Computational protocol: Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice

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Protocol publication

[…] A total of 2,767,159 and 1,857,845 SNPs (minor allele frequency ≥0.05; the number of accessions with minor alleles ≥6) were used for GWAS in indica and japonica subpopulations, respectively (). Linear mixed models (LMM) were used to make associations by running the Fast-LMM program (). Population structure was controlled using a kinship matrix constructed with all SNPs. Using a method described by (), the effective numbers of independent SNPs were calculated as 571,843 and 245,348 for both indica and japonica subpopulations, respectively. The suggested P-values were specified as 1.8 × 10-6 in indica and 1.3 × 10-6 in japonica (). The thresholds were then set at P = 8.0 × 10-7 in Wuhan and P = 3.8 × 10-7 in Hainan to identify significant association signals via LMM. To obtain independent association signals, multiple SNPs exceeding the threshold in a 5-Mb sliding window were clustered by r2 of linkage disequilibrium ≥0.25, and SNPs with the minimum P-value in a cluster were considered lead SNPs. The detailed method was previously described (; ). […]

Pipeline specifications

Software tools FaST-LMM, kinship
Applications Population genetic analysis, GWAS
Organisms Oryza sativa, Oryza sativa Japonica Group
Chemicals Nitroprusside