Table 6.

Frequency of candidate genes, by gene category and trait, that included or were within a 100 kb window of a significant single nucleotide polymorphisms (SNPs) detected in a genome-wide association study (GWAS) for a panel of 470 Oryza sativa accessions, composed of rice diversity panel 1 (RDP1, n = 379) (Eizenga et al., 2014) and the aus subset (n = 91) of the 3,000 rice genome project (Li et al., 2014a).

Gene category	Emerg	SOE	SDW	ML	Total
Phytohormone biosynthesis/signaling	10 + 1*		1*		11
Cell wall biosynthesis and defense response	5 + 1*	1*		1	7
Abiotic stress response	4		2		6
Biotic stress response	6				6
Detoxification	2 + 1*	1*	1		4
Nutrient uptake	3				3
Protein synthesis	2		1		3
Sugar transport/metabolism	3				3
Cellular development			2		2
DNA damage response/DNA repair	2				2
Metabolite modification	2				2
Other	4				4
Total	43 + 3*	2*	6 + 1*	1	53

*Same gene identified for two or more traits.

QTL, quantitative trait loci; Chr, chromosome; pos, position (Mb); PVE, phenotypic variance explained (%).

Traits included emergence (%), speed of emergence measured and shoot dry weight measured in a field trial at Los Baños, Philippines in which seed were planted 8 cm deep, and mesocotyl length (ML, cm) measured in a test tube experiment after five days incubation in the dark at 30°C in a controlled environment chamber.