Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice

doi:10.1016/j.rsci.2020.11.009

Abstract

Abstract:

Cadmium (Cd) is a non-essential toxic metal that is harmful to plants. To investigate the genetic mechanism of Cd tolerance in rice, quantitative trait loci (QTLs) associated with Cd tolerance at the seedling stage were analyzed using a recombinant inbred line (RIL) population derived from a cross between PA64s and 93-11. A total of 36 QTLs associated with shoot length, root length, shoot dry weight, root dry weight and total dry weight were detected in Hangzhou and Lingshui of China. Among them, 15 QTLs were identified under the control condition and 15 QTLs were identified under the Cd stress condition, and 6 QTLs for Cd tolerant coefficient were detected on chromosomes 1, 3, 7 and 9. The qCDSL1.1 and qCDSL1.2 were identified in Hangzhou and Lingshui, respectively, and had overlapping intervals on chromosome 1. To further confirm the effects of qCDSL1.1 and qCDSL1.2, we developed a chromosome segment substitution line (CSSL), CSSL^qCDSL1, in 93-11 background harboring qCDSL1.1/ qCDSL1.2 from PA64s. Compared to 93-11, CSSL^qCDSL1 had increased shoot length under the Cd stress condition. These results pave the way for further isolation of those genes controlling Cd tolerance in rice and marker-assistant selection of rice elite varieties with Cd tolerance.

Key words: cadmium tolerance, recombinant inbred line, qCDSL1, rice, quantitative trait locus

Shilin Ding, Chaolei Liu, Lianguang Shang, Shenglong Yang, Anpeng Zhang, Hongzhen Jiang, Banpu Ruan, Guonan Fang, Biao Tian, Guoyou Ye, Longbiao Guo, Qian Qian, Zhenyu Gao. Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice[J]. Rice Science, 2021, 28(1): 81-88.

Figures/Tables 5

References 36

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Cd content (μmol/L)	Root length (cm)			Shoot length (cm)		Root dry weight (mg)							Total dry weight (mg)
Cd content (μmol/L)	93-11	PA64s		93-11	PA64s	93-11		PA64s		93-11		PA64s	93-11	PA64s
0	13.34 ± 0.85	11.15 ± 1.09	27.27 ± 1.23		31.15 ± 1.23**	21.8 ± 1.1	18.8 ± 1.2**		91.4 ± 9.4		69.0 ± 5.3**		113.2 ± 6.7	87.8 ± 2.3**
10	11.59 ± 0.77	11.35 ± 0.39	24.06 ± 1.12		27.83 ± 1.29*	18.1 ± 1.7	18.4 ± 0.3		67.3 ± 3.2		62.0 ± 2.2**		84.4 ± 2.5	80.4 ± 4.5*
20	8.33 ± 0.87	10.74 ± 0.87*	23.86 ± 0.98		26.62 ± 1.98*	16.1 ± 1.5	18.1 ± 0.4*		67.0 ± 2.1		61.4 ± 3.5**		83.1 ± 6.3	79.5 ± 1.9*
30	8.20 ± 0.74	9.60 ± 0.57*	23.75 ± 0.99		26.59 ± 1.23*	15.0 ± 1.0	17.9 ± 0.9*		67.0 ± 2.3		60.2 ± 2.4**		82.0 ± 6.5	78.1 ± 2.3*
40	8.10 ± 0.57	9.55 ± 0.91*	23.45 ± 1.33		26.78 ± 1.32*	12.0 ± 0.9	17.7 ± 0.2**		66.1 ± 2.3		59.9 ± 3.1**		78.1 ± 2.1	77.6 ± 4.4
50	8.01 ± 0.54	9.52 ± 0.87*	20.16 ± 0.56		26.67 ± 0.99**	10.1 ± 0.4	17.6 ± 0.3**		52.6 ± 3.7		59.0 ± 2.4**		62.7 ± 3.3	76.6 ± 4.7**
100	7.50 ± 0.14	7.63 ± 0.81	20.93 ± 0.67		26.20 ± 1.12**	7.0 ± 0.5	4.5 ± 0.1**		51.4 ± 4.2		40.2 ± 1.2**		58.4 ± 2.6	44.7 ± 3.4**
150	7.52 ± 0.69	7.84 ± 1.06	19.66 ± 0.87		26.15 ± 0.92**	4.6 ± 0.3	3.9 ± 0.3*		36.2 ± 5.6		37.1 ± 3.1		40.8 ± 4.1	41.0 ± 3.1

Cd content (μmol/L)	Root length (cm)			Shoot length (cm)		Root dry weight (mg)							Total dry weight (mg)
Cd content (μmol/L)	93-11	PA64s		93-11	PA64s	93-11		PA64s		93-11		PA64s	93-11	PA64s
0	13.34 ± 0.85	11.15 ± 1.09	27.27 ± 1.23		31.15 ± 1.23**	21.8 ± 1.1	18.8 ± 1.2**		91.4 ± 9.4		69.0 ± 5.3**		113.2 ± 6.7	87.8 ± 2.3**
10	11.59 ± 0.77	11.35 ± 0.39	24.06 ± 1.12		27.83 ± 1.29*	18.1 ± 1.7	18.4 ± 0.3		67.3 ± 3.2		62.0 ± 2.2**		84.4 ± 2.5	80.4 ± 4.5*
20	8.33 ± 0.87	10.74 ± 0.87*	23.86 ± 0.98		26.62 ± 1.98*	16.1 ± 1.5	18.1 ± 0.4*		67.0 ± 2.1		61.4 ± 3.5**		83.1 ± 6.3	79.5 ± 1.9*
30	8.20 ± 0.74	9.60 ± 0.57*	23.75 ± 0.99		26.59 ± 1.23*	15.0 ± 1.0	17.9 ± 0.9*		67.0 ± 2.3		60.2 ± 2.4**		82.0 ± 6.5	78.1 ± 2.3*
40	8.10 ± 0.57	9.55 ± 0.91*	23.45 ± 1.33		26.78 ± 1.32*	12.0 ± 0.9	17.7 ± 0.2**		66.1 ± 2.3		59.9 ± 3.1**		78.1 ± 2.1	77.6 ± 4.4
50	8.01 ± 0.54	9.52 ± 0.87*	20.16 ± 0.56		26.67 ± 0.99**	10.1 ± 0.4	17.6 ± 0.3**		52.6 ± 3.7		59.0 ± 2.4**		62.7 ± 3.3	76.6 ± 4.7**
100	7.50 ± 0.14	7.63 ± 0.81	20.93 ± 0.67		26.20 ± 1.12**	7.0 ± 0.5	4.5 ± 0.1**		51.4 ± 4.2		40.2 ± 1.2**		58.4 ± 2.6	44.7 ± 3.4**
150	7.52 ± 0.69	7.84 ± 1.06	19.66 ± 0.87		26.15 ± 0.92**	4.6 ± 0.3	3.9 ± 0.3*		36.2 ± 5.6		37.1 ± 3.1		40.8 ± 4.1	41.0 ± 3.1

Location and treatment	Trait	Parent		RIL population
Location and treatment	Trait	93-11	PA64s	Mean	Range	Skewness	Kurtosis
Hangzhou
Control	Root length (cm)	13.70 ± 1.01	11.80 ± 0.51*	11.76	6.35‒16.57	-0.29	0.87
	Shoot length (cm)	28.83 ± 1.23	33.64 ± 1.31*	31.30	22.31‒45.01	0.38	0.59
	Root dry weight (mg)	13.3 ± 1.1	10.3 ± 1.2*	9.1	2.5‒18.1	0.77	0.62
	Shoot dry weight (mg)	44.5 ± 3.1	36.5 ± 2.5**	36.3	10.3‒64.8	0.41	0.02
	Total dry weight (mg)	57.8 ± 3.6	46.8 ± 4.1**	45.2	10.3‒83.0	0.41	0.26
Cd stress	Root length (cm)	12.78 ± 1.30	11.81 ± 1.53	11.71	6.68‒17.43	-0.03	0.81
	Shoot length (cm)	20.23 ± 1.01	24.73 ± 1.34*	22.72	17.93‒29.68	0.52	0.27
	Root dry weight (mg)	10.1 ± 1.4	10.6 ± 1.3	9.3	3.7‒19.2	0.65	0.40
	Shoot dry weight (mg)	37.9 ± 2.5	35.4 ± 3.4	32.7	18.7‒52.8	0.41	-0.38
	Total dry weight (mg)	48.0 ± 4.1	46.0 ± 3.5	41.9	22.4‒71.7	0.36	-0.40
CTC	Relative root length (cm)	0.93 ± 0.09	1.06 ± 0.04*	0.98	0.57‒1.24	-1.22	3.95
	Relative shoot length (cm)	0.70 ± 0.06	0.74 ± 0.09	0.73	0.55‒0.93	-0.14	0.35
	Relative root dry weight (mg)	0.76 ± 0.04	1.03 ± 0.07**	1.05	0.26‒1.87	0.15	1.32
	Relative shoot dry weight (mg)	0.85 ± 0.03	0.99 ± 0.08*	0.90	0.47‒1.33	0.36	1.47
	Relative total dry weight (mg)	0.83 ± 0.04	0.98 ± 0.05*	0.93	0.45‒1.41	0.43	1.66
Lingshui
Control	Root length (cm)	14.24 ± 2.24	11.26 ± 2.11*	11.89	6.21‒17.41	-0.26	1.50
	Shoot length (cm)	28.87 ± 1.23	31.89 ± 0.96*	31.16	20.94‒44.98	0.42	0.85
	Root dry weight (mg)	13.2 ± 0.6	10.4 ± 0.5*	8.8	3.5‒20.5	0.83	1.77
	Shoot dry weight (mg)	46.5 ± 3.2	35.7 ± 3.4**	36.4	14.7‒72.4	0.58	1.03
	Total dry weight (mg)	59.7 ± 4.0	46.1 ± 3.3**	45.2	18.7‒92.8	0.65	1.35
Cd stress	Root length (cm)	13.13 ± 1.54	12.61 ± 2.10	11.80	6.16‒16.75	-0.21	0.48
	Shoot length (cm)	18.41 ± 1.23	23.71 ± 1.11**	23.07	15.85‒31.24	0.40	0.67
	Root dry weight (mg)	11.4 ± 1.5	12.6 ± 2.2	9.3	4.5‒17.7	0.67	0.26
	Shoot dry weight (mg)	34.4 ± 2.5	35.0 ± 3.3	32.3	18.1‒55.3	0.53	0.19
	Total dry weight (mg)	45.9 ± 4.6	47.6 ± 4.9	41.6	23.6‒70.9	0.51	-0.04
CTC	Relative root length (cm)	0.92 ± 0.08	1.12 ± 0.09**	1.00	0.51‒1.20	-1.85	6.10
	Relative shoot length (cm)	0.64 ± 0.06	0.74 ± 0.05*	0.75	0.48‒0.94	-0.26	0.92
	Relative root dry weight (mg)	0.86 ± 0.09	1.26 ± 0.08**	1.11	0.46‒1.95	0.70	1.44
	Relative shoot dry weight (mg)	0.74 ± 0.12	0.98 ± 0.09**	0.92	0.48‒1.48	0.64	1.60
	Relative total dry weight (mg)	0.77 ± 0.11	1.00 ± 0.08**	0.95	0.47‒1.45	0.54	1.00

Location and treatment	Trait	Parent		RIL population
Location and treatment	Trait	93-11	PA64s	Mean	Range	Skewness	Kurtosis
Hangzhou
Control	Root length (cm)	13.70 ± 1.01	11.80 ± 0.51*	11.76	6.35‒16.57	-0.29	0.87
	Shoot length (cm)	28.83 ± 1.23	33.64 ± 1.31*	31.30	22.31‒45.01	0.38	0.59
	Root dry weight (mg)	13.3 ± 1.1	10.3 ± 1.2*	9.1	2.5‒18.1	0.77	0.62
	Shoot dry weight (mg)	44.5 ± 3.1	36.5 ± 2.5**	36.3	10.3‒64.8	0.41	0.02
	Total dry weight (mg)	57.8 ± 3.6	46.8 ± 4.1**	45.2	10.3‒83.0	0.41	0.26
Cd stress	Root length (cm)	12.78 ± 1.30	11.81 ± 1.53	11.71	6.68‒17.43	-0.03	0.81
	Shoot length (cm)	20.23 ± 1.01	24.73 ± 1.34*	22.72	17.93‒29.68	0.52	0.27
	Root dry weight (mg)	10.1 ± 1.4	10.6 ± 1.3	9.3	3.7‒19.2	0.65	0.40
	Shoot dry weight (mg)	37.9 ± 2.5	35.4 ± 3.4	32.7	18.7‒52.8	0.41	-0.38
	Total dry weight (mg)	48.0 ± 4.1	46.0 ± 3.5	41.9	22.4‒71.7	0.36	-0.40
CTC	Relative root length (cm)	0.93 ± 0.09	1.06 ± 0.04*	0.98	0.57‒1.24	-1.22	3.95
	Relative shoot length (cm)	0.70 ± 0.06	0.74 ± 0.09	0.73	0.55‒0.93	-0.14	0.35
	Relative root dry weight (mg)	0.76 ± 0.04	1.03 ± 0.07**	1.05	0.26‒1.87	0.15	1.32
	Relative shoot dry weight (mg)	0.85 ± 0.03	0.99 ± 0.08*	0.90	0.47‒1.33	0.36	1.47
	Relative total dry weight (mg)	0.83 ± 0.04	0.98 ± 0.05*	0.93	0.45‒1.41	0.43	1.66
Lingshui
Control	Root length (cm)	14.24 ± 2.24	11.26 ± 2.11*	11.89	6.21‒17.41	-0.26	1.50
	Shoot length (cm)	28.87 ± 1.23	31.89 ± 0.96*	31.16	20.94‒44.98	0.42	0.85
	Root dry weight (mg)	13.2 ± 0.6	10.4 ± 0.5*	8.8	3.5‒20.5	0.83	1.77
	Shoot dry weight (mg)	46.5 ± 3.2	35.7 ± 3.4**	36.4	14.7‒72.4	0.58	1.03
	Total dry weight (mg)	59.7 ± 4.0	46.1 ± 3.3**	45.2	18.7‒92.8	0.65	1.35
Cd stress	Root length (cm)	13.13 ± 1.54	12.61 ± 2.10	11.80	6.16‒16.75	-0.21	0.48
	Shoot length (cm)	18.41 ± 1.23	23.71 ± 1.11**	23.07	15.85‒31.24	0.40	0.67
	Root dry weight (mg)	11.4 ± 1.5	12.6 ± 2.2	9.3	4.5‒17.7	0.67	0.26
	Shoot dry weight (mg)	34.4 ± 2.5	35.0 ± 3.3	32.3	18.1‒55.3	0.53	0.19
	Total dry weight (mg)	45.9 ± 4.6	47.6 ± 4.9	41.6	23.6‒70.9	0.51	-0.04
CTC	Relative root length (cm)	0.92 ± 0.08	1.12 ± 0.09**	1.00	0.51‒1.20	-1.85	6.10
	Relative shoot length (cm)	0.64 ± 0.06	0.74 ± 0.05*	0.75	0.48‒0.94	-0.26	0.92
	Relative root dry weight (mg)	0.86 ± 0.09	1.26 ± 0.08**	1.11	0.46‒1.95	0.70	1.44
	Relative shoot dry weight (mg)	0.74 ± 0.12	0.98 ± 0.09**	0.92	0.48‒1.48	0.64	1.60
	Relative total dry weight (mg)	0.77 ± 0.11	1.00 ± 0.08**	0.95	0.47‒1.45	0.54	1.00

Location and treatment	Trait	QTL ^a	Chr	Marker interval	Genetic distance (cM)	LOD ^b	Add ^c	Var (%)
Hangzhou
Control	RL	qRL3	3	SNP3-140‒SNP3-154	98.70‒113.51	4.58	1.246	12.6
		qRL4	4	SNP4-90‒SNP4-127	29.71‒38.56	5.87	-1.497	18.1
		qRL5	5	SNP5-257‒SNP5-299	186.46‒202.23	2.89	0.984	7.8
	RDW	qRDW1.2	1	SNP1-328‒SNP1-347	211.14‒241.11	3.08	-0.002	11.6
	SDW	qSDW2	2	SNP2-252‒SNP2-269	136.03‒155.15	3.64	-0.007	12.3
		qSDW11.2	11	SNP11-76‒SNP11-106	99.58‒119.73	3.01	-0.006	10.2
	TDW	qTDW2	2	SNP2-252‒SNP2-268	136.03‒154.58	3.71	-0.009	12.6
		qTDW11.2	11	SNP11-76‒SNP11-106	99.58‒119.73	2.86	-0.008	9.7
Cd stress	RL	qCDRL2	2	SNP2-265‒SNP2-288	150.74‒167.38	3.02	-1.259	11.4
	SL	qCDSL1.1	1	SNP1-311‒SNP1-347	201.79‒241.11	2.94	-1.450	9.9
		qCDSL5	5	SNP5-275‒SNP5-299	194.83‒202.23	3.07	1.503	10.7
	RDW	qCDRDW4.1	4	SNP4-1‒SNP4-29	0.00‒11.51	2.06	-0.017	0. 9
		qCDRDW5	5	SNP5-210‒SNP5-232	155.42‒176.84	2.60	0.002	11.7
	SDW	qCDSDW2	2	SNP2-252‒SNP2-267	136.03‒154.38	3.71	-0.006	12.8
		qCDSDW11	11	SNP11-70‒SNP11-114	97.21‒124.18	2.24	-0.005	7.9
	TDW	qCDTDW2	2	SNP2-252‒SNP2-269	136.03‒155.15	2.58	-0.007	9.2
		qCDTDW11	11	SNP11-70‒SNP11-114	97.21‒124.18	2.03	-0.006	6.6
CTC	RL	qRRL9	9	SNP9-136‒SNP9-168	76.32‒97.61	2.26	-0.088	8.8
CTC	SL	qRSL9	9	SNP9-160‒SNP9-180	90.45‒104.07	2.57	0.043	10.8
Lingshui Control
	SL	qSL3	3	SNP3-110‒SNP3-121	73.36‒82.84	3.07	2.413	9.2
		qSL9	9	SNP9-26‒SNP9-52	11.10‒27.03	4.43	2.914	13.4
		qSL10	10	SNP10-7‒SNP10-26	2.06‒20.03	3.03	2.374	8.9
	RDW	qRDW1.1	1	SNP1-163‒SNP1-193	104.79‒127.33	3.78	-0.002	12.5
		qRDW5	5	SNP5-267‒SNP5-299	190.72‒202.23	3.17	0.002	10.8
	SDW	qSDW11.1	11	SNP11-39‒SNP11-57	32.54‒53.91	2.93	0.006	11.1
	TDW	qTDW11.1	11	SNP11-39‒SNP11-59	32.54‒57.47	2.71	0.008	10.4
	Cd stress	RL	qCDRL10	10	SNP10-112‒SNP10-147	66.22‒81.82	3.01	1.288	11.8
SL		qCDSL1.2	1	SNP1-312‒SNP1-347	202.18‒241.11	3.44	-2.489	11.8
		qCDSL4	4	SNP4-220‒SNP4-259	81.03‒104.36	2.36	-2.080	8.3
RDW		qCDRDW4.2	4	SNP4-270‒SNP4-285	108.33‒139.91	2.75	-0.002	11.8
SDW		qCDSDW4	4	SNP4-1‒SNP4-19	0.00‒8.33	2.67	-0.005	10.5
TDW		qCDTDW4	4	SNP4-1‒SNP4-19	0.00‒8.33	2.65	-0.006	10.5
CTC	RL	qRRL7	7	SNP7-230‒SNP7-263	102.30‒119.81	2.44	0.090	9.4
	RDW	qRRDW3	3	SNP3-265‒SNP3-284	199.55‒221.41	3.99	-0.241	15.4
	SDW	qRSDW1	1	SNP1-177‒SNP1-197	108.96‒129.65	2.81	0.141	10.6
	TDW	qRTDW1	1	SNP1-177‒SNP1-197	108.96‒129.65	2.99	0.149	11.3