Classification by Nuclear Markers and Phenotype Analysis of C. annuum Accessions

We used data collected previously by Lee et al. (2016) to classify the C. annuum accessions by nuclear markers and phenotype. Lee et al. (2016) applied 48 SNP markers developed by transcriptome sequencing to a large Capsicum collection comprising 3,821 accessions. They divided the accessions into 10 clusters based on the SNP markers using the STRUCTURE program ver.2.3.4. They then created a core collection containing 240 accessions based on the 48 SNP markers and 32 phenotypic traits. The phenotype data were obtained in 2014 at a research farm (Seoul National University, Suwon, Republic of Korea) as described previously (Lee et al., 2016). The measurement of phenotype was performed in three independent individuals, and the average values were used for further analysis. We determined the differences between the mean values of groups classified by mtDNA or nuclear markers using Duncan’s multiple range tests (P < 0.05) following one-way ANOVA with the IBM SPSS statistics software (IBM Corp., Armonk, NY, USA).