Table 5 Marker-trait associations for percentage of head rice (PHR) and percentage of chalky grain (GC) traits in indica and tropical japonica rice breeding populations. Chromosome position (bp), year, effect of the alternative allele, and score (-log10(p-value)) are shown in the table
indica
MarkerChrPositionYearAlt allele effect (%)Score
PHR
S1_1015065110150652010−1.624.98
S2_2421061422421061420122.957.20
S3_88809793888097920101.324.60
S3_102479583102479582010−2.129.97
S3_153657263153657262010−1.857.19
S4_2972898242972898220101.304.68
20122.375.66
S6_829223682922320101.765.04
S6_110221016110221012012−2.105.30
S6_132159236132159232010−1.245.47
S6_2132750362132750320122.635.54
S7_1479860671479860620101.255.05
S10_673755410673755420102.405.64
S11_24425810112442581020101.924.70
GC
S1_10668941106689420111.334.06
S1_2249206612249206620121.455.74
S3_1603736031603736020110.724.07
S4_2248072142248072120111.244.14
tropical japonica
PHR
S1_3868631213868631220132.03.20
S2_276600462276600462013−1.04.41
S3_13951653139516520111.06.18
S6_278347726278347722011−2.04.89
2013−1.03.44
S8_233803958233803952013−2.04.11
GC
S6_2740226062740226020112.004.62
20132.003.94