4.4. Genotyping via 6K SNP Array

A total of 230 ILs of plant genomic DNA were extracted from leaf tissue using the cetyl trimethylammonium bromide (CTAB) method [145] and quantified by a NanoDrop 8000 spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA). The concentration of DNA was adjusted to 50 ng μL⁻¹, and approximately 200 ng of DNA from each genotype used in the SNP array. The complete set of the BC₁F₅ mapping population, along with the parents used for the genotyping with 6K SNP array technology, was followed by DNA quantification, incubation, and hybridization of bead chips, staining, and image scanning according to the manufacturer’s instructions for the Illumina Infinium assay, and this work was conducted in the Genotyping Services Laboratory of the International Rice Research Institute. The resulting intensity data were processed using the genotyping module V2011.1 of Genome Studio software (Illumina Inc., San Diego, CA, USA) for SNP calling. The generated genotypic data indicated that 704 high-quality SNP markers were identified and further used in the construction of high-density linkage maps for NuUE QTLs, related to agronomic and yield-attributed traits.