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Additional file 1: Figure S1. The distribution of the InDel (20-90 bp) on the whole genome. Figure S2. The frequency of the InDel between 20 and 90 bp. Figure S3. Comparation of potential LInDel markers among three genomes. Figure S4. Dendrogram of 22 rice varieties derived by UPGMA from 312 LInDel markers. Figure S5. Detection of the hybrids Shanyou 63 from ZS97 and MH63 (MH63 as female parent). Figure S6. The genetic linkage map of 20 LInDel markers on chromosome 1. Four breeding markers were labeled on the corresponding position.

Figure S1. Development and genome composition of the rice populations. Figure S2. Genetic interaction analysis among Ghd7, Ghd8, PRR37 and Hd1 in the 4-gene segregating populations under NLD and NSD conditions. Figure S3. Genetic interaction analysis of Ghd7, Ghd8, PRR37 and Hd1 in the merged PRR37-segregating populations (NIL-F4) under NLD and NSD conditions. Figure S4. PRR37 delays the heading date in the ghd7ghd8Hd1 background under both LD and SD conditions. Table S1. Characteristics of four heading date genes and linked markers. Table S2. The monthly average day length of growing seasons at Wuhan and Lingshui. Table S3. Haplotypes of 10 heading date genes in ZS97. Table S4. The genetic interactions in the 4-gene segregating populations under NLD and NSD conditions. Table S5. The genetic interactions among four genes on the basis of the merged PRR37-segragating populations (NIL-F4) under NLD and NSD conditions. Table S6. The heading date and spikelets per panicle of 16 homozygous 4-gene combinations under NLD and NSD conditions. Table S7. Primers used in this study. (DOCX 1337 kb)

List of twenty most dormant accessions that retained their dormancy in After-ripened seeds. This table contains names of twenty most dormant accessions, sub- population, country of origin and the germination percentages in FHS and ARS. (PDF 95 kb)

List of most dormant accessions that lost their dormancy in After-ripened seeds. This table contains names of most dormant accessions, sub- population, country of origin and the germination percentages in FHS and ARS. (PDF 105 kb)

Estimated effective number of SNPs and significant Thresholds in populations: This table shows the effective number of independent SNPs (Me) after a modified Bonferroni correction calculated using informative SNPs (M) in Whole population, Aus, indica and japonica populations. (PDF 85 kb)

The Genome-wide association mapping results for Germination Percentage (GP) of the freshly harvested seeds (FHS) in whole, Aus, indica and japonica populations. The figure shows neighbor-joining tree, histogram of the phenotypes (GP), quantile-quantile plot of the expected null distribution and the observed P-value and the Manhattan plots of GP of freshly harvested seeds in populations using LMM and LR methods. (PDF 795 kb)

The Genome-wide association mapping results for Germination Percentage (GP) of the after-ripened seeds (ARS) in whole, Aus, indica and japonica populations. The figure shows neighbor-joining tree, histogram of the phenotypes (GP), quantile-quantile plot of the expected null distribution and the observed P-value and the Manhattan plots of GP of after-ripened seeds in populations using LMM and LR methods. (PDF 823 kb)

Neighbor-joining tree of the 350 rice accessions with reference to GP: A neighbor-joining tree showing the divergent groups of the 350 rice accessions used in this study with reference to germination percentage (GP). (PDF 123 kb)

Non-synonymous SNPs in Sdr4 and GA2ox3 genes in 350 accessions used in our study. This file contains two tables (a) and (b). Table (a) contains the non-synonymous SNPs in Sdr4 and GA2ox3 genes, the SNPs position within the chromosomes, the minor and major alleles for the SNPs and the Amino acid changes in relation to the nucleotide change from major to minor alleles. The tables also shows the haplotype diversity within these two genes. Table (b) shows the number of accessions in individual sub-populations possessing any of the Sdr4 and GA2ox3 haplotypes. (PDF 101 kb)