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...

水稻（Oryza sativa L.）因其起源于热带与亚热带区域，易受到15℃以下低温的不利影响，进而制约其生长与籽粒产量。在苗期与营养生长期，冷胁迫会导致叶片卷曲、分蘖减少、生长迟缓、失绿及坏死。鉴于该性状的重要性，从更广范围的种质资源库中挖掘遗传资源以鉴定新的耐寒性种质来源，将是关键研究步骤。为此，我们针对由238份水稻种质组成的新型多样性群体，使用C7AIR单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片开展了全基因组关联分析（Genome-wide Association Study, GWAS）。本实验在可控生长条件下进行，针对7个性状与4个指标进行了评估，相关数据分别在三个时间节点采集：冷处理前、冷胁迫处理后及恢复培养阶段。最终共鉴定出77个与21个耐寒性及相关目标性状相关的显著GWAS-数量性状位点（Quantitative Trait Locus, QTL），其中34个[原文内容未完整呈现]。
# 数据集来源：水稻苗期耐寒性及恢复相关性状的全基因组关联分析研究
https://doi.org/10.5061/dryad.k6djh9wg4

用于水稻耐寒性全基因组关联分析的基因型数据SNP矩阵文件（SNP标记以行表示，水稻种质以列表示）。本研究使用了源自Cornell_7K_Array_Infinium_Rice Array（C7AIR; Morales等，2020）的基因型数据，该芯片包含7098个SNP标记。

## 数据与文件结构说明
为获取238份水稻种质的基因型数据，本研究使用了包含7098个SNP标记的Cornell_7K_Array_Infinium_Rice Array（C7AIR; Morales等，2020）芯片。经筛选（次要等位基因频率（Minor Allele Frequency, MAF）≥5%、SNP检出率≥90%）后，最终共保留4902个SNP标记用于全基因组关联分析（详见补充表S3）。

## 共享与获取说明
本数据源自以下来源：
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224494/](https://www.ncbi.nlm...)