Genome-wide SNP genotyping of rice breeding lines

In total 431, 816, 1491, and 1029 advanced breeding lines of F₇-F₉ generations along with five released varieties (BRRI dhan28, BRRI dhan29, BRRI dhan67, BRRI dhan74, and BRRI dhan89, were evaluated for yield at multi-locations during Boro season of 2018–19, 2019–20, 2020–21, and 2021–22, respectively. The trial meta-data can be seen the Supplementary Table S1. Green leaf tissues from a representative plant of each breeding line was collected in labeled glassine bag at 4–5 weeks after transplanting and stored immediately on ice. The samples were stored in a −80°C freezer until processing for genotyping. DNA was isolated and purified according to the modified Cetyltrimmethyl Ammonium Bromide (CTAB) protocol (Aboul-Maaty and Oraby 2019 (link)). Genotyping with genome-wide 1024 SNP markers including 92 trait-specific markers named as 1K-RiCA panel (Arbelaez et al., 2019 (link)) was performed at an outsourcing genotyping service provider with the help of IRRI Genotyping Services Laboratory, The Philippines. The genotyping data of 1k-RiCA SNPs were filtered using TASSEL v5.0 (Bradbury et al., 2007 (link)) following the criteria that the individuals with more than 15% of heterozygous loci were removed, markers with more than 15% of missing values and minor allele frequency below 0.05 were removed. After filtering, 814–889 markers were retained for doing downstream analysis.