长
2.3 months
期刊介绍: Publishing the best original research papers in all key areas of modern plant biology from the world"s leading laboratories, The Plant Journal provides a dynamic forum for this ever growing international research community. Plant science research is now at the forefront of research in the biological sciences, with breakthroughs in our understanding of fundamental processes in plants matching those in other organisms. The impact of molecular genetics and the availability of model and crop species can be seen in all aspects of plant biology. For publication in The Plant Journal the research must provide a highly significant new contribution to our understanding of plants and be of general interest to the plant science community.
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