芝麻产量相关性状的多位点全基因组关联分析及候选基因预测

doi:10.3864/j.issn.0578-1752.2022.01.018

Abstract

Abstract:

【Objective】 Genome-wide association studies (GWAS) were performed using multi-locus random-SNP-effect mixed linear (mrMLM) model to identify the significantly associated SNPs and candidate genes with yield traits, and lay a foundation for molecular marker-assisted selection breeding for sesame high yield.【Method】 In this study, 363 diverse sesame lines were assembled into an association-mapping panel. Eight yield-related traits, including seed yield per plant, capsule number per plant, seed number per capsule, 1000-seed weight, plant height, capsule axis length, first capsule height and apparent harvest index, were investigated. Genome-wide association studies were performed using mrMLM to detect significantly associated SNPs and predict important candidate genes related to yield traits.【Result】 Eight yield-related traits measured in four environments exhibited extensive phenotypic variation with 1.63%-17.29% of phenotypic variation coefficients. The seed yield per plant was positively correlated with capsule number per plant, plant height, capsule axis length, and apparent harvest index respectively. Analysis of variance indicated that significant variations were observed across environment, genotype, and the genotype × environment interaction. GWAS were performed and a total of 210 SNPs were detected for yield traits. Among these SNPs, 47, 35, 35, 53, and 75 SNPs were detected in 2018NY, 2019NY, 2018PY, 2019PY and BLUP, explaining 1.63%-17.29%, 1.94%-11.90%, 2.15%-15.90%, 1.25%-11.13% and 1.44%-13.58% of phenotypic variation, respectively. These 210 SNPs corresponded to 175 loci, and 10 loci were detected in more than 3 environments. A total of 214 candidate genes were identified, including 156 genes involved in metabolism, biological regulation, and developmental and growth process. Among these genes, 4 genes were selected as important candidate genes. SIN_1006338, encoding 1-aminocyclopropane-1-carboxylate synthase 3-like protein, was involved in ethylene biosynthesis. SIN_1024330, encoding transcription factor IBH1-like 1, was involved in regulating cell and organ elongation. SIN_1014512, encoding indole-3-acetic acid-amido synthetase GH3.6, was involved in shoot and hypocotyl cell elongation. SIN_1011473, encoding protein DA1-like, was involved in restricting the period of cell proliferation.【Conclusion】 One hundred and seventy-five loci were identified by mrMLM, and 4 important genes related to yield traits were selected.

Key words: Sesamum indicum L., yield-related traits, genome-wide association studies, function annotation, candidate gene

CUI ChengQi, LIU YanYang, JIANG XiaoLin, SUN ZhiYu, DU ZhenWei, WU Ke, MEI HongXian, ZHENG YongZhan. Multi-Locus Genome-Wide Association Analysis of Yield-Related Traits and Candidate Gene Prediction in Sesame (Sesamum indicum L.)[J].Scientia Agricultura Sinica, 2022, 55(1): 219-232.

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Figures/Tables 7

Table 1

Descriptive statistics for yield-related traits of the association population"

环境 Environment	性状 Traits	变异范围 Range	均值 Mean	标准差 SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
2018年平舆 2018PY	单株产量SY	3.00–17.36	8.30	2.52	30.33	0.50	0.04
	单株蒴数CN	31.65–108.05	62.27	14.69	23.60	0.52	0.13
	蒴粒数SN	36.07–112.98	64.64	8.53	13.20	0.74	3.46
	千粒重SW	2.04–3.77	3.00	0.32	10.49	-0.30	-0.15
	株高PH	100.00–183.50	138.41	13.16	9.51	-0.01	0.01
	主茎果轴长CAL	32.15–94.50	60.50	11.49	18.99	0.06	-0.23
	始蒴高度FCH	49.50–102.50	72.82	9.72	13.35	0.21	0.22
	表观收获指数HI	0.18–0.44	0.31	0.05	16.13.	-0.16	-0.25
2018年南阳 2018NY	单株产量SY	2.50–17.80	7.63	2.17	28.46	0.54	1.03
	单株蒴数CN	56.00–166.20	103.16	20.56	19.93	0.28	-0.07
	蒴粒数SN	43.71–106.07	64.31	8.36	12.99	0.85	2.74
	千粒重SW	2.29–3.86	3.07	0.31	10.02	0.18	-0.38
	株高PH	137.60–240.00	183.19	15.96	8.71	-0.10	0.40
	主茎果轴长 CAL	74.80–151.00	113.57	12.44	10.96	-0.08	0.11
	始蒴高度FCH	36.50–102.80	60.98	10.16	16.66	0.36	1.26
	表观收获指数HI	0.10–0.42	0.21	0.04	19.05	0.71	3.73
2019年平舆 2019PY	单株产量SY	3.01–20.09	9.12	3.06	33.57	0.59	0.63
	单株蒴数CN	21.20–152.90	82.29	21.87	26.58	0.28	0.18
	蒴粒数SN	30.68–102.49	64.71	9.86	15.24	0.91	2.83
	千粒重SW	1.63–3.93	2.98	0.41	13.78	-0.33	-0.20
	株高PH	80.60–200.60	141.81	17.36	12.24	0.09	1.01
	主茎果轴长 CAL	22.00–123.70	78.10	15.05	19.27	-0.06	0.46
	始蒴高度FCH	22.40–146.50	60.57	14.55	24.03	0.55	2.78
	表观收获指数HI	0.08–0.39	0.22	0.05	22.73	-0.31	0.45
2019年南阳 2019NY	单株产量SY	4.88–17.54	11.17	2.41	21.56	0.05	-0.48
	单株蒴数CN	35.95–124.20	75.59	15.29	20.22	0.22	0.03
	蒴粒数SN	52.83–120.25	69.18	9.41	13.60	1.74	4.69
	千粒重SW	2.25–4.20	3.08	0.35	11.20	0.09	-0.49
	株高PH	113.65–207.65	150.65	16.17	10.73	0.37	0.14
	主茎果轴长CAL	55.93–116.40	84.61	12.49	14.76	0.19	-0.47
	始蒴高度FCH	29.65–99.60	59.18	10.89	18.40	0.57	0.67
	表观收获指数HI	0.11–0.35	0.23	0.05	21.74	-0.10	-0.62
综合 BLUP	单株蒴数CN	53.05–89.01	71.69	7.03	9.79	0	-0.31
	蒴粒数 SN	54.96–91.76	66.26	5.86	8.85	1.46	3.02
	千粒重 SW	2.48–3.60	3.06	0.20	6.51	-0.14	-0.39
	单株产量SY	6.82–11.05	8.55	0.77	9.01	0.53	0.21
	株高PH	121.4–169.0	145.7	9.70	6.66	0.04	-0.46
	主茎果轴长CAL	50.95–85.69	69.33	7.61	10.98	-0.15	-0.75
	始蒴高度FCH	47.10–90.10	64.78	7.55	11.65	0.34	0.14
	表观收获指数 HI	0.17–0.27	0.22	0.02	9.10	-0.11	-0.35

Table 1

Fig. 1

Table 2

Correlation coefficients among yield-related traits in the association mapping population"

环境 Environment	性状 Trait	单株产量 SY	单株蒴数 CN	蒴粒数 SN	千粒重 SW	株高 PH	主茎果轴长 CAL	始蒴高度 FCH
2018年平舆 2018PY	单株蒴数 CN	0.53**
	蒴粒数 SN	0.10	-0.12*
	千粒重 SW	0.10	0.03	-0.15**
	株高 PH	0.35**	0.31**	0.03	0.16**
	主茎果轴长 CAL	0.46**	0.40**	0.04	0.18**	0.74**
	始蒴高度 FCH	0.01	-0.02	0.02	0.08	0.62**	-0.25**
	表观收获指数 HI	0.60**	0.28**	0.08	-0.21**	-0.02	0.17**	-0.23**
2018年南阳 2018NY	单株蒴数 CN	0.80**
	蒴粒数 SN	0.17**	0.01
	千粒重 SW	0.08	-0.04	-0.36**
	株高 PH	0.45**	0.348**	0.08	0.14**
	主茎果轴长 CAL	0.40**	0.32**	-0.09	0.20**	0.76**
	始蒴高度 FCH	0.126*	0.10	0.258**	-0.05	0.43**	-0.25**
	表观收获指数 HI	0.55**	0.29**	0.15**	-0.06	0.05	0.14**	-0.12*
2019年平舆 2019PY	单株蒴数 CN	0.56**
	蒴粒数 SN	0.01	-0.13*
	千粒重 SW	0.28**	0.00	-0.26**
	株高 PH	0.44**	0.32**	0.07	0.18**
	主茎果轴长 CAL	0.43**	0.29**	-0.07	0.36**	0.58**
	始蒴高度 FCH	0.07	0.07	0.157**	-0.140**	0.551**	-0.36**
	表观收获指数 HI	0.63**	0.21**	-0.03	0.22**	0.10	0.63**	-0.18**
2019年南阳 2019NY	单株蒴数 CN	0.56**
	蒴粒数 SN	0.03	-0.22**
	千粒重 SW	0.01	-0.08	-0.18**
	株高 PH	0.32**	0.45**	0.09	0.26**
	主茎果轴长 CAL	0.44**	0.52**	-0.08	0.18**	0.77**
	始蒴高度 FCH	-0.09	-0.04	0.236**	0.25**	0.50**	-0.15**
	表观收获指数 HI	0.30**	0.28**	-0.12*	-0.13*	0.06	0.32**	-0.34**
综合BLUP	单株蒴数 CN	0.68**
	蒴粒数 SN	-0.03	-0.26 **
	千粒重 SW	0.12*	-0.15**	-0.30**
	株高 PH	0.38**	0.27**	0.09	0.21**
	主茎果轴长 CAL	0.51**	0.35**	-0.08	0.25**	0.65**
	始蒴高度 FCH	-0.02	-0.02	0.23**	0.03	0.59**	-0.21**
	表观收获指数 HI	0.57**	0.39**	-0.03	-0.10	-0.04	0.35**	-0.40**

Table 2

Table 3

Fig. 2

Table 4

Ten significantly associated loci that could be detected in more than 3 environments"

位点 Loci	连锁群 LG	环境 Environments	性状 Traits	标记 SNP	物理位置 Position (bp)	LOD值 LOD	贡献率 R² (%)
1	4	2018年南阳2018NY	单株蒴数 CN	S4_12077666	12077666	4.88	4.52
1	4	2018年平舆2018PY	单株蒴数 CN	S4_12175895	12175895	4.74	5.34
1	4	2019年平舆2019PY	单株蒴数 CN	S4_12175895	12175895	7.23	5.75
1	4	综合 BLUP	单株蒴数 CN	S4_12175895	12175895	8.84	7.38
2	4	2018年南阳2018NY	蒴粒数 SN	S4_12175895	12175895	7.45	4.65
2	4	2018年平舆2018PY	蒴粒数 SN	S4_12175895	12175895	14.19	12.89
2	4	2019年南阳2019NY	蒴粒数 SN	S4_12175895	12175895	8.97	6.60
2	4	2019年平舆2019PY	蒴粒数 SN	S4_12175895	12175895	8.41	8.16
2	4	综合 BLUP	蒴粒数 SN	S4_12175895	12175895	11.97	7.34
3	6	2018年平舆2018PY	千粒重 SW	S6_20401909	20401909	3.91	3.88
3	6	2019年南阳2019NY	千粒重 SW	S6_20401885	20401885	3.14	2.60
3	6	2019年平舆2019PY	千粒重 SW	S6_20401885	20401885	4.05	3.31
3	6	综合 BLUP	千粒重 SW	S6_20401885	20401885	3.21	2.39
4	4	2018年平舆2018PY	株高 PH	S4_2965202	2965202	11.61	9.70
4	4	2019南阳2019NY	株高 PH	S4_2999295	2999295	5.60	7.45
4	4	2019年平舆2019PY	株高 PH	S4_2965202	2965202	3.13	2.87
5	6	2018年南阳2018NY	株高 PH	S6_3944096	3944096	3.29	10.37
5	6	2018年平舆2018PY	株高 PH	S6_3944096	3944096	4.66	4.21
5	6	综合 BLUP	株高 PH	S6_3944096	3944096	3.41	4.22
6	1	2018年南阳2018NY	始蒴高度 FCH	S1_5656292	5656292	6.11	5.46
6	1	2019年平舆2019PY	始蒴高度 FCH	S1_5656292	5656292	8.20	6.52
6	1	综合 BLUP	始蒴高度 FCH	S1_5656292	5656292	5.78	6.25
7	4	2018年南阳2018NY	始蒴高度 FCH	S4_12175895	12175895	6.54	4.12
7	4	2018年平舆2018PY	始蒴高度 FCH	S4_12175895	12175895	3.23	2.15
7	4	2019年南阳2019NY	始蒴高度 FCH	S4_12175895	12175895	9.00	4.91
7	4	2019年平舆2019PY	始蒴高度 FCH	S4_12175895	12175895	3.10	2.03
7	4	综合 BLUP	始蒴高度 FCH	S4_12175895	12175895	10.01	6.95
8	10	2018年南阳2018NY	始蒴高度 FCH	S10_3435751	3435751	6.30	17.29
8	10	2019年平舆2019PY	始蒴高度 FCH	S10_3389829	3389829	3.38	2.17
8	10	2019年南阳2019NY	始蒴高度 FCH	S10_3441972	3441972	3.28	6.68
9	12	2018年南阳2018NY	始蒴高度 FCH	S12_7500712	7500712	7.67	8.91
9	12	2019年南阳2019NY	始蒴高度 FCH	S12_7510215	7510215	6.97	2.68
9	12	综合 BLUP	始蒴高度 FCH	S12_7500712	7500712	3.36	3.48
10	5	2018年南阳2018NY	表观收获指数 HI	S5_1942861	1942861	3.13	3.87
10	5	2019年平舆2019PY	表观收获指数 HI	S5_1861592	1861592	3.21	8.11
10	5	综合 BLUP	表观收获指数 HI	S5_1942861	1942861	4.25	2.14

Table 4

Fig. 3

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性状Trait	变异来源Source	离均差平方和 Type sum of squares	自由度 Df	均方 Mean square	F值F value
单株产量 SY	基因型G	7277.22	362	20.10	3.00**
	环境E	12743.45	3	4247.82	633.22**
	基因型×环境 G×E	12598.92	1086	11.60	1.73**
	误差 Error	9740.36	1452	6.71
	总变异Total	250355.40	2904
单株蒴数 CN	基因型G	362349.02	362	1000.96	4.05**
	环境E	353079.52	3	117693.17	476.59**
	基因型×环境 G×E	422589.91	1086	389.13	1.58**
	误差Error	358570.49	1452	246.95
	总变异Total	15197261.65	2904
蒴粒数 SN	基因型G	154208.88	362	425.99	6.27**
	环境E	8841.06	3	2947.02	43.36**
	基因型×环境 G×E	130872.51	1086	120.51	1.77**
	误差Error	98692.38	1452	67.97
	总变异Total	13566244.22	2904
千粒重 SW	基因型G	207.75	362	0.57	9.27**
	环境E	25.70	3	8.57	138.44**
	基因型×环境G×E	114.06	1086	0.11	1.70**
	误差Error	89.84	1452	0.06
	总变异Total	28640.90	2904
株高 PH	基因型G	380243.82	362	1050.40	8.44**
	环境E	520433.78	3	173477.93	1393.93**
	基因型×环境 G×E	239288.84	1086	220.34	1.77**
	误差Error	180705.09	1452	124.45
	总变异Total	60234518.86	2904
主茎果轴长 CAL	基因型G	249490.48	362	689.20	5.94**
	环境E	223064.77	3	74354.92	640.81**
	基因型×环境 G×E	205442.35	1086	189.17	1.63**
	误差Error	168479.54	1452	116.03
	总变异Total	16679958.27	2904
始蒴高度 FCH	基因型 G	239089.39	362	660.47	9.20**
	环境E	163719.63	3	54573.21	759.93**
	基因型×环境G×E	122236.79	1086	112.56	1.57**
	误差Error	104273.55	1452	71.81
	总变异Total	12056126.18	2904
表观收获指数 HI	基因型G	30750.48	362	84.95	3.42**
	环境E	125145.68	3	41715.23	1679.68**
	基因型×环境 G×E	44030.95	1086	40.54	1.63**
	误差Error	36035.85	1451	24.84
	总变异Total	1743682.01	2903

Multi-Locus Genome-Wide Association Analysis of Yield-Related Traits and Candidate Gene Prediction in Sesame (Sesamum indicum L.)

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