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There was discontinuity in the distribution of the japonica accessions, with 10 accessions with a very wide root cone angle (above 115°).
Indica haplotypes are variable in allele composition and include accessions with or without a SUB1A gene.
Number of ORSC accessions with hull color and pericarp color phenotypes, grouped by subpopulation.
There were 49 accessions with ambiguous genotypes, which were grouped into an undefined group.
TASSEL was used to produce a dendrogram of these accessions with the 135 Sri Lankan landraces.
SNPs were then filtered based on a frequency test; only SNPs with a significant frequency difference between O. sativa accessions with white pericarp and ORSC accessions with red pericarp (P value cutoff: 1.0e −05) were used.
The lines involved were different from marker to marker and generally included accessions with extremes phenotypes (from subpopulations J4 or J6) associated with one or several accessions with rather average phenotypes from the same or other subpopulations.
Datapoints for dehulled caryopses of 126 non glutinous cultivars, grouped according to the haplotype at the SNP of intron 1 (47 accessions with G allele; 79 accessions with T allele).
Accessions with membership coefficients ≥0.7 were assigned to a specific sub-population, whereas the remaining genotypes were identified as admixed.
To get the specific variation information, we compared the potential SNPs in four accessions with the dbSNP.
However, three other accessions with the same substitution, Asamurasaki, KSWSK, and O. rufipogon, had blackish purple leaf sheath.
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