A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome
Author:
Wang Rui1, Yang Yang1ORCID, Tian Hongli1, Yi Hongmei1, Xu Liwen1, Lv Yuanda2ORCID, Ge Jianrong1, Zhao Yikun1, Wang Lu1, Zhou Shiliang3, Wang Fengge1
Affiliation:
1. Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China 2. Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China 3. State Key Laboratory of Systematic and Evolutionary Botany (LSEB), Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
Abstract
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.
Funder
Beijing Academy of Agricultural and Forestry Sciences
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