基于杂交种群体的玉米产量及其配合力的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.09.001

摘要/Abstract

摘要：

【目的】通过分析陕A群和陕B群选育自交系组配的杂交种产量,评估自交系的配合力,并开展以产量和配合力为目标性状的全基因组关联分析,挖掘产量及其配合力的关联位点,为陕A群和陕B群选育玉米自交系的改良及育种中的应用提供依据。【方法】基于NCⅡ遗传设计,以陕A群和陕B群选育的85份优良玉米自交系为亲本,构建包含246份F₁的杂交种群体,在3个环境下进行产量测试,并评估产量的一般配合力和特殊配合力;利用6H90K芯片进行亲本基因型检测,获得63 879个高质量SNP标记,并进行群体遗传特征分析,在杂交种群体推测出高质量SNP标记55 951个,采用加性模型和非加性模型对杂交种产量、一般配合力和特殊配合力开展了全基因组关联分析,并基于B73参考基因组对显著关联SNPs内的基因进行挖掘和功能注释。【结果】3个环境下的产量表现符合正态分布且变异广泛,产量广义遗传力为59.04%,环境效应显著;杂交种产量、一般配合力和特殊配合力三者之间均达到极显著相关性,杂交种产量与特殊配合力的相关性（r=0.95）大于与一般配合力的相关性（r=0.62）;陕A群与陕B群遗传特征具有一定差异,陕A群具有较高的一般配合力。全基因组关联分析分别检测到7、5和9个SNP与杂交种产量、一般配合力和特殊配合力显著相关（-log₁₀(P)>3.86）,其中4个SNP为杂交种产量和特殊配合力共定位,最终锚定了17个关联SNP。对不同性状关联位点的优势等位基因型分析发现,4个GCA关联SNP受加性效应控制,F₁产量BLUE关联位点可分为4种表现形式,以显性效应为主,其杂合基因型为最优等位基因型或次优等位基因型。通过功能注释发现,候选基因在玉米生长发育和籽粒建成中特异表达,例如GRMZM2G165828、GRMZM2G057557均与玉米籽粒发育相关。【结论】一般配合力和特殊配合力共同影响杂交种的产量,特殊配合力效应影响更大;一般配合力和特殊配合力具有不同的遗传基础,可通过有利等位基因聚集提高一般配合力。在F₁杂交种群体采用全基因组关联分析策略可开展配合力相关遗传解析,挖掘产量及其配合力相关遗传位点,可加速关联位点在分子育种中的应用。

关键词: 玉米, 杂交种, 一般配合力, 特殊配合力, 全基因组关联分析

Abstract:

【Objective】By analyzing the yield of the hybrids from the inbred lines bred from the Shaan A and Shaan B group, the combining ability of the inbred lines were evaluated, genome-wide association analysis, and mining associated loci for yield and its combining ability conducted. It will provide references for improving maize inbred lines selected from Shaan A group and Shaan B group and applying them in varieties breeding. 【Method】Based on NCⅡ genetic design, 85 excellent inbred lines from Shaan A group and Shaan B group were used to construct a hybrid population containing 246 F₁. Then, the yield of the hybrid population was tested in three environments to evaluate their general combining ability (GCA) and special combining ability (SCA). Using the 6H90K maize array to detect the parental genotypes, 63 879 high-quality SNPs were obtained, which were used to analyze the genetic characteristics of parental lines. According to the parental genotypes, 55 951 high-quality SNPs were inferred in the hybrid population for genome-wide association analysis of hybrid yield, GCA, and SCA using additive model and non-additive model. Meanwhile, candidate genes around the significant SNPs were screened and annotated based on the maize B73 reference genome.【Result】The yield in the three environments accorded to the normal distribution with wide variation, the broad-sense heritability of yield was 59.04%, and the environmental effect was significant. There was significant positive correlation between hybrid yield and combining ability, and the correlation between hybrid yield and SCA (r=0.95) was higher than that between hybrid yield and GCA (r=0.62). The genetic characteristic of Shaan A group and Shaan B group was different, and inbred lines from Shaan A group have higher general combining ability. Totally, five, seven and nine significant SNPs were detected (-log₁₀(P)>3.86) for GCA, hybrid yield and SCA, respectively. Among them, four SNPs were co-located in hybrid yield and SCA. Ultimately, 17 associated SNPs were anchored. Dominant allele analysis of different trait-associated loci showed that four GCA-associated SNPs were controlled by additive effects, and the F₁ BLUE-associated loci could be divided into 4 types mainly by the dominant effect, and the heterozygous genotype is the favorite allele or sub-optimal allele for yield in F₁. Through functional annotation, the candidate genes were specifically expressed in maize growth and kernel establishment, for example, GRMZM2G165828 and GRMZM2G057557 were related to maize kernel development. 【Conclusion】Based on this study, we consider that GCA and SCA jointly affect the yield of hybrids, and the effect of SCA is greater. Moreover, GCA and SCA may have different genetic basis, and GCA can be increased with the accumulation of favorable alleles. Using the genome-wide association analysis in the F₁ hybrid population can carry out genetic analysis related to combining ability, mine the genetic loci related to yield and combining ability, and accelerated the application of the associated loci in molecular breeding.

Key words: maize, hybrids, general combining ability, special combining ability, genome-wide association analysis

李周帅,董远,李婷,冯志前,段迎新,杨明羡,徐淑兔,张兴华,薛吉全. 基于杂交种群体的玉米产量及其配合力的全基因组关联分析[J]. 中国农业科学, 2022, 55(9): 1695-1709.

LI ZhouShuai,DONG Yuan,LI Ting,FENG ZhiQian,DUAN YingXin,YANG MingXian,XU ShuTu,ZHANG XingHua,XUE JiQuan. Genome-Wide Association Analysis of Yield and Combining Ability Based on Maize Hybrid Population[J]. Scientia Agricultura Sinica, 2022, 55(9): 1695-1709.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2022.09.001

https://www.chinaagrisci.com/CN/Y2022/V55/I9/1695

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候选基因预测"

标记位点 SNP ID	性状 Trait	SNPs位置 Position (bp)	候选基因 Candidate genes	功能注释 Annotation
SNP_1	GCA	Chr.1:296696400	AC206957.1_FG005	转座元件Transposable_element
SNP_2	GCA	Chr.2:228845613	GRMZM2G559383	-
SNP_3	GCA	Chr.4:80111618	GRMZM2G175827(Zm00001d050350)	Kan3转录因子Kan3 transcription factor
SNP_4	GCA	Chr.4:155406944	GRMZM2G137029(Zm00001d051447)	F-box蛋白PP2-A13 F-box protein PP2-A13
SNP_5	GCA	Chr.4:176561593	GRMZM2G097081(Zm00001d052102)	AP2-EREBP-转录因子57 AP2-EREBP-transcription factor 57(ereb57)
SNP_6	CO_ADD	Chr.10:146974725	GRMZM2G149932(Zm00001d026580)	外泌素家族蛋白 Exostosin family protein
SNP_7	CO_DOM	Chr.10:4152732	GRMZM2G101928(Zm00001d023342)	-
SNP_8	CO_DOM	Chr.2:24634902	GRMZM2G124371(Zm00001d002876)	具有FYVE锌指结构域的染色体凝聚（RCC1）家族的调控因子 Regulator of chromosome condensation (RCC1) family with FYVE zinc finger domain
SNP_9	CO_DOM	Chr.2:28002879	GRMZM2G133012(Zm00001d002980)	-
SNP_10	F₁BLUE	Chr.2:4377056	GRMZM2G363066(Zm00001d002013)	水稻凝集素蛋白激酶家族蛋白同源基因 OsRLCK168, homologous gene of lectin protein kinase family protein
SNP_11	F₁BLUE	Chr.4:153499376	GRMZM2G101388	转座元件Transposable_element
SNP_12	F₁BLUE	Chr.10:146837618	GRMZM2G464157(Zm00001d026572)	羧酯酶SOBER1 Carboxylesterase SOBER1
SNP_13	SCA	Chr.1:8628332	GRMZM2G474258(Zm00001d027598)	CCT结构域相关基因（cct101） CO CO-LIKE TIMING OF CAB1 protein domain101(cct101)
SNP_14	SCA	Chr.2:194691551	GRMZM2G079109(Zm00001d006153)	1-酰基甘油-3-磷酸O-酰基转移酶 1-acylglycerol-3-phosphate O-ac= yltransferase
SNP_15	SCA	Chr.2:193402735	GRMZM2G378215	-
SNP_16	SCA	Chr.7:805187	GRMZM2G165828(Zm00001d018615)	类似于谷氨酸受体3.4前体（配体门控离子通道3.4）（AtGLR 4） Similar to Glutamate receptor 3.4 precursor (Ligand-gated ion channel 3.4) (AtGLR4)
SNP_17	SCA	Chr.10:1148101	GRMZM2G057557(Zm00001d023220)	外膜OMP85家族蛋白 Outer membrane OMP85 family protein

表5

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环境 Env.	重复 Rep.	最小值 Minimum (kg·hm^-2)	最大值 Maximum (kg·hm^-2)	均值 Mean (kg·hm^-2)	标准差 SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV	广义遗传力 H²(%)	F值 F value
环境 Env.	重复 Rep.	最小值 Minimum (kg·hm^-2)	最大值 Maximum (kg·hm^-2)	均值 Mean (kg·hm^-2)	标准差 SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV	广义遗传力 H²(%)	基因型 Gen.	环境 Env.	基因×环境 Gen.×Env.
杨凌 Yangling	1	5095.60	12917.48	9527.95	1243.25	-0.60	0.96	0.13	59.04	6.60**	6318.72**	3.89**
杨凌 Yangling	2	4286.95	12709.47	9286.99	1437.99	-0.64	0.63	0.15
榆林 Yulin	1	12325.73	20036.29	15794.53	1367.89	0.17	0.20	0.09
榆林 Yulin	2	12066.87	20488.13	15533.07	1441.90	0.20	0.36	0.09
旬邑 Xunyi	1	9401.12	20342.91	14038.85	1889.22	0.41	0.25	0.13
旬邑 Xunyi	2	10093.17	19664.45	14115.04	1783.91	0.26	-0.04	0.13
BLUE		10775.45	17180.75	13831.91	988.61	-0.28	0.59	0.07

性状 Trait	数量 Number	最小值 Minimum	最大值 Maximum	标准差 SD	偏度 Skewness	峰度 Kurtosis	相关系数 Correlation coefficient
性状 Trait	数量 Number	最小值 Minimum	最大值 Maximum	标准差 SD	偏度 Skewness	峰度 Kurtosis	GCA	SCA	BLUE
GCA	82	-565.87	316.87	172.54	-0.68	0.49		0.51***	0.62***
SCA	246	-1772.11	1621.62	520.94	-0.30	0.65			0.95***

性状 Trait	标记名称 SNPs	染色体 Chr.	物理位置 Position (bp)	基因型 Genotype	最小等位基因频率 MAF	P值 P value	表型解释率 PVE (%)
GCA	Affx-291398318	1	296696400	A/G	0.36	1.02E-04	23.37
GCA	Affx-291395842	2	228845613	T/C	0.22	1.13E-04	11.91
GCA	Affx-291375443	4	80111618	G/A	0.12	7.12E-05	12.29
GCA	Affx-291425877	4	155406944	G/A	0.29	2.77E-05	8.26
GCA	Affx-159192088	4	176561593	C/A	0.41	1.31E-04	7.97
F₁_ADD	●Affx-291424805	10	146974725	T/C	0.24	6.27E-05	1.55
F₁_DOM	Affx-88979942	2	4377056	G/A	0.31	1.07E-04	1.75
F₁_DOM	■Affx-291385286	2	24634902	T/G	0.37	8.43E-05	4.12
F₁_DOM	▲Affx-88980445	2	28002879	G/A	0.42	1.36E-04	0.43
F₁_DOM	Affx-158919359	4	153499376	C/T	0.08	9.46E-05	5.96
F₁_DOM	Affx-291394192	10	146837618	A/C	0.43	8.24E-05	3.30
F₁_DOM	★Affx-291431456	10	4152732	C/T	0.47	3.52E-05	3.57
SCA_ADD	●Affx-291424805	10	146974725	T/C	0.24	2.82E-05	1.77
SCA_DOM	Affx-291423507	1	8628332	C/T	0.44	3.13E-05	1.21
SCA_DOM	■Affx-291385286	2	24634902	T/G	0.37	3.78E-05	3.26
SCA_DOM	▲Affx-88980445	2	28002879	G/A	0.42	6.80E-06	1.22
SCA_DOM	Affx-291382512	2	194691551	G/A	0.49	9.30E-05	0.92
SCA_DOM	Affx-158945854	2	193402735	A/C	0.49	3.64E-05	1.76
SCA_DOM	Affx-291445414	7	805187	G/C	0.42	1.13E-04	1.42
SCA_DOM	Affx-291393021	10	1148101	C/T	0.31	1.06E-04	6.31
SCA_DOM	★Affx-291431456	10	4152732	C/T	0.47	6.97E-05	3.15

标记位点 SNP ID	性状 Trait	标记名称 SNPs	染色体位置 Position (bp)	基因型 Genotype	不同性状下的有利等位基因 Favorable bases in different traits			主效应模式 SNP effect
标记位点 SNP ID	性状 Trait	标记名称 SNPs	染色体位置 Position (bp)	基因型 Genotype	GCA	F₁	SCA	主效应模式 SNP effect
SNP_1	GCA	Affx-291398318	Chr.1:296696400	A/G	AA***	AA***	AA***	A
SNP_2	GCA	Affx-291395842	Chr.2:228845613	T/C	CC**	CC**	CC**	A
SNP_3	GCA	Affx-291375443	Chr.4:80111618	G/A	GG**	\	\	\
SNP_4	GCA	Affx-291425877	Chr.4:155406944	G/A	AA**	GA/GG	GA	A=D
SNP_5	GCA	Affx-159192088	Chr.4:176561593	C/A	CC	CC	CC	A
SNP_6	CO_ADD	Affx-291424805	Chr.10:146974725	T/C	CC***	TC	TC*	D
SNP_7	CO_DOM	Affx-291431456	Chr.10:4152732	C/T	TT	TT/CC*	TT/CC*	A
SNP_8	CO_DOM	Affx-291385286	Chr.2:24634902	T/G	GG	TG*	TG**	D
SNP_9	CO_DOM	Affx-88980445	Chr.2:28002879	G/A	AA	GA*	GA*	D
SNP_10	F₁BLUE	Affx-88979942	Chr.2:4377056	G/A	GG**	GG*	AA/GG	A
SNP_11	F₁BLUE	Affx-158919359	Chr.4:153499376	C/T	CC**	CC***	CC**	A
SNP_12	F₁BLUE	Affx-291394192	Chr.10:146837618	A/C	CC*	AC**	AC*	D
SNP_13	SCA	Affx-291423507	Chr.1:8628332	C/T	TT*	CT	CT*	D
SNP_14	SCA	Affx-291382512	Chr.2:194691551	G/A	AA/GG	GA*	GA**	D
SNP_15	SCA	Affx-158945854	Chr.2:193402735	A/C	CC	AC*	AC**	D
SNP_16	SCA	Affx-291445414	Chr.7:805187	G/C	CC	GC*	GC**	D
SNP_17	SCA	Affx-291393021	Chr.10:1148101	C/T	CC	CC/CT***	CC/CT***	A=D