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

中国农业科学 ›› 2022, Vol. 55 ›› Issue (1): 219-232.doi: 10.3864/j.issn.0578-1752.2022.01.018

• 研究简报 • 上一篇

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

崔承齐¹(),刘艳阳¹(),江晓林¹,孙知雨²,杜振伟¹,武轲¹,梅鸿献¹(),郑永战¹()

¹河南省农业科学院芝麻研究中心,郑州 450008
²华南师范大学生命科学学院,广州 510631

收稿日期:2021-06-23 接受日期:2021-09-18 出版日期:2022-01-01 发布日期:2022-01-07
通讯作者: 梅鸿献,郑永战
作者简介:崔承齐,E-mail： chengqicui_1986@126.com。|刘艳阳,E-mail： liuyanyang001@163.com。
基金资助:
财政部和农业农村部：国家现代农业产业技术体系(CARS-14-1-01);河南省重大科技专项(201300110600);河南省重点研发与推广专项(202102110026);河南省农业科学院优秀青年科技基金(2020YQ26);河南省农业科学院科技创新创意项目(2020CX25);河南省农业科学院基础性科研项目(2020JC008);河南省农业科学院基础性科研项目(2021JC013);河南省农业科学院基本科研业务费(2021ZC69)

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

CUI ChengQi¹(),LIU YanYang¹(),JIANG XiaoLin¹,SUN ZhiYu²,DU ZhenWei¹,WU Ke¹,MEI HongXian¹(),ZHENG YongZhan¹()

¹Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450008
²College of Life Sciences, South China Normal University, Guangzhou 510631

Received:2021-06-23 Accepted:2021-09-18 Online:2022-01-01 Published:2022-01-07
Contact: HongXian MEI,YongZhan ZHENG

摘要/Abstract

摘要：

【目的】通过对芝麻产量相关性状的全基因组关联分析,挖掘与产量性状关联的SNP位点及预测候选基因,为通过分子标记辅助选择育种等方式提高芝麻产量提供技术基础。【方法】以363份不同遗传背景和地理来源的芝麻种质资源构成的自然群体为研究对象,调查2年2点4环境下8个产量相关性状（单株产量、单株蒴数、蒴粒数、千粒重、株高、主茎果轴长、始蒴高度和表观收获指数）的表型值,借助覆盖全基因组的42 781个SNP标记,利用多位点SNP随机效应混合线性模型（multi-locus random-SNP-effect mixed linear model,mrMLM）对8个产量相关性状进行全基因组关联分析,检测与产量相关性状显著关联的SNP位点,并预测候选基因。【结果】在4个不同环境下,8个产量相关性状表现出广泛的表型变异,变异系数为6.51%—33.57%;相关性分析表明单株产量与单株蒴数、株高、主茎果轴长、表观收获指数呈极显著正相关;方差分析表明产量相关性状的基因型效应、环境效应、基因型与环境互作效应均达到了极显著水平。通过多位点全基因组关联分析共检测到210个与产量相关性状显著关联的SNP,在2018年南阳环境下检测到47个SNP,解释表型变异的1.63%—17.29%;在2019年南阳环境下检测到35个SNP,解释表型变异的1.94%—11.90%;在2018年平舆环境下检测到35个SNP,解释表型变异的2.15%—15.90%;在2019年平舆环境下检测到53个SNP,解释表型变异的1.25%—11.13%;在4个环境的综合BLUP条件下检测到75个SNP,解释表型变异的1.44%—13.58%。上述210个SNP涉及到175个位点,其中10个位点在3个及以上环境中被重复检测到。在这10个位点基因组区域内,共鉴定到214个候选基因,其中156个候选基因具有功能注释,主要涉及植物代谢、生物调控、生长发育等生物学过程。根据功能注释筛选出4个可能与芝麻产量相关的候选基因,其中SIN_1006338编码1-氨基环丙烷-1-羧酸合酶3（1-aminocyclopropane-1-carboxylate synthase 3-like）,参与乙烯的生物合成;SIN_1024330编码碱性螺旋-环-螺旋（basic helix-loop-helix）转录因子,负向调控植物细胞和器官的伸长;SIN_1014512编码吲哚-3-乙酸-酰胺合成酶GH3.6（indole-3-acetic acid-amido synthetase GH3.6）,参与调控茎和下胚轴细胞的伸长生长;SIN_1011473编码泛素受体蛋白DA1（protein DA1-like）,参与调节植物细胞增殖周期。【结论】通过多位点SNP随机效应混合线性模型的全基因组关联分析,检测到175个与产量相关性状显著关联的位点,筛选出4个可能与产量相关的重要候选基因。

关键词: 芝麻, 产量性状, 多位点全基因组关联分析, 功能注释, 候选基因

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

崔承齐, 刘艳阳, 江晓林, 孙知雨, 杜振伟, 武轲, 梅鸿献, 郑永战. 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[J]. 中国农业科学, 2022, 55(1): 219-232.

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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图/表 7

表1

芝麻8个产量相关性状的描述统计分析"

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

表1

图1

表2

表3

图2

表4

在3种以上环境同时检测到的10个显著关联位点"

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

表4

图3

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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**

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

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

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

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