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Thirteen accessions (Table 1) were used in the analysis.
Currently, IRRI holds the largest collection of African Oryza totaling to about 3601 accessions (Table 2).
The uniquely mapped reads covered approximately 94% of the Nipponbare genome in all five accessions (Table 1).
A total of 19 InDel markers were used to evaluate genetic diversity in 101 rice accessions (Table 1).
One of the three accession, W1238 also carried rufipogon-type nuclear INDELs but meridionalis-type organelle genomes like Jpn1 accessions (Table 3).
The germplasm collection of 127 rice accessions (Table 1) was chosen to evaluate the effectiveness of known molecular markers in predicting Apparent Amylose Content.
On average, the ratio of non-synonymous to synonymous SNPs was 1.16 in the five accessions (Table 3), which is similar to that found in a previous study (McNally et al. 2009).
The study employed 15 O. sativa accessions (Table 1) selected from the publically available Rice Diversity Panel 1 (Eizenga et al. 2013) and provided by Susan McCouch, Cornell University.
Mo showed the most variation with 44 significant pairwise differences between accessions (Table S1).
Several elements showed large variation between the lowest and highest accumulating accessions (Table 2).
We used 21 biallelic base-change and minisatellite sites to analyze the cpDNA haplogroups in the 200 accessions (Table S2).
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