Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.
Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus.
a Department of Horticulture and Breeding, Andong National University, Andong, Gyeongsangbukdo, 760-749, Republic of Korea.|b Department of Eco-Friendly Horticulture, Cheonan Yonam College, Cheonan, Chungcheongnamdo, 331-709, Republic of Korea.
Hyun Jung
HJ
Kim
a Department of Horticulture and Breeding, Andong National University, Andong, Gyeongsangbukdo, 760-749, Republic of Korea.
Jungsu
J
Jung
c Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Myung-Shin
MS
Kim
d Department of Horticultural Science, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea.
Je Min
JM
Lee
c Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Doil
D
Choi
a Department of Horticulture and Breeding, Andong National University, Andong, Gyeongsangbukdo, 760-749, Republic of Korea.|e Institute of Agricultural Science and Technology, Andong National University, Andongsi, Gyeongsangbukdo, 760-749, Republic of Korea.
Inhwa
I
Yeam
D000483:Alleles; D001483:Base Sequence; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D017343:Genes, Plant; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D031238:Platycodon / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
D018744:DNA, Plant; D005819:Genetic Markers; D018749:RNA, Plant
Platycodon grandiflorum; SNP; SSR; analyse phylogénétique; phylogenetic analysis; transcriptome