Explore the genetics of weedy traits using rice 3K database

Botanical Studies

Table 2 Phenotype prediction accuracy based on genotype of selected trait-associated SNPs

Trait	Pop	No. Ind	SNP	Genotype	Freq	Prediction accuracy
AWN	aus	145	S6_7624195	AA	0.74	73.8% awn-less
				GG	0.26	68.4% awned
AWN	trop	375	S8_24022229	GG	0.9	80.1% awn-less
				AA	0.1	89.1% awned
PTH	trop	378	S7_13096799	GG	0.76	73.4% difficult (41.6%) to intermediate (31.8) threshing
				AA	0.23	90.9% easy (38.6%) to intermediate (52.2%) threshing
SCCO	aus	153	S7_6068017	CC	0.68	96.1% colored seed coat
				AA	0.31	93.8% white seed coat
SCCO	aus	153	S8_9105408	GG	0.65	86% colored seed coat
				AA	0.33	66.7% white seed coat
SCCO	ind	645	S7_6067855	GG	0.92	96.1% white seed coat
				AA	0.07	91.5% colored seed coat
SCCO	trop	362	S7_6062746	TT	0.9	90.5% white seed coat
				GG	0.1	88.9% colored seed coat
SDHT	ind	641	S11_24872440	CC	0.85	92.1% short (21%) to intermediate (70%) seedling
				TT	0.13	95.2% intermediate (71%) to tall (23%) seedling
SDHT	temp	137	S1_31283533	AA	0.75	62.1% short seedling
				GG	0.25	94% intermediate seedling

The meaning for each trait abbreviation is as follows: AWN: awn color; PTH: panicle threshability, SCCO: seed coat color; SDHT: seedling height. Sub-population × trait combinations are shown in the table if the genotype of trait-associated SNP can predict the phenotype with at least 60% of chance to accuracy. Otherwise we do not present the Sub-population × trait combinations for a clear and concise presentation