Construction of a SNP-Based Genetic Map and QTL Mapping for Salt Tolerance in a Rice DH Population Derived from Aigela and Xudao 10

doi:10.16819/j.1001-7216.2026.250604

Abstract

Abstract:

【Objective】Soil salinization is an important abiotic factor affecting agricultural production in China, and the identification of salt tolerance-related genes/QTLs in rice is crucial for ensuring stable rice production in saline-alkali soils. 【Method】Aigela and Xudao 10, which exhibit significant differences in salt tolerance related traits, were used as parent plants to create a doubled haploid (DH) population. Salt tolerance was identified under field and hydroponic conditions. Genotyping of the targeted population was performed using the rice 1 K mGPS SNP chip. Phenotypic data combined with genotype data of DH population were used for QTL mapping with the QTL IciMapping 4.2 software. 【Result】Through QTL mapping analysis, a total of 22 salt tolerance related QTLs were detected, including 10 QTLs for grain yield per plant, 4 for grains per panicle, 2 for root length, and 6 for root dry weight. These QTLs are located on chromosomes 1, 6, 8, 10, 11, and 12, explaining phenotypic variation of 3.37%−15.52% with LOD values ranging from 4.04 to 9.65. Based on the gene annotation, Arabidopsis homologous gene comparison, spatiotemporal expression analysis and sequence comparison within the mapping interval of qST11, a candidate gene (LOC_Os11g30560) encoding a hydroxysteroid dehydrogenase (OsHSD1) was identified. 【Conclusion】Among the 22 QTLs detected in this study, 11 were known genes or loci related to salt tolerance, and the remaining 11 were newly identified. Meanwhile, the candidate gene analysis was conducted on the newly identified salt tolerance QTL (qST11), laying a foundation for cloning of salt-tolerance related genes and deciphering their genetic regulatory networks.

Key words: salt tolerance-related trait, doubled haploid population, QTL mapping, candidate gene

摘要：

【目的】土壤盐碱化是一个影响我国农业生产的重要非生物胁迫因素，挖掘水稻耐盐相关性状基因/QTL对保障盐碱地水稻的安全生产至关重要。【方法】以耐盐性差异较大的矮格拉和徐稻10号为亲本构建定位群体，利用田间和室内水培进行耐盐性鉴定，利用水稻1 K mGPS SNP芯片对定位群体进行基因分型，结合表型数据和基因型数据，利用QTL IciMapping 4.2软件进行QTL定位。【结果】通过QTL定位分析，最终鉴定出22个耐盐相关QTL，其中单株产量QTL 10个，每穗粒数QTL 4个，根长QTL 2个，根干质量QTL 6个，这些QTL位于水稻1、6、8、10、11和12号染色体上，LOD值为4.04~9.65，表型贡献率为3.37%~15.52%。根据新发现QTL(qST11)定位区间内的基因注释、与拟南芥的同源基因比对、时空表达分析和序列分析，最终筛选到1个编码羟基类固醇脱氢酶的候选基因LOC_Os11g30560 (OsHSD1)。【结论】在本研究检测到的22个QTL中，11个为已知耐盐性基因位点，11个是新鉴定位点。同时，本研究对新鉴定耐盐QTL(qST11)进行了候选基因分析，为进一步开展耐盐基因的克隆和遗传调控的解析奠定了基础。

关键词: 耐盐相关性状, 双单倍体群体, QTL定位, 候选基因

LIU Yan, LI Jingfang, CHI Ming, ZHANG Yuqin, SUN Zhiguang, LI Jian, YANG Bo, XU Bo, XING Yungao, ZHOU Qun, WANG Derong, CHEN Tingmu, LIU Jinbo, LU Baiguan, XU Dayong, WANG Baoxiang. Construction of a SNP-Based Genetic Map and QTL Mapping for Salt Tolerance in a Rice DH Population Derived from Aigela and Xudao 10[J]. Chinese Journal OF Rice Science, 2026, 40(3): 351-359.

刘艳, 李景芳, 迟铭, 章雨沁, 孙志广, 李健, 杨波, 徐波, 邢运高, 周群, 王德荣, 陈庭木, 刘金波, 卢百关, 徐大勇, 王宝祥. 矮格拉/徐稻10号DH群体的SNP标记图谱构建及耐盐QTL定位分析[J]. 中国水稻科学, 2026, 40(3): 351-359.

Figures/Tables 6

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处理 Treatment	性状 Trait	矮格拉 Aigela	徐稻10号 Xudao 10	群体Population
				均值±标准差	变幅	变异系数	峰度	偏度
				Mean ± SD	Range	CV (%)	Kurtosis	Skewness
对照 CK	单株产量	24.38**	36.90	21.19±7.46	0.00~43.76	35.21	0.46	0.13
	GYPP(g)	24.38**	36.90	21.19±7.46	0.00~43.76	35.21	0.46	0.13
	每穗粒数	138.20	144.01	166.80±37.95	70.39~268.70	22.75	−0.32	−0.13
	NGPP	138.20	144.01	166.80±37.95	70.39~268.70	22.75	−0.32	−0.13
	根长	81.02	89.65	89.67±18.82	30.46~134.50	20.98	0.14	−0.42
	RL(mm)	81.02	89.65	89.67±18.82	30.46~134.50	20.98	0.14	−0.42
	根干质量	0.07*	0.08	0.07±0.07	0.01~0.94	95.98	142.00	11.41
	RDW(g)	0.07*	0.08	0.07±0.07	0.01~0.94	95.98	142.00	11.41
盐胁迫 Salt stress	单株产量	22.82*	18.92	7.77±5.07	1.50~34.56	65.25	5.42	1.76
	GYPP(g)	22.82*	18.92	7.77±5.07	1.50~34.56	65.25	5.42	1.76
	每穗粒数	125.91	120.50	99.04±41.17	29.05~218.30	41.57	−0.67	0.42
	NGPP	125.91	120.50	99.04±41.17	29.05~218.30	41.57	−0.67	0.42
	根长	102.83**	82.43	91.16±18.35	38.21~148.00	20.13	0.33	−0.17
	RL(mm)	102.83**	82.43	91.16±18.35	38.21~148.00	20.13	0.33	−0.17
	根干质量	0.04*	0.06	0.06±0.02	0.02~0.12	34.34	0.26	0.36
	RDW(g)	0.04*	0.06	0.06±0.02	0.02~0.12	34.34	0.26	0.36
比值 Ratio	单株产量	0.94**	0.51	0.33±0.24	0.00~1.23	72.36	1.01	1.02
	GYPP	0.94**	0.51	0.33±0.24	0.00~1.23	72.36	1.01	1.02
	每穗粒数	0.91*	0.84	0.61±0.24	0.20~1.32	39.81	0.23	0.73
	NGPP	0.91*	0.84	0.61±0.24	0.20~1.32	39.81	0.23	0.73
	根长	1.27*	0.92	1.03±0.18	0.64~1.71	16.95	2.44	0.87
	RL	1.27*	0.92	1.03±0.18	0.64~1.71	16.95	2.44	0.87
	根干质量	0.60*	0.75	0.89±0.50	0.07~4.73	56.17	20.28	3.25
	RDW	0.60*	0.75	0.89±0.50	0.07~4.73	56.17	20.28	3.25

处理 Treatment	性状 Trait	矮格拉 Aigela	徐稻10号 Xudao 10	群体Population
				均值±标准差	变幅	变异系数	峰度	偏度
				Mean ± SD	Range	CV (%)	Kurtosis	Skewness
对照 CK	单株产量	24.38**	36.90	21.19±7.46	0.00~43.76	35.21	0.46	0.13
	GYPP(g)	24.38**	36.90	21.19±7.46	0.00~43.76	35.21	0.46	0.13
	每穗粒数	138.20	144.01	166.80±37.95	70.39~268.70	22.75	−0.32	−0.13
	NGPP	138.20	144.01	166.80±37.95	70.39~268.70	22.75	−0.32	−0.13
	根长	81.02	89.65	89.67±18.82	30.46~134.50	20.98	0.14	−0.42
	RL(mm)	81.02	89.65	89.67±18.82	30.46~134.50	20.98	0.14	−0.42
	根干质量	0.07*	0.08	0.07±0.07	0.01~0.94	95.98	142.00	11.41
	RDW(g)	0.07*	0.08	0.07±0.07	0.01~0.94	95.98	142.00	11.41
盐胁迫 Salt stress	单株产量	22.82*	18.92	7.77±5.07	1.50~34.56	65.25	5.42	1.76
	GYPP(g)	22.82*	18.92	7.77±5.07	1.50~34.56	65.25	5.42	1.76
	每穗粒数	125.91	120.50	99.04±41.17	29.05~218.30	41.57	−0.67	0.42
	NGPP	125.91	120.50	99.04±41.17	29.05~218.30	41.57	−0.67	0.42
	根长	102.83**	82.43	91.16±18.35	38.21~148.00	20.13	0.33	−0.17
	RL(mm)	102.83**	82.43	91.16±18.35	38.21~148.00	20.13	0.33	−0.17
	根干质量	0.04*	0.06	0.06±0.02	0.02~0.12	34.34	0.26	0.36
	RDW(g)	0.04*	0.06	0.06±0.02	0.02~0.12	34.34	0.26	0.36
比值 Ratio	单株产量	0.94**	0.51	0.33±0.24	0.00~1.23	72.36	1.01	1.02
	GYPP	0.94**	0.51	0.33±0.24	0.00~1.23	72.36	1.01	1.02
	每穗粒数	0.91*	0.84	0.61±0.24	0.20~1.32	39.81	0.23	0.73
	NGPP	0.91*	0.84	0.61±0.24	0.20~1.32	39.81	0.23	0.73
	根长	1.27*	0.92	1.03±0.18	0.64~1.71	16.95	2.44	0.87
	RL	1.27*	0.92	1.03±0.18	0.64~1.71	16.95	2.44	0.87
	根干质量	0.60*	0.75	0.89±0.50	0.07~4.73	56.17	20.28	3.25
	RDW	0.60*	0.75	0.89±0.50	0.07~4.73	56.17	20.28	3.25

处理 Treatment	性状 Trait	性状位点 Trait locus	染色体 Chr.	标记区间 Marker interval	物理位置 Physical position (bp)	LOD值 LOD score	表型贡献率 PVE (%)	加性效应 Additive effect	已知位点 Known loci
田间 Field	单株产量 GYPP (g)	qGYPP1	1	Bin1-12−Bin1-14	9298140−9492186	4.44	3.79	−0.25
		qGYPP6-1	6	Bin6-12−Bin6-15	7458474−7668549	6.64	7.43	0.21	qSIS6.7 ^[13]
		qGYPP6-2	6	Bin6-29−Bin6-30	8234582−8374658	8.21	3.86	0.24
		qGYPP6-3	6	Bin6-36−Bin6-40	17802740−18211466	5.87	5.12	0.23	qDSW6.1 ^[14]
		qGYPP10-1	10	Bin10-14−Bin10-19	3582800−3974958	4.99	4.34	0.18
		qGYPP10-2	10	Bin10-30−Bin10-31	4667214−5334672	6.73	9.57	−0.25
		qGYPP11-1	11	Bin11-2−Bin11-3	6034232−6542007	5.96	6.29	0.23	qRWCs11.1 ^[15]
		qGYPP11-2	11	Bin11-26−Bin11-27	6544143−6946407	7.92	7.11	0.24	qW2SES11.1^[16]
		qGYPP11-3	11	Bin11-38−Bin11-41	17699906−18106609	6.95	15.52	0.17
		qGYPP12	12	Bin12-18−Bin12-19	2398764−2967519	6.21	6.44	−0.15	CYP94C2b ^[20]
	每穗粒数 NGPP	qNGPP6	6	Bin6-12−Bin6-15	7458474−7668549	5.02	12.94	0.22	qSIS6.7 ^[13]
		qNGPP8	8	Bin8-14−Bin8-15	15795996−16513772	4.71	5.43	−0.07
		qNGPP11	11	Bin11-38−Bin11-41	17699906−18106609	7.07	14.51	0.20
		qNGPP12	12	Bin12-18−Bin12-19	2398764−2967519	5.41	7.25	−0.19	CYP94C2b ^[20]
室内 Green- house	根长 RL (mm)	qRC1	1	Bin1-12−Bin1-14	9298140−9492186	4.83	12.35	−0.25
	根长 RL (mm)	qRC8	8	Bin8-22−Bin8-24	19682575−20333667	4.91	8.00	−0.23	qRTL8.19 ^[13]
	根干质量 RDW (g)	qRDW1	1	Bin1-12−Bin1-14	9298140−9492186	5.51	3.37	−0.82
		qRDW6	6	Bin6-12−Bin6-15	7458474−7668549	4.86	6.86	0.63	qSIS6.7 ^[13]
		qRDW8-1	8	Bin8-14−Bin8-15	15795996−16513772	4.04	10.63	0.68
		qRDW8-2	8	Bin8-16−Bin8-20	16513924−17029875	4.90	8.74	0.65	OsELF4c ^[21]
		qRDW10-1	10	Bin10-14−Bin10-19	3582800−3974958	4.95	5.12	0.70
		qRDW10-2	10	Bin10-67−Bin10-68	11325178−11843441	9.65	7.99	0.19	GH5BG ^[22]

处理 Treatment	性状 Trait	性状位点 Trait locus	染色体 Chr.	标记区间 Marker interval	物理位置 Physical position (bp)	LOD值 LOD score	表型贡献率 PVE (%)	加性效应 Additive effect	已知位点 Known loci
田间 Field	单株产量 GYPP (g)	qGYPP1	1	Bin1-12−Bin1-14	9298140−9492186	4.44	3.79	−0.25
		qGYPP6-1	6	Bin6-12−Bin6-15	7458474−7668549	6.64	7.43	0.21	qSIS6.7 ^[13]
		qGYPP6-2	6	Bin6-29−Bin6-30	8234582−8374658	8.21	3.86	0.24
		qGYPP6-3	6	Bin6-36−Bin6-40	17802740−18211466	5.87	5.12	0.23	qDSW6.1 ^[14]
		qGYPP10-1	10	Bin10-14−Bin10-19	3582800−3974958	4.99	4.34	0.18
		qGYPP10-2	10	Bin10-30−Bin10-31	4667214−5334672	6.73	9.57	−0.25
		qGYPP11-1	11	Bin11-2−Bin11-3	6034232−6542007	5.96	6.29	0.23	qRWCs11.1 ^[15]
		qGYPP11-2	11	Bin11-26−Bin11-27	6544143−6946407	7.92	7.11	0.24	qW2SES11.1^[16]
		qGYPP11-3	11	Bin11-38−Bin11-41	17699906−18106609	6.95	15.52	0.17
		qGYPP12	12	Bin12-18−Bin12-19	2398764−2967519	6.21	6.44	−0.15	CYP94C2b ^[20]
	每穗粒数 NGPP	qNGPP6	6	Bin6-12−Bin6-15	7458474−7668549	5.02	12.94	0.22	qSIS6.7 ^[13]
		qNGPP8	8	Bin8-14−Bin8-15	15795996−16513772	4.71	5.43	−0.07
		qNGPP11	11	Bin11-38−Bin11-41	17699906−18106609	7.07	14.51	0.20
		qNGPP12	12	Bin12-18−Bin12-19	2398764−2967519	5.41	7.25	−0.19	CYP94C2b ^[20]
室内 Green- house	根长 RL (mm)	qRC1	1	Bin1-12−Bin1-14	9298140−9492186	4.83	12.35	−0.25
	根长 RL (mm)	qRC8	8	Bin8-22−Bin8-24	19682575−20333667	4.91	8.00	−0.23	qRTL8.19 ^[13]
	根干质量 RDW (g)	qRDW1	1	Bin1-12−Bin1-14	9298140−9492186	5.51	3.37	−0.82
		qRDW6	6	Bin6-12−Bin6-15	7458474−7668549	4.86	6.86	0.63	qSIS6.7 ^[13]
		qRDW8-1	8	Bin8-14−Bin8-15	15795996−16513772	4.04	10.63	0.68
		qRDW8-2	8	Bin8-16−Bin8-20	16513924−17029875	4.90	8.74	0.65	OsELF4c ^[21]
		qRDW10-1	10	Bin10-14−Bin10-19	3582800−3974958	4.95	5.12	0.70
		qRDW10-2	10	Bin10-67−Bin10-68	11325178−11843441	9.65	7.99	0.19	GH5BG ^[22]