Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

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.