Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.)

Panax ginseng C. A. Mey., a perennial herb belonging to the family Araliaceae, is a valuable medicinal plant with distinctive biological characteristics. However, comprehensive analyses of the mitochondrial genome (mitogenome) are lacking. In this study, we sequenced the complete mitogenome of ginse...

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Published inAgronomy (Basel) Vol. 10; no. 12; p. 1868
Main Authors Jang, Woojong, Lee, Hyun Oh, Kim, Jang-Uk, Lee, Jung-Woo, Hong, Chi-Eun, Bang, Kyong-Hwan, Chung, Jong-Wook, Jo, Ick-Hyun
Format Journal Article
LanguageEnglish
Published Basel MDPI AG 01.12.2020
Subjects
Alleles
breeding
Chloroplasts
Comparative analysis
Cultivars
Deoxyribonucleic acid
DNA
Error correction & detection
Genetic diversity
Genomes
Genomics
Genotypes
Ginseng
Herbal medicine
Kompetitive allele-specific PCR
Markers
Medicinal plants
Mitochondria
mitochondrial genome
Mutation
Mutation rates
Panax ginseng
Panax ginseng C. A. Mey
Porosity
Single-nucleotide polymorphism
Thermal cycling
United Kingdom > UK
United States > US
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Summary:Panax ginseng C. A. Mey., a perennial herb belonging to the family Araliaceae, is a valuable medicinal plant with distinctive biological characteristics. However, comprehensive analyses of the mitochondrial genome (mitogenome) are lacking. In this study, we sequenced the complete mitogenome of ginseng based on long-read data from the Nanopore sequencing platform. The mitogenome was assembled into a “master circle” form of 464,705 bp and contained 72 unique genes. The genome had three large repeat regions, and 10.42% of the sequences were mitogenome sequences of plastid origin (MTPTs). In total, 278 variants (213 SNPs and 65 InDels) were discovered, most of which were identified in intergenic regions. The MTPT regions were mutational hotspots, harboring 74.5% of the variants. The ginseng mitogenome showed a higher mutation rate than that of the chloroplast genome, and this pattern is uncommon in plants. In addition, 10 Kompetitive allele-specific PCR (KASP) markers were developed from 10 SNPs, excluding those in MTPT regions. These markers accurately identified the genotypes of 59 Korean ginseng accessions and elucidated mitogenome diversity. These results provide insight into organellar genomes and genetic diversity in ginseng. Moreover, the complete mitogenome sequence and 10 KASP markers will be useful for ginseng research and breeding.
ISSN:2073-4395
2073-4395
DOI:10.3390/agronomy10121868