Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

Fan, Jiongjiong; Hua, Hua; Luo, Zhaowei; Zhang, Qi; Chen, Mengjiao; Gong, Junyi; Wei, Xin; Huang, Zonghua; Huang, Xuehui; Wang, Qin

doi:10.1186/s12284-022-00550-y

Rice

Table 3 QTLs for the three traits detected in the set of CSSLs in Shanghai and Hangzhou

From: Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

Environment	Trait	QTL	Chromosome	Location (bin)	Location (Mb)	LOD	PVE (%)^a	Add^b	Known QTL/gene
Shanghai	HD	qHD1-1	chr01	chr01_357	35.7–40.2	3.2	1.7	− 1.7	OsMADS51
Shanghai	HD	qHD4-2	chr04	chr04_196	18.5–22.0	14.1	9.3	3.4
Shanghai	HD	qHD6-1	chr06	chr06_10	1.0–3.0	41.7	52.3	11.2	Hd3a/RFT1
Shanghai	HD	qHD8-1	chr08	chr08_41	3.9–4.6	22.9	18.4	8.1	Ghd8
Shanghai	HD	qHD10-1	chr10	chr10_159	15.9–17.3	14.5	9.7	4.8	Ehd1
Shanghai	PH	qPH1-1	chr01	chr01_357	35.7–40.2	34.5	71.7	19.2	sd1
Shanghai	PH	qPH6-1	chr06	chr06_10	1.0–3.0	3.5	3.6	5.0	Hd3a/RFT1
Shanghai	PL	qPL3-2	chr03	chr03_243	24.3–26.5	3.8	12.5	− 0.9
Shanghai	PL	qPL10-1	chr10	chr10_174	15.9–19.0	3.0	9.8	− 1.2
Hangzhou	HD	qHD4-1	chr04	chr04_185	18.5–22.0	9.6	3.8	1.8
Hangzhou	HD	qHD6-1	chr06	chr06_10	1.0–3.0	49.7	50.5	8.5	Hd3a/RFT1
Hangzhou	HD	qHD7-1	chr07	chr07_0	0.0–5.1	10.9	4.4	4.3
Hangzhou	HD	qHD7-2	chr07	chr07_207	20.3–27.7	5.2	1.9	2.8
Hangzhou	HD	qHD8-1	chr08	chr08_41	3.9–4.6	18.4	8.8	4.3	Ghd8
Hangzhou	HD	qHD10-1	chr10	chr10_159	15.9–17.3	15.5	7.0	3.2	Ehd1
Hangzhou	HD	qHD10-2	chr10	chr10_195	19.5–22.3	5.2	1.9	2.0
Hangzhou	HD	qHD11-1	chr11	chr11_193	18.9–20.4	6.5	2.4	1.9
Hangzhou	HD	qHD11-2	chr11	chr11_288	28.8–28.9	6.5	2.4	1.9
Hangzhou	HD	qHD12-1	chr12	chr12_57	2.7–9.0	5.2	1.9	2.8
Hangzhou	HD	qHD12-2	chr12	chr12_91	8.0–20.4	15.8	7.2	− 5.5
Hangzhou	HD	qHD12-3	chr12	chr12_204	20.4–21.1	43.4	37.5	7.3
Hangzhou	HD	qHD12-4	chr12	chr12_212	21.1–27.4	11.6	4.8	− 4.5
Hangzhou	PH	qPH1-1	chr01	chr01_357	35.7–40.2	17.4	46.7	13.8	sd1
Hangzhou	PH	qPH8-1	chr08	chr08_238	22.6–28.3	3.1	6.2	5.7
Hangzhou	PL	qPL3-1	chr03	chr03_130	12.8–26.5	3.9	14.0	− 2.7

^aThe percentage of phenotypic variation explained (PVE) by the detected QTL; ^b Additive effects (Add), the positive value suggests that alleles from BAS increase the effect

Back to article page