Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice

To investigate the genetic architecture underlying 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 from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following 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 (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis.  The dataset representing the genotype data of 5,185 SNP markers by 257 rice acce...

为探究水稻（Oryza sativa）萌发期耐冷性的遗传基础，我们使用源自全球的257份水稻种质资源构建的新型多样性群体，结合7K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记阵列得到的5185个SNP标记，开展全基因组关联研究（Genome-Wide Association Study, GWAS）。基因分型实验采用定制化Illumina iSelect基因分型阵列，并严格遵循Infinium HD阵列超检测方案完成。该7K阵列命名为C7AIR，由康奈尔大学Susan McCouch博士实验室开发，共包含7098个SNP标记（Morales等，2020年，同行评审中）。使用该7K阵列（C7AIR）对257份水稻种质资源完成基因分型后，我们剔除了质量不合格的SNP标记：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均被从数据集中移除。本研究最终选用过滤后得到的5185个高质量SNP标记开展全基因组关联分析。本数据集包含257份水稻种质资源的5185个SNP标记基因型数据……