Data from: 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 after cold
stress, and 43 were detected during the post-recovery phase. A total of 42
QTL regions were significant at FDR<0.001 and -log10(P-values)
> 5. In addition, 31 novel GWAS-QTLs, three colocalized GWAS-QTL
hotspots, and eight colocalized GWAS-QTLs for two traits sharing the same
genomic location were also identified. The results of this study may help
in further elucidating the molecular mechanisms underlying cold tolerance
as well as aid in developing climate-smart rice varieties for chilling
stress conditions.