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Table 2 QTLs for eating-quality traits on CSSLs in the ‘Koshihikari’ genetic background in 2016 and 2017

From: Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Trait Locus name CSSLs Position Flanking marker interval Year Additive effect
Amylose content (%) qAC1–1 SL1204 Chr1 RM1196-RM7594 2016 1.8
     2017 1.5
qAC1–2 SL1205   RM6648-RM6321 2016 −1.1
qAC2–1 SL1206, SL1207 Chr2 RM5897-RM1234 2016 0.9
     2017 0.6
qAC4 SL1214 Chr4 RM16260-RM1305 2016 −0.9
qAC5 SL1219 Chr5 RM6034-RM1386 2016 0.6
     2017 0.8
qAC6 SL1223, SL1224 Chr6 RM1340-RM1370 2016 −1.0
qAC7 SL1225 Chr7 RM4584-RM5481 2017 0.8
qAC9 SL1233 Chr9 RM6235-RM6797 2016 −1.8
qAC10 SL1235 Chr10 RM4455-RM6673 2016 −0.9
qAC11 SL1237 Chr11 RM3701-RM1341 2016 −1.2
qAC12 SL1239 Chr12 Bb77A02-RM2935 2016 −1.0
Protein content (%) qPC2 SL1209 Chr2 RM6933-RM3850 2016 −0.3
qPC5 SL1218 Chr5 RM6034-RM1386 2016 0.3
qPC8 SL1230, SL1231 Chr8 RM3634-RM4997 2016 0.3
Eating quality score (−) qEQ2 SL1208, SL1209 Chr2 RM3515-RM3850 2016 −12.4
     2017 −6.0
qEQ3–1 SL1210 Chr3 RM7332-RM5748 2016 −4.7
     2017 −3.2
qEQ3–2 SL1213   RM2334-RM7389 2016 −5.4
qEQ4 SL1217 Chr4 RM3839-RM5608 2016 −8.0
     2017 −3.4
qEQ5 SL1219 Chr5 RM6034-RM1386 2017 −3.4
qEQ6 SL1222 Chr6 RM5855-RM7193 2016 −5.0
qEQ8 SL1228, SL1229 Chr8 RM6369-RM22709 2016 −5.4
qEQ10 SL1235 Chr10 RM4455-RM6673 2016 −4.7
qEQ11 SL1237 Chr11 RM3701-RM1341 2016 −9.0
     2017 −3.5
qEQ12–1 SL1239 Chr12 Bb77A02-RM2935 2016 −4.9
qEQ12–2 SL1241   RM3326-RM1226 2016 −12.0
     2017 −5.0
Stickiness S1 (N/m2 × 102) qST1 SL1204 Chr1 RM1196-RM7594 2016 −5.1
qST2 SL1208 Chr2 RM1211-RM3316 2016 −8.2
     2017 −7.7
qST3–1 SL1210 Chr3 RM7332-RM5748 2016 −5.4
     2017 −7.1
qST3–2 SL1213   RM2334-RM7389 2016 −5.9
     2017 −8.3
qST5 SL1219 Chr5 RM6034-RM1386 2016 −4.8
     2017 −6.9
qST9 SL1233 Chr9 RM6235-RM6797 2016 −5.7
qST11 SL1237 Chr11 RM3701-RM1341 2016 −6.6
     2017 −7.8
Hardness H2 (N/m2 × 104) qHA1 SL1204 Chr1 RM1196-RM7594 2017 2.1
qHA2 SL1206 Chr2 RM6842-RM5699 2017 1.4
qHA4–1 SL1214, SL1215 Chr4 RM5414-RM5633 2016 1.5
     2017 2.2
qHA4–2 SL1217   RM3839-RM5608 2016 1.4
     2017 2.4
qHA5–1 SL1218 Chr5 RM1248-RM3838 2017 1.8
qHA5–2 SL1220   RM1386-RM3286 2017 2.0
qHA6–1 SL1221 Chr6 RM6467-RM5855 2017 2.0
qHA7 SL1227 Chr7 RM6394-RM7601 2017 1.9
qHA9 SL1232 Chr9 RM23654-RM6235 2017 −1.5
qHA10 SL1235 Chr10 RM4455-RM6673 2017 −1.4
qHA11 SL1237 Chr11 RM3701-RM1341 2016 1.8
     2017 2.0
Whiteness (−) qWH1 SL1204 Chr1 RM1196-RM7594 2016 0.8
     2017 0.9
qWH2–1 SL1208, SL1209 Chr2 RM3515-RM3850 2016 −1.3
qWH3 SL1212, SL1213 Chr3 RM3513-RM6970 2016 0.5
qWH4–1 SL1214 Chr4 RM16260-RM1305 2017 1.0
qWH4–2 SL1216, SL1217   RM1359-RM3916 2016 0.7
     2017 0.8
qWH5 SL1219 Chr5 RM6034-RM1386 2016 0.5
     2017 0.7
qWH6–1 SL1222 Chr6 RM5855-RM7193 2016 1.4
     2017 1.3
qWH6–2 SL1224   RM5957-RM5463 2016 −1.5
qWH7 SL1225 Chr7 RM4584-RM5481 2016 −1.9
qWH10 SL1234 Chr10 RM7492-RM1859 2016 −1.4
  qWH11 SL1237, SL1238 Chr11 RM5824-RM6623 2017 0.8
  1. Positive additive effect means ‘Takanari’ allele increasing the trait values
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