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Fig. 7 | Botanical Studies

Fig. 7

From: Explore the genetics of weedy traits using rice 3K database

Fig. 7

Relationship between genotype and phenotype for seed coat/pericarp color-associated SNP inside or close to the known candidate gene Rc. a Position of the SNPs were indicated by arrows on the diagram of the structure of Rc. E1 to E6 stand for exon 1 to exon 6. The gene structure of Rc is proportional to the actual base-pair length, except for intron 2 which is ca. 2.7 kb. sig. sub indicates the sub-population from which the corresponding seed coat color-associated SNP was identified. The color-less or colored seed coat-associated allele, as well as the associated functional alteration were indicated. b For each trait-associated marker, its number of individuals used for the calculation of frequency of individuals carrying the “colored” genotype (FGc), the number of individuals carrying the “colored” genotype which had seed coat color information (No. Gc∩P), and the frequency that the individuals carrying colored genotype had indeed colored seed coat (Freq(Col | Gc)). Within a sub-population, SNPs whose alleles correspond well to phenotypes are highlighted in orange. Meanwhile, only SNP × sub-population combinations with No. Gc∩P exceeding 20 are highlighted

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