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Journal of Integrative Agriculture  2024, Vol. 23 Issue (7): 2178-2195    DOI: 10.1016/j.jia.2023.06.032
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize
Peng Liu1*, Langlang Ma1*, Siyi Jian1, Yao He1, Guangsheng Yuan1, Fei Ge1, Zhong Chen1, Chaoying Zou1, Guangtang Pan1, Thomas Lübberstedt2, Yaou Shen1#
1 State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
2 Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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摘要  

玉米遗传转化高度依赖于幼胚诱导的胚性愈伤组织(embryonic callus, EC),而玉米胚性愈伤组织的诱导能力具有严重的基因型限制。本研究对具有不同胚性愈伤组织诱导能力的80份玉米自交系进行了基因组测序,利用新开发的流程工具(MQ2Gpipe)构建了该群体的高密度变异图谱。基于胚性愈伤组织诱导率(ratio of embryonic callus induction, REC)表型,将该群体划分成三个亚群。与高REC亚群相比,低REC亚群具有更丰富的遗传多样性。结合全基因组受选择区域分析与候选区段关联分析,本研究鉴定了与REC相关的95.23 Mb的遗传分化区域及43个关联REC的遗传变异。这些变异位点可以解释21.46%–49.46%的REC表型变异。在这些显著关联位点的连锁不平衡区域内共鉴定到103个与愈伤诱导能力相关的候选基因。这些基因主要参与了细胞周期调控、细胞分裂素调控等过程,其中MYB15EMB2745基因位于前人报道的一个与愈伤组织诱导相关的主效QTL区间。本研究发现,多个具有正效应的穗上叶面积遗传位点与几个高REC 关联的位点紧密连锁,这意味着在现代玉米自交系的选育过程中,高REC自交系可能在育种家选择优良株叶型的同时受到了协同负向选择而被淘汰。



Abstract  

Genetic transformation has been an effective technology for improving the agronomic traits of maize.  However, it is highly reliant on the use of embryonic callus (EC) and shows a serious genotype dependence.  In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline (MQ2Gpipe).  Based on the induction rate of EC (REC), these inbred lines were categorized into three subpopulations.  The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.  By integrating a genome-wide selective signature screen and region-based association analysis, we revealed 95.23 Mb of selective regions and 43 REC-associated variants.  These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.  In total, 103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.  These genes mainly participate in regulation of the cell cycle, regulation of cytokinesis, and other functions, among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.  Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci, implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Keywords:  maize       genetic transformation       embryonic callus       selective signal       association analysis  
Received: 13 March 2023   Accepted: 18 May 2023
Fund: This work was supported by the National Key Research and Development Program of China (2021YFF1000303), the National Nature Science Foundation of China (32072073, 32001500, and 32101777), and the Sichuan Science and Technology Program, China (2021JDTD0004 and 2021YJ0476).
About author:  Peng Liu, E-mail: sicau_liupeng@163.com; Langlang Ma, E-mail: sxyljxml@163.com; #Correspondence Yaou Shen, Tel: +86-28-86291865, E-mail: shenyaou@sicau.edu.cn * These authors contributed equally to this study.

Cite this article: 

Peng Liu, Langlang Ma, Siyi Jian, Yao He, Guangsheng Yuan, Fei Ge, Zhong Chen, Chaoying Zou, Guangtang Pan, Thomas Lübberstedt, Yaou Shen. 2024. Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize. Journal of Integrative Agriculture, 23(7): 2178-2195.

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