TY - JOUR
T1 - Development of SNP Markers for the Identification of Commercial Korean Watermelon Cultivars Using Fluidigm Genotyping Analysis
AU - Park, Jun Young
AU - Jang, Yoon Jeong
AU - Jung, Jin Kee
AU - Shim, Eun Jo
AU - Sim, Sung Chr
AU - Chung, Sang Min
AU - Lee, Gung Pyo
N1 - Publisher Copyright:
© 2022 Korean Society for Horticultural Science.
PY - 2022
Y1 - 2022
N2 - Molecular markers based on simple sequence repeats (SSRs) from expressed sequence tags (ESTs) have been used to identify the registered commercial cultivars in watermelon (Citrullus lanatus). To characterize diversity in watermelon cultivars, molecular markers based on genome-wide single nucleotide polymorphisms (SNPs) are needed. Here, we used Fluidigm genotyping for the development of a core set of SNPs to differentiate Korean watermelon commercial cultivars. A candidate subset of SNPs was discovered by genotyping-by-sequencing using 48 F1 cultivars. The cultivars could be divided into three subpopulations with 97.5% similarity by unweighted pair group method with arithmetic mean (UPGMA) clustering based on 2,300 SNPs. After filtering loci with a high poly-morphism information content (PIC), a subset of 238 SNPs was selected and analyzed in 92 F1 cultivars on the Fluidigm genotyping system. Among these, 141 polymorphic, bi-allelic SNPs were obtained. To evaluate genetic diversity in 92 cultivars, a principal component analysis (PCA) and hierarchical clustering analysis were performed. The first two axes of the PCA explained only 30.5% of the total variance; however, the 92 cultivars clustered into three subgroups with similar sizes. Approximately 90% of the subgroups remained unchanged in the UPGMA clustering analysis. In addition, when the subset of 141 SNPs was filtered with a threshold PIC of 0.36, a core set of 96 SNP markers were obtained, without identical clustering results. The core set of SNP markers can be used for the identification of commercial Korean watermelon cultivars and for the protection of proprietary rights for new cultivar development.
AB - Molecular markers based on simple sequence repeats (SSRs) from expressed sequence tags (ESTs) have been used to identify the registered commercial cultivars in watermelon (Citrullus lanatus). To characterize diversity in watermelon cultivars, molecular markers based on genome-wide single nucleotide polymorphisms (SNPs) are needed. Here, we used Fluidigm genotyping for the development of a core set of SNPs to differentiate Korean watermelon commercial cultivars. A candidate subset of SNPs was discovered by genotyping-by-sequencing using 48 F1 cultivars. The cultivars could be divided into three subpopulations with 97.5% similarity by unweighted pair group method with arithmetic mean (UPGMA) clustering based on 2,300 SNPs. After filtering loci with a high poly-morphism information content (PIC), a subset of 238 SNPs was selected and analyzed in 92 F1 cultivars on the Fluidigm genotyping system. Among these, 141 polymorphic, bi-allelic SNPs were obtained. To evaluate genetic diversity in 92 cultivars, a principal component analysis (PCA) and hierarchical clustering analysis were performed. The first two axes of the PCA explained only 30.5% of the total variance; however, the 92 cultivars clustered into three subgroups with similar sizes. Approximately 90% of the subgroups remained unchanged in the UPGMA clustering analysis. In addition, when the subset of 141 SNPs was filtered with a threshold PIC of 0.36, a core set of 96 SNP markers were obtained, without identical clustering results. The core set of SNP markers can be used for the identification of commercial Korean watermelon cultivars and for the protection of proprietary rights for new cultivar development.
KW - Additional F hybrids
KW - Genetic relationship
KW - Genotyping-by-sequencing
KW - PCA
KW - Population structure
UR - http://www.scopus.com/inward/record.url?scp=85125748880&partnerID=8YFLogxK
U2 - 10.7235/HORT.20220008
DO - 10.7235/HORT.20220008
M3 - Article
AN - SCOPUS:85125748880
SN - 1226-8763
VL - 40
SP - 75
EP - 84
JO - Horticultural Science and Technology
JF - Horticultural Science and Technology
IS - 1
ER -