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.

为探究水稻（Oryza sativa）萌发期的耐寒性，本研究利用包含257份水稻种质的新型多样性群体，以及源自7K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记阵列的5185个SNP标记，开展了全基因组关联分析（Genome-Wide Association Study, GWAS）。基因分型采用遵循Infinium HD Array Ultra实验流程的7K Illumina iSelect定制阵列完成。这款命名为C7AIR的7K阵列由康奈尔大学Susan McCouch博士实验室开发，共包含7098个SNP位点（Morales等人，2020，待刊）。在对257份水稻种质完成7K阵列基因分型后，我们剔除了分型质量不佳的SNP标记：即检出率低于90%、次要等位基因频率低于5%或杂合率高于20%的SNP位点。经过滤后获得的5185个高质量SNP标记被用于开展全基因组关联分析，本数据集公开了257份水稻种质对应的5185个SNP标记的基因型数据。