Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (<i>Oryza sativa</i> L.).

Haplotype Analysis for Candidate Genes We screened potential candidate genes for cold tolerance when they met at least one of the following criteria: (1) We would match the genes with extremely significant as-sociation SNPs ( p -value < 1/N) in each characteristic (the downstream genes are selected if the SNP is located between the genes) as important candidate genes; (2) The funRiceGenes database [ 24 ] and the Nipponbare reference genome IRGSP 1.0 [ 25 ] were used to locate genes with abiotic stress-related functional annotations.

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