A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome
文献类型： 外文期刊
作者： Wang, Rui 1 ; Yang, Yang 1 ; Tian, Hongli 1 ; Yi, Hongmei 1 ; Xu, Liwen 1 ; Lv, Yuanda 2 ; Ge, Jianrong 1 ; Zhao, Yikun 1 ; Wang, Lu 1 ; Zhou, Shiliang 3 ; Wang, Fengge 1 ;
作者机构： 1.Beijing Acad Agr & Forest Sci BAAFS, Maize Res Inst, Beijing Key Lab Maize DNA Fingerprinting & Mol Bre, Key Lab Crop DNA Fingerprinting Innovat & Utilizat, Beijing 100097, Peoples R China
2.Jiangsu Acad Agr Sci, Nanjing 210014, Peoples R China
3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot LSEB, Beijing 100093, Peoples R China
关键词： chloroplast; SNP; InDel; high throughput; genotyping; maize
期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）
ISSN：
年卷期： 2024 年 15 卷 3 期
页码：
收录情况： SCI
摘要： Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.
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