Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

Table 4 Levels of nucleotide variation at the two studied genes

Gene	Ecotype	Indel	SNP	S	π_tot	θ_tot	dN/dS	D	D*	F*
Wx	Glutinous	6	1	23	0.0053	0.0043	-	1.7295	1.7295	1.8583
	Nonglutinous	17	7	31	0.0043	0.0033		1.1825	0.9145	1.369
OsC1	Colored	2	1	6	0.0023	0.0020	-	0.8109	1.0088	1.1449
	Colorless	3	8	10	0.0010	0.0021	1.00	−1.7683	−1.2847	−1.7178

S, number of segregating sites; π, average number of nucleotide differences per site between two sequences [33] calculated on the total number of polymorphic sites (π_tot); silent sites (π_sil); synonymous sites (π_syn); nonsynonymous sites (π_nonsyn); θ, Watterson’s estimator of nucleotide polymorphism per base pair [32] calculated on the total number of polymorphic sites (θ_tot); silent sites (θ_sil); synonymous sites (θ_syn); nonsynonymous sites (θ_nonsyn); D, Tajima’s D[34]; D*, Fu and Li’s D*; F*, Fu and Li’s F* [35].
Tajima’s D, *Fu and Li’s D* and F* not significant (P > 0.10).

ISSN: 2730-6844