Genome-wide association study for traits related to cold tolerance and recovery during seedling stage in rice

Rice (Oryza sativa L.), due to its tropical and sub-tropical origin, is adversely affected by low temperatures below 15°C, restricting growth and yield. During the seedling and vegetative stage, cold stress causes curled leaves, fewer tillers, retarded growth, chlorosis, and necrosis. Due to the significance of this trait, exploring the wealth of genetic resources from a wider pool of germplasm to identify new sources of tolerance will be a crucial step. Toward this goal, we performed a genome-wide association study on a novel diversity panel of 238 rice accessions using the C7AIR SNP array. The experiment was conducted in controlled growth conditions, and rice accessions were evaluated for seven traits and four indices, which were recorded at three different time points, i.e., prior to cold treatment, after cold treatment and post-recovery phase. A total of 77 significant GWAS-QTLs were identified for 21 cold tolerance and related traits of interest. Out of these, 34 were detected afte..., , , # Data from: Genome-wide association study for traits related to cold tolerance and recovery during seedling stage in rice

[https://doi.org/10.5061/dryad.k6djh9wg4](https://doi.org/10.5061/dryad.k6djh9wg4)

SNP matrix file of genotypic data for GWAS for rice cold tolerance (SNP markers are rows, rice accessions are columns). Gentoype data obtained from the Cornell_7K_Array_Infinium_Rice Array (C7AIR; Morales et al., 2020) comprising 7,098 SNPs was used. 

## Description of the data and file structure

To access the genotypic data for the 238 rice accessions, the Cornell_7K_Array_Infinium_Rice Array (C7AIR; Morales et al., 2020) comprising 7,098 SNPs was used. After filtering for the minor allele frequency (MAF) criterion of 5% and SNP call rate of ≥90%, only a total of 4,902 SNPs were used for GWAS analysis (Supplemental Table S3).

## Sharing/Access information

Data was derived from the following sources:

* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224494/](https://www.ncbi.nlm...