Genome-wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery during Germination in Rice

To investigate cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array using the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array, poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. A subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The genotype data of 5,185 SNP markers by 257 rice accessions is presented here.