*2.5. DNA Extraction and Fluidigm Genotyping*

Young leaves of each plant from all materials used in this study were collected for DNA extraction at the tillering stage. Genomic DNA was extracted using the modified cetyltrimethylammonium bromide (CTAB) method, as described by Murray and Thompson [31]. The concentration and purity of DNA samples were measured with a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). DNA samples, showing absorbance ratios above 1.8 at 260/280 nm, were diluted to 50 ng/μ<sup>L</sup> and used for genotyping.

Genotyping was performed using the BioMark™ HD system (Fluidigm) and 96.96 Dynamic Array IFCs (Fluidigm), according to the manufacturer's protocol in National Instrumentation Center for Environmental Management (NICEM), Seoul National University (Pyeongchang, Korea). Specific Target Amplification (STA) was performed prior to SNP genotyping analysis. PCR was performed in a 5 μL reaction containing 50 ng of the DNA sample, according to the manufacturer's protocol. For genotyping, SNPtype assays were performed using STA products, according to the manufacturer's protocol. The genotyping result was acquired using Fluidigm SNP Genotyping Analysis software. All the genotype-calling results were manually checked and any obvious errors in the homozygous or heterozygous clusters were curated.
