Table 3.

Estimated effects of quantitative trait loci (QTLs).

Trait	Chr	Nearest marker	Position (cM)	LOD	PVE	Koshihikari-allele	Habataki-allele
Primary branch number	1	Geno_NIAS04066	202.3	3.960	0.216	13.033 ± 0.269	10.728 ± 0.431
Primary branch number	2	Geno_NIAS10171	204.9	3.054	0.171	12.867 ± 0.264	10.618 ± 0.507
Total primary branch length	6	Geno_NIAS26448	168.7	0.261	0.016	12.241 ± 0.288	12.927 ± 0.553
Total primary branch length	1	Geno_NIAS01002	45.0	8.737	0.387	92.583 ± 2.253	121.571 ± 4.343
Total secondary branch number	1	Geno_NIAS01002	45.0	6.904	0.317	30.082 ± 1.520	46.694 ± 2.778
Total spikelet number	1	Geno_NIAS01002	45.0	8.558	0.365	161.982 ± 6.360	239.123 ± 11.797
Primary branch length PC1	6	Geno_NIAS09083	167.5	3.738	0.187	0.017 ± 0.025	–0.024 ± 0.034
Primary branch length PC2	2	Geno_NIAS09998	197.5	4.608	0.230	0.016 ± 0.017	–0.042 ± 0.028
Secondary branch number PC2	2	Geno_NIAS09051	162.5	4.519	0.224	0.038 ± 0.052	–0.053 ± 0.068
Secondary branch number PC2	3	Geno_NIAS14274	171.2	3.042	0.170	–0.083 ± 0.044	0.259 ± 0.075
Secondary branch number PC2	8	Geno_NIAS32135	68.4	3.026	0.170	0.075 ± 0.042	–0.306 ± 0.088
Spikelet number PC2	2	Geno_NIAS10171	207.5	3.927	0.200	0.035 ± 0.025	–0.098 ± 0.042
Spikelet number PC2	8	Geno_NIAS32135	68.4	3.055	0.171	0.040 ± 0.023	–0.167 ± 0.047

LOD, Logarithm of odds score.

PVE, Proportion of variance explained.