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

Hori, Kiyosumi; Suzuki, Keitaro; Ishikawa, Haruka; Nonoue, Yasunori; Nagata, Kazufumi; Fukuoka, Shuichi; Tanaka, Junichi

doi:10.1186/s12284-020-00447-8

Rice

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

Positive additive effect means ‘Takanari’ allele increasing the trait values

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