QTL Mapping and Candidate Gene Analysis of Vitamin E in Rice Grain

doi:10.11983/CBB21216

Abstract

Abstract:

Vitamin E (V_E) is an important index of rice nutritional quality. Rice (Oryza sativa) is the most widely planted crop in China. To increase rice V_E content is a convenient and effective way to improve its nutrient composition. In this study, 120 recombinant inbred line (RIL) populations were constructed with indica rice HZ as male parent and japonica rice Nekken2 as female parent. The content of vitamin E isomer in the population was determined by high performance liquid chromatography (HPLC). Quantitative trait loci (QTL) mapping was carried out based on the constructed high-density molecular genetic map. After pedigree analysis, 122 V_E related QTLs were identified, which were distributed on 12 chromosomes. Some loci have high LOD scores, such as qT3α/to2-1 with 10.32 LOD score, qT3α2-1 of 9.91 LOD score. There are multiple major QTLs associated with the content of different conformations, and some V_E biosynthesis genes are within the intervals, e.g., OsGGR1, OsGGR2, OsTC and OsγTMT. The expression of these genes were analyzed by qRT-PCR. The results showed that their expression in HZ was significantly higher than that in Nekken2. It is speculated that the high expression of these genes is the reason of why tocopherol and tocotrienol in HZ are higher than in Nekken2. The number of QTLs and the scores of LOD are large, which provides a molecular basis for further screening and cultivating rice varieties with high V_E content also conductive to clarify the molecular regulation mechanism of rice V_E biosynthesis through QTLs.

Key words: rice, vitamin E, QTL mapping, candidate genes, rice quality

Hanfei Ye, Wenjing Yin, Yian Guan, Kairu Yang, Qianyu Chen, Shuying Yu, Xudong Zhu, Dedong Xin, Wei Zhang, Yuexing Wang, Yuchun Rao. QTL Mapping and Candidate Gene Analysis of Vitamin E in Rice Grain[J]. Chinese Bulletin of Botany, 2022, 57(2): 157-170.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB21216

https://www.chinbullbotany.com/EN/Y2022/V57/I2/157

Figures/Tables 9

References 30

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Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)
LOC_Os01g16020-F-qrt	CCATGGCCTACTACGACGAC	60.05	150
LOC_Os01g16020-R-qrt	CCGACTGGAGCCTCTTGATC	59.95	150
LOC_Os02g07160-F-qrt	AGGAGCAGATCAACGAGTGC	60.11	172
LOC_Os02g07160-R-qrt	TTCTGGTACTCCTGCCCACT	60.28	172
LOC_Os02g17650-F-qrt	TCGACGCAACAAGCAACATG	59.95	161
LOC_Os02g17650-R-qrt	ACCAGGGGGCTTGAGAAATG	59.75	161
LOC_Os02g47310-F-qrt	CGGCAGAGCAAGGGTTATCA	59.96	223
LOC_Os02g47310-R-qrt	GACTCTTCGGATGGCTCGAG	60.39	223
LOC_Os02g51080-F-qrt	GATGATTTCGCCGTCCAACG	60.05	200
LOC_Os02g51080-R-qrt	TGTAGTGCACCACGTACGAC	60.03	200
LOC_Os06g43880-F-qrt	CCGTGCAAGTCCAGGAAGAT	59.96	196
LOC_Os06g43880-R-qrt	TCACCAGCAATGGCATAGCA	60.00	196
LOC_Os06g44840-F-qrt	CCTTGGATGGGCTGTTGGAT	59.99	223
LOC_Os06g44840-R-qrt	TGGCCTGGTAAAGACTGCTG	60.08	223
LOC_Os07g08200-F-qrt	ACCGAGGACATGAGGGATGA	59.98	179
LOC_Os07g08200-R-qrt	TTCTGCCTGGCCTTCTCAAG	60.07	179
LOC_Os12g42090-F-qrt	CTCAAGGGCGTCACCATCAT	60.12	224
LOC_Os12g42090-R-qrt	AGCATCCACATGTCAGCGAA	59.98	224

Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)
LOC_Os01g16020-F-qrt	CCATGGCCTACTACGACGAC	60.05	150
LOC_Os01g16020-R-qrt	CCGACTGGAGCCTCTTGATC	59.95	150
LOC_Os02g07160-F-qrt	AGGAGCAGATCAACGAGTGC	60.11	172
LOC_Os02g07160-R-qrt	TTCTGGTACTCCTGCCCACT	60.28	172
LOC_Os02g17650-F-qrt	TCGACGCAACAAGCAACATG	59.95	161
LOC_Os02g17650-R-qrt	ACCAGGGGGCTTGAGAAATG	59.75	161
LOC_Os02g47310-F-qrt	CGGCAGAGCAAGGGTTATCA	59.96	223
LOC_Os02g47310-R-qrt	GACTCTTCGGATGGCTCGAG	60.39	223
LOC_Os02g51080-F-qrt	GATGATTTCGCCGTCCAACG	60.05	200
LOC_Os02g51080-R-qrt	TGTAGTGCACCACGTACGAC	60.03	200
LOC_Os06g43880-F-qrt	CCGTGCAAGTCCAGGAAGAT	59.96	196
LOC_Os06g43880-R-qrt	TCACCAGCAATGGCATAGCA	60.00	196
LOC_Os06g44840-F-qrt	CCTTGGATGGGCTGTTGGAT	59.99	223
LOC_Os06g44840-R-qrt	TGGCCTGGTAAAGACTGCTG	60.08	223
LOC_Os07g08200-F-qrt	ACCGAGGACATGAGGGATGA	59.98	179
LOC_Os07g08200-R-qrt	TTCTGCCTGGCCTTCTCAAG	60.07	179
LOC_Os12g42090-F-qrt	CTCAAGGGCGTCACCATCAT	60.12	224
LOC_Os12g42090-R-qrt	AGCATCCACATGTCAGCGAA	59.98	224

Trait	RILs			Parents
Trait	Means±SD	Range	Skewness	HZ	Nekken2
Total-V_E (μg∙g^-1)	33.9489±8.24636	11.64-62.93	0.7220	39.0169	25.1275
Total-toco (μg∙g^-1)	13.9571±6.54920	4.19-43.16	1.7550	15.6586	7.3524
Total-t3 (μg∙g^-1)	19.9918±4.44004	7.45-30.41	0.0940	23.3583	17.7751
α-toco (μg∙g^-1)	11.0692±6.46111	2.34-41.33	1.9120	11.8855	4.7839
γ-toco (μg∙g^-1)	2.7072±1.11795	0.74-6.73	0.3200	3.6121	2.3390
δ-toco (μg∙g^-1)	0.1807±0.12540	0.03-0.92	2.1220	0.1610	0.2295
α-t3 (μg∙g^-1)	2.3057±1.33266	0.60-6.10	1.1710	1.4780	5.1269
γ-t3 (μg∙g^-1)	16.0730±4.3067	5.76-26.14	0.1970	20.4400	11.2289
δ-t3 (μg∙g^-1)	1.6131±0.63116	0.56-4.46	1.4040	1.4404	1.4193
α-toco/total-toco	0.7618±0.12004	0.36-0.96	0.7610	0.7596	0.6344
α-t3/total-t3	0.1203±0.07395	0.04-0.34	1.0980	0.0634	0.2881

Trait	RILs			Parents
Trait	Means±SD	Range	Skewness	HZ	Nekken2
Total-V_E (μg∙g^-1)	33.9489±8.24636	11.64-62.93	0.7220	39.0169	25.1275
Total-toco (μg∙g^-1)	13.9571±6.54920	4.19-43.16	1.7550	15.6586	7.3524
Total-t3 (μg∙g^-1)	19.9918±4.44004	7.45-30.41	0.0940	23.3583	17.7751
α-toco (μg∙g^-1)	11.0692±6.46111	2.34-41.33	1.9120	11.8855	4.7839
γ-toco (μg∙g^-1)	2.7072±1.11795	0.74-6.73	0.3200	3.6121	2.3390
δ-toco (μg∙g^-1)	0.1807±0.12540	0.03-0.92	2.1220	0.1610	0.2295
α-t3 (μg∙g^-1)	2.3057±1.33266	0.60-6.10	1.1710	1.4780	5.1269
γ-t3 (μg∙g^-1)	16.0730±4.3067	5.76-26.14	0.1970	20.4400	11.2289
δ-t3 (μg∙g^-1)	1.6131±0.63116	0.56-4.46	1.4040	1.4404	1.4193
α-toco/total-toco	0.7618±0.12004	0.36-0.96	0.7610	0.7596	0.6344
α-t3/total-t3	0.1203±0.07395	0.04-0.34	1.0980	0.0634	0.2881

Trait		QTL	Chromosome	Physical distance (bp)	Position of support (cM)	LOD
Total		qVE2-1	02	3467582-15790369	14.86-67.69	2.82
		qVE2-2	02	30526267-30670565	130.86-131.48	3.11
		qVE5-1	05	27292002-27936693	116.99-119.76	3.05
		qVE7-1	07	25017683-25489862	107.24-109.27	3.50
		qVE8-1	08	10042712-11311929	43.05-48.49	3.69
		qVE8-2	08	14098425-15488141	60.44-66.39	4.00
		qVE8-3	08	19014129-21020793	81.51-90.11	4.85
		qVE10-1	10	10714090-13003806	45.93-55.74	3.70
Total-t3		qT3to1-1	01	7035569-8460131	30.16-36.27	3.51
		qT3to3-1	03	11975352-12205246	51.34-52.32	2.93
		qT3to5-1	05	27199002-27292002	116.59-116.99	2.88
		qT3to10-1	10	13003806-15914330	55.74-68.22	2.96
Total-toco		qTto2-1	02	7154574-16772608	30.67-71.90	3.63
		qTto8-1	08	10042712-15565426	43.05-66.72	2.68
		qTto8-2	08	19301150-20349908	82.74-87.23	3.65
		qTto10-1	10	57733-5856857	0.25-25.11	3.46
		qTto10-2	10	10573976-13003806	45.33-55.74	7.39
		qTto11-1	11	9677541-9808325	41.48-42.05	2.65
α-t3		qT3α1-1	01	8235815-8460131	35.30-36.27	3.57
		qT3α2-1	02	20415024-32383695	87.51-138.82	9.91
		qT3α2-2	02	32754542-35824426	140.41-153.57	3.64
		qT3α5	05	4080644-6619616	17.49-28.38	3.58
		qT3α7-1	07	42757-572873	0.18-2.46	3.27
		qT3α8-1	08	4857563-6004458	20.82-25.74	3.43
		qT3α8-2	08	8917564-15791348	38.23-67.69	4.66
		qT3α8-3	08	24746469-25177340	106.08-107.93	2.50
		qT3α8-4	08	25195867-25340928	108.01-108.63	2.55
		qT3α9-1	09	13620974-14832840	58.39-63.58	3.10
		qT3α9-2	09	16630835-22938953	71.29-98.33	5.28
α-t3/total-t3		qT3α/to1-1	01	8235815-9438021	35.30-40.46	3.66
		qT3α/to2-1	02	20415024-35824426	87.51-153.57	10.32
		qT3α/to3-1	03	5183108-6234241	22.22-26.72	3.25
		qT3α/to3-2	03	6743718-6982005	28.91-29.93	3.31
		qT3α/to5-1	05	4080644-6619616	17.49-28.38	3.31
		qT3α/to6-1	06	20854685-21217545	89.40-90.95	2.81
		qT3α/to6-2	06	21507916-21913927	92.20-93.94	2.66
		qT3α/to6-3	06	22256655-24198880	95.41-103.73	3.57
		qT3α/to7-1	07	42757-875466	0.18-3.75	2.88
		qT3α/to8-1	08	5469252-5970122	23.45-25.59	3.53
		qT3α/to8-2	08	13109769-13402076	56.20-57.45	3.79
		qT3α/to8-3	08	24432953-25340928	104.74-108.63	2.96
		qT3α/to9-1	09	13572882-14761639	58.18-63.28	3.42
		qT3α/to9-2	09	16699350-17528726	71.59-75.14	2.78
		qT3α/to9-3	09	17822997-22938953	76.40-98.33	6.47
		qT3α/to10-1	10	12856184-13003806	55.11-55.74	3.65
		qT3α/to10-2	10	19066686-19211967	81.73-82.36	2.57
α-toco		qTα2-1	02	10650561-10928729	45.66-46.85	3.41
		qTα2-2	02	11181757-11319097	47.932-48.52	2.54
		qTα8-1	08	10119315-15791348	43.38-67.69	2.77
		qTα8-2	08	19301150-20108258	82.74-86.20	3.10
		qTα10-1	10	1624313-5776626	6.96-24.76	3.17
		qTα10-2	10	10635436-11008219	45.59-47.19	3.90
		qTα11-1	11	9677541-9808325	41.48-42.05	2.96
		qTα11-2	11	21463452-22167073	92.01-95.02	3.06
α-toco/total-toco		qTα/to1-1	01	1663060-2070966	7.13-8.88	2.61
		qTα/to2-1	02	10650561-10928729	45.66-46.85	3.83
		qTα/to2-2	02	27158525-28132392	116.42-120.60	2.83
		qTα/to2-3	02	28499903-30078981	122.17-128.94	3.76
		qTα/to2-4	02	35381094-35525300	151.67-152.29	3.24
		qTα/to3-1	03	786808-1156051	3.37-4.96	4.36
		qTα/to3-2	03	1531836-1753422	6.57-7.52	2.81
		qTα/to4-1	04	4147493-4739169	17.78-20.32	4.23
		qTα/to4-2	04	6047670-9068118	25.92-38.87	4.23
		qTα/to4-3	04	13341761-14630459	57.19-62.72	4.18
		qTα/to5-1	05	6526040-6673100	27.98-28.61	2.80
		qTα/to5-2	05	7886106-8030564	33.81-34.42	4.14
		qTα/to5-3	05	19534829-19659074	83.74-84.27	2.67
		qTα/to6-1	06	3108218-3378992	13.32-14.48	3.02
		qTα/to6-2	06	16365713-16951387	70.16-72.67	2.53
		qTα/to6-3	06	24956043-25093708	106.98-107.57	2.79
		qTα/to6-4	06	26359832-27156405	113.00-116.41	3.18
		qTα/to7-1	07	13014544-13768860	55.79-59.02	3.42
		qTα/to7-2	07	17441086-17530313	74.77-75.15	2.70
		qTα/to8-1	08	712661-860780	3.05-3.69	4.14
		qTα/to8-2	08	1152527-1753671	4.94-7.52	4.58
		qTα/to8-3	08	5341420-5646427	22.90-24.20	3.94
	qTα/to9-1		09	11654883-11744700	49.96-50.35	2.52
	qTα/to11-1		11	8467466-8766502	36.30-37.58	3.04
	qTα/to11-2		11	21077880-22646003	90.36-97.08	4.92
	qTα/to12-1		12	260226-401477	1.12-1.72	2.50
	qTα/to12-2		12	6824561-7508660	29.25-32.19	3.34
	qTα/to12-3		12	17175063-18091161	73.62-77.55	3.32
γ-t3	qT3γ1-1		01	7128319-9521270	30.56-40.82	3.31
	qT3γ2-1		02	29846956-31331712	127.95-134.31	3.26
	qT3γ2-2		02	35381094-35675126	151.67-152.93	3.15
	qT3γ6-1		06	27333693-28446541	117.17-121.94	3.54
	qT3γ8-1		08	712661-860780	3.05-3.69	3.78
γ-toco	qTγ1-1		01	1663060-1775390	7.13-7.61	2.56
	qTγ2-1		02	24818487-35305635	106.39-151.35	6.20
	qTγ3-1		03	5859763-6008076	25.12-25.75	2.50
	qTγ4-1		04	5922401-6230638	25.39-26.71	2.92
	qTγ4-2		04	6451666-6599549	27.66-28.29	2.54
	qTγ5-1		05	6983157-10879499	29.93-46.64	2.91
	qTγ5-2		05	27199002-27292002	116.59-116.99	2.73
	qTγ6-1		06	6452921-6720585	27.66-28.81	3.22
	qTγ7-1		07	572873-936652	2.46-4.02	2.64
	qTγ8-1		08	712661-860780	3.05-3.69	2.72
	qTγ9-1		09	21030827-21162733	90.15-90.72	2.51
δ-t3	qT3δ1-1		01	19435110-19915117	83.31-85.37	3.36
	qT3δ1-2		01	25117984-25257953	107.67-108.27	5.75
	qT3δ2-1		02	7215671-8736288	30.93-37.45	2.66
	qT3δ2-2		02	30228480-32985884	129.58-141.40	2.66
	qT3δ3-1		03	29597075-29806859	126.87-127.77	2.86
	qT3δ4-1		04	17170511-23608260	73.61-101.20	3.31
	qT3δ4-2		04	26410305-31423289	113.21-134.70	4.71
	qT3δ8-1		08	20195421-20349908	86.57-87.23	2.97
	qT3δ10-1		10	57733-13172007	0.25-56.46	3.88
	qT3δ10-2		10	19963553-20188240	85.58-86.54	4.49
	qT3δ12-1		12	4509538-4663215	19.33-19.99	3.16
	qT3δ12-2		12	19235536-26139939	82.46-112.05	4.90
δ-toco	qTδ1-1		01	38537755-39791276	165.20-170.57	4.28
	qTδ2-1		02	7215671-7350401	30.93-31.51	2.89
	qTδ2-2		02	31043939-32985884	133.08-141.40	2.57
	qTδ3-1		03	5785084-6008076	24.80-25.75	3.49
	qTδ5-1		05	853216-1082203	3.66-4.64	3.23
	qTδ5-2		05	6983157-7138974	29.93-30.60	6.17
	qTδ5-3		05	13569180-13776389	58.17-59.06	2.70
	qTδ6-1		06	6452921-6720585	27.67-28.81	3.80
	qTδ7-1		07	7351588-15250540	31.51-65.37	2.73
	qTδ8-1		08	1152527-5163244	4.94-22.13	3.51
	qTδ9-1		09	10102157-12363787	43.31-53.00	3.73
	qTδ12-1		12	9212254-15247966	39.49-65.36	7.16