玉米杂交种穗部性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.13.001

摘要/Abstract

摘要：

【目的】玉米穗部性状是产量的重要构成因子,利用全基因组关联分析（genome-wide association study,GWAS）方法解析玉米杂交种穗部性状的遗传基础、挖掘与穗部性状相关的位点,为功能基因克隆和高产玉米品种培育提供参考。【方法】选用115份来源于陕A群和陕B群的优良玉米自交系和4份国内骨干作为亲本,以基于NCⅡ遗传交配设计获得的442份玉米杂交种为材料构建关联群体,调查2个环境中群体材料的穗长、穗粗、穗行数等8个穗部性状;利用tGBS技术检测亲本基因型,推测出F₁杂交种的19 461个高质量SNP,结合杂交种表型和基因型开展基于加性、显性及上位性模型的穗部性状的全基因组关联分析,并利用公共数据库中玉米穗发育相关组织的转录组数据和基因的注释信息预测候选基因。【结果】表型数据分析结果显示,试验群体的8个穗部性状均符合正态分布,表型变异为3.78%—45.25%。方差分析表明,8个穗部性状的环境效应和基因型效应均呈现极显著水平（P<0.001）,广义遗传力为54.15%—68.89%。同时玉米杂交种穗部性状间呈现显著正相关或显著负相关。利用加性和显性模型分别检测到16个和3个显著SNP,上位性模型检测到79个上位性位点。3种模型检测的显著位点累积解释各性状38.21%—60.69%的表型变异,其中,加性模型检测到的显著SNP累积解释的表型变异为0.00—41.26%,上位性模型检测到的位点累积解释的表型变异为15.18%—45.36%。基于加性和显性模型检测的显著SNP的效应分析发现多数位点呈现加性和部分显性效应,仅2个为超显性。进一步分析发现,7个单SNP和5个上位性位点能够解释5%以上的表型变异。根据SNP的位置以及基因的表达信息预测了17个候选基因。【结论】玉米杂交种穗部性状主要受加性、上位性效应影响,显性效应影响较小;加性和显性模型检测的SNP主要表现为加性和部分显性效应,可通过聚合有利等位基因改良目标性状。

关键词: 玉米, 杂交种, 穗部性状, 全基因组关联分析, 遗传效应, 候选基因

Abstract:

【Objective】Ear traits are important components of grain yield in maize. Dissecting their genetic basis and mining significant SNPs using genome-wide association study (GWAS) can provide references for cloning functional genes and breeding high-yield maize varieties. 【Method】A total of 115 superior inbred lines from Shaan A group and Shaan B group, as well as four domestic backbone lines were selected as parents. Based on NCⅡ genetic design, an association population consisting of 442 hybrids was constructed, which was planted in two different environments to collect phenotype data of ear traits. Meanwhile, all parental lines were sequenced by the tunable genotyping by sequencing (tGBS) protocols. According to the genotype of inbred lines, altogether 19 461 high-quality SNPs were inferred in the association population. Then, GWAS was performed using 19 461 SNPs and phenotype data by three models including additive, dominance and epistasis, respectively. Combining with the transcriptome data of maize ear related tissues in the public database and the annotation information of genes, candidate genes were predicted. 【Result】Phenotypic data analysis showed that eight ear traits followed a continuous distribution, and there were 3.78%-45.25% of phenotypic variation. Analysis of variance indicated that environment and genotype effects reached an extremely significant level (P<0.001), and the range of broad-sense heritability was from 54.15% to 68.89%. And there were significantly positive or negative correlations among ear traits of hybrids. In total, 16, 3, 79 significant SNPs/pairs were identified under additive, dominant, and epistatic models, respectively. The significant loci detected by the three models cumulatively explained 38.21%-60.69% of the phenotypic variation of each trait. The cumulative phenotypic variation of significant SNP detected by additive model and epistatic model was 0.00-41.26% and 15.18%-45.36%, respectively. Effect analysis of significant SNPs identified by additive and dominant models showed most SNPs with additive or partial dominance effects, and only two with over-dominance effects. Further, only seven single-SNPs and five interaction pairs explained more than 5% of the phenotypic variation, and 17 candidate genes were predicted based on the SNP locations and gene expression information. 【Conclusion】Ear traits of maize hybrids were mainly affected by additive and epistasis effects, but less by dominance effects. Multiple SNPs identified by additive and dominant models showed additive and partially dominance effects, and aggregating favorable alleles of these SNPs could improve the target traits.

Key words: maize, hybrids, ear traits, genome wide association study, genetic effect, candidate gene

李婷,董远,张君,冯志前,王亚鹏,郝引川,张兴华,薛吉全,徐淑兔. 玉米杂交种穗部性状的全基因组关联分析[J]. 中国农业科学, 2022, 55(13): 2485-2499.

LI Ting,DONG Yuan,ZHANG Jun,FENG ZhiQian,WANG YaPeng,HAO YinChuan,ZHANG XingHua,XUE JiQuan,XU ShuTu. Genome-Wide Association Study of Ear Related Traits in Maize Hybrids[J]. Scientia Agricultura Sinica, 2022, 55(13): 2485-2499.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2022.13.001

https://www.chinaagrisci.com/CN/Y2022/V55/I13/2485

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候选基因预测"

序号 Number	标记 SNP marker	类型 Type	性状 Trait	候选基因 Candidate gene	表型解释率 PVE (%)	注释 Annotation
SNP_1	Chr.6: 142154022	外显子Exon	EL,FL,KNR	●Zm00001d037925	21.69	ASF/SF2样pre-mRNA剪接因子SRP31 ASF/SF2-like pre-mRNA splicing factor SRP31
SNP_3	Chr.7: 136117199	内含子Intron	EL,FL	●Zm00001d020902	6.81	推测的DUF1664结构域家族蛋白 Putative DUF1664 domain family protein
SNP_5	Chr.9: 103073562	基因间区Intergenic	EL,FL	Zm00001d046716	9.24	RNA结合（RRM/RBD/RNP基序）家族蛋白 RNA-binding (RRM/RBD/RNP motifs) family protein
SNP_9	Chr.1: 63127746	内含子Intron	ERN	●Zm00001d029226	5.08	菱形蛋白19 Rhomboid-like protein 19
SNP_10	Chr.3: 140533299	基因间区Intergenic	ERN	Zm00001d041847	22.21	SWI/SNF复合亚单位SWI3C-like SWI/SNF complex subunit SWI3C-like
SNP_12	Chr.3: 24937775	基因间区Intergenic	ED	Zm00001d040051	14.61	ARM重复超家族蛋白 ARM repeat superfamily protein
SNP_16	Chr.5: 77126549	下游Downstream	KNE	●Zm00001d015153	8.61	BZIP转录因子160 BZIP transcription factor 160
Pair_21	Chr.1: 258346354 Chr.5: 219936403	外显子Exon 基因间区Intergenic	ERN	Zm00001d033309 Zm00001d018394	7.34	蛋白质多效性调节基因座1 Protein pleiotropic regulatory locus 1 DBP转录因子2 DBP-transcription factor 2
Pair_28	Chr.1: 269687016 Chr.4: 17283434	内含子Intron 内含子Intron	KNR	●Zm00001d033652 ●Zm00001d049135	5.38	推测的LRR受体样丝氨酸/苏氨酸蛋白 Putative LRR receptor-like serine/threonine-protein kinase 推测的bZIP转录因子超家族蛋白 Putative bZIP transcription factor superfamily protein
Pair_46	Chr.1: 61044255 Chr.9: 156420734	非翻译区UTR3 外显子Exon	BTL	●Zm00001d029177 Zm00001d048438	6.52	核仁GTP结合蛋白2 Nucleolar GTP-binding protein 2 表皮模式因子样蛋白4 Epidermal patterning factor-like protein 4
Pair_50	Chr.1: 7694515 Chr.4: 14565656	内含子Intron 上游Upstream	BTL	●Zm00001d027536 Zm00001d049060	5.20	丝氨酸乙酰转移酶4 Serine acetyltransferase4 非特征蛋白质 Uncharacterized protein
Pair_63	Chr.5: 88161699 Chr.6: 153042725	上游Upstream 下游Downstream	SSR	●Zm00001d015395 ●Zm00001d038274	16.32	脲酶辅助蛋白D Urease accessory protein D 四三肽重复序列（TPR）样超家族蛋白 Tetratricopeptide repeat (TPR) like superfamily protein

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环境 Environment	性状 Trait	均值 Mean	最小值 Minimum	最大值 Maximum	标准差 SD	变异系数 CV (%)	偏度 Skew	峰度 Kurtosis
杨凌Yangling	穗长EL (cm)	14.46	10.85	18.78	1.27	8.81	0.22	0.34
	结实长FL (cm)	12.94	9.29	18.44	1.53	11.82	0.39	0.18
	穗行数ERN	15.14	12.00	18.80	1.08	7.13	0.12	0.03
	行粒数KNR	27.16	18.20	36.20	2.97	10.94	0.06	-0.06
	穗粗ED (cm)	4.33	3.72	4.91	0.21	4.79	0.25	-0.06
	秃尖长BTL (cm)	1.52	0.02	4.42	0.69	45.25	0.63	0.86
	结实率SSR (%)	89.36	70.11	99.86	4.92	5.50	-0.52	0.26
	穗粒数KNE	410.73	254.80	576.92	49.85	12.14	0.11	-0.01
榆林Yulin	穗长EL (cm)	16.57	13.15	20.50	1.23	7.41	0.13	0.10
	结实长FL (cm)	15.20	11.05	19.14	1.39	9.16	0.01	0.10
	穗行数ERN	17.29	14.00	21.80	1.32	7.66	0.08	-0.18
	行粒数KNR	33.03	24.70	41.50	2.67	8.07	0.07	0.12
	穗粗ED (cm)	4.65	4.13	5.40	0.21	4.50	0.27	0.35
	秃尖长BTL (cm)	1.38	0.07	3.15	0.55	39.90	0.31	0.07
	结实率SSR (%)	91.66	80.39	99.56	3.47	3.78	-0.39	0.13
	穗粒数KNE	570.30	420.32	748.80	58.25	10.21	0.03	-0.12
最佳线性无偏估计BLUE	穗长EL (cm)	15.52	13.00	18.78	1.06	6.84	0.29	0.06
	结实长FL (cm)	14.08	10.95	18.36	1.26	8.92	0.32	-0.01
	穗行数ERN	16.21	13.10	19.52	1.03	6.38	-0.07	-0.09
	行粒数KNR	30.13	22.50	37.15	2.37	7.86	0.17	0.03
	穗粗ED (cm)	4.49	4.05	5.05	0.17	3.88	0.23	0.25
	秃尖长BTL (cm)	1.45	0.19	3.35	0.51	35.13	0.40	0.16
	结实率SSR (%)	90.49	77.65	98.84	3.49	3.86	-0.40	0.07
	穗粒数KNE	490.97	347.00	619.70	45.57	9.28	0.08	-0.20

性状 Trait	基因型×环境 Line×Environment	基因型 Line	环境 Environment	广义遗传力 H²(%)
穗长EL (cm)	0.32***	0.64***	2.28***	60.45
结实长FL (cm)	0.36***	0.99***	2.59***	65.78
穗长数ERN	0.18***	0.71***	2.34***	68.89
行粒数KNR	1.13***	3.24***	17.39***	61.43
穗粗ED (cm)	0.01***	0.02***	0.05***	57.71
秃尖长BTL (cm)	0.04*	0.13***	0.01***	54.15
结实率SSR (%)	0.00*	0.00***	0.00***	56.39
穗粒数KNE	263.80*	1280.50***	12878.90***	65.24

编号 Number	标记 SNP	染色体 Chromosome	位置 Position (bp)	基因型 Genotype	有利等位基因 Favorable allele	性状 Trait	P值 <BOLD>P</BOLD> value	模型 Model	表型解释率 PVE (%)
? SNP_1	Chr.6:142154022	6	142154022	A/T	AA***	EL	3.06E-05	Add	21.69
					AA***	FL	9.52E-06	Add	18.79
					AA***	KNR	2.75E-06	Add	16.88
SNP_2	Chr.7:10328617	7	10328617	T/C	\	EL	5.71E-05	Add	1.97
? SNP_3	Chr.7:136117199	7	136117199	C/A	AA***	EL	6.55E-07	Add	2.78
? SNP_3	Chr.7:136117199	7	136117199	C/A	AA***	FL	4.30E-05	Add	6.81
SNP_4	Chr.7:139654593	7	139654593	G/A	AA***	EL	8.53E-05	Add	1.77
? SNP_5	Chr.9:103073562	9	103073562	C/T	CC***	EL	4.69E-05	Add	7.29
? SNP_5	Chr.9:103073562	9	103073562	C/T	CC***	FL	3.22E-05	Add	9.24
? SNP_6	Chr.1:31507749	1	31507749	A/T	TT***	FL	9.54E-06	Add	3.92
? SNP_6	Chr.1:31507749	1	31507749	A/T	TT***	SSR	2.20E-05	Add	3.35
SNP_7	Chr.9:103896805	9	103896805	G/A	AA***	FL	1.73E-05	Add	1.17
? SNP_8	Chr.9:142603978	9	142603978	C/T	CC***	FL	6.76E-05	Add	1.33
? SNP_8	Chr.9:142603978	9	142603978	C/T	CC***	KNR	8.59E-05	Add	1.85
SNP_9	Chr.1:63127746	1	63127746	C/T	\	ERN	7.29E-05	Add	5.08
SNP_10	Chr.3:140533299	3	140533299	T/G	\	ERN	9.24E-05	Add	22.21
SNP_11	Chr.5:217554704	5	217554704	A/G	AA***	ERN	5.95E-05	Add	3.38
SNP_12	Chr.3:24937775	3	24937775	C/T	TT***	ED	4.39E-05	Add	14.61
SNP_13	Chr.4:17756435	4	17756435	T/C	\	ED	5.18E-05	Add	3.52
SNP_14	Chr.6:33388399	6	33388399	C/T	TT***	ED	1.33E-05	Add	4.42
SNP_15	Chr.6:71642919	6	71642919	A/G	\	ED	2.15E-05	Add	1.92
SNP_16	Chr.5:77126549	5	77126549	G/C	GG***	KNE	9.17E-05	Add	8.61
SNP_17	Chr.7:174762752	7	174762752	T/C	CT***	ED	1.95E-05	Dom	1.48
SNP_18	Chr.1:5822204	1	5822204	C/T	TT***	BTL	1.02E-04	Dom	1.46
SNP_19	Chr.4:243712772	4	243712772	T/C	TT*	KNE	8.85E-06	Dom	1.78