玉米雌穗产量相关性状全基因组关联分析与候选基因鉴定

doi:10.3724/SP.J.1006.2023.23021

Abstract

Abstract:

Ear traits directly affect the final yield of maize, and the analysis of its genetic mechanisms can provide useful guidance for yield enhancement in maize. In this study, 733 maize inbred lines were planted in randomized block designs under two environments, and three yield-related traits, kernel row number (KRN), ear length (EL), and ear diameter (ED), were investigated. Genotyping was performed using MaizeSNP3072 chip and FarmCPU (fixed and random model circulating probability unification) model was used to conduct genome-wide association study (GWAS). 16, 13, and 24 single nucleotide polymorphism (SNP) loci significantly associated with the three traits were identified, and the values of phenotypic variation explained (PVE) for single locus were 0.01%-7.08%, 0.01%-5.34%, and 0.07%-4.34%, respectively. Further, six, two, and five high confidence (HC) SNPs that were repeatedly detected in multiple environments for KRN, EL, and ED were retrieved, among which two SNPs were simultaneously associated with KRN and ED traits, and one KRN HC-SNP and three ED HC-SNPs were firstly reported in this study. By searching 200 kb regions around the 11 HC-SNPs loci, 33 important candidate genes were identified, including a known gene PIN1a regulating ear development via auxin polar transport located in the confidence interval of chromosome 9 SNP marker PZE-109003046. Other candidate genes encoded transcription factors, hormone (such as auxin, gibberellin, and ethylene) pathway related proteins, DNA methylation, and protein phosphorylation related proteins, which might regulate ear traits by different mechanisms. The 11 HC-SNPs and 33 important candidate genes detected in this study can provide valuable information for further cloning of functional genes and reveal the molecular regulatory mechanisms and marker-assisted selection for ear trait in maize.

Key words: maize, yield related ear traits, genome-wide association study (GWAS), candidate gene

YIN Fang-Bing, LI Ya-Nan, BAO Jian-Xi, MA Ya-Jie, QIN Wen-Xuan, WANG Rui-Pu, LONG Yan, LI Jin-Ping, DONG Zhen-Ying, WAN Xiang-Yuan. Genome-wide association study and candidate genes predication of yield related ear traits in maize[J].Acta Agronomica Sinica, 2023, 49(2): 377-391.

Figures/Tables 8

Table 1

Fig. 1

Table 2

Fig. 2

Fig. 3

Table S1

Summary of the SNPs significantly associated with KRN, EL, and ED in different environments"

性状 Trait	标记名称 Maker name	染色体 Chr.	物理位置 Position (bp)	环境 Environment	P值 P-value	表型变异解释率 PVE (%)	最小等位基因频率 MAF
穗行数KRN	PZE-103149597	3	206,991,538	BLUP/2019	1.28E-06/1.60E-07	1.13/1.46	0.21
	PZE-104041818	4	59,704,298	BLUP/2020	1.58E-06/1.52E-05	6.44/6.18	0.36
	PZE-104124173	4	205,899,298	2019	7.02E-08	3.21	0.34
	PZE-104126211	4	208,732,552	BLUP/2020	1.46E-10/4.08E-07	7.08/6.74	0.47
	PZE-105105740	5	164,510,203	2019	1.90E-05	0.11	0.35
	PZE-106038186	6	89,083,642	2020	4.83E-05	0.37	0.44
	SYN4194	6	162,814,863	BLUP/2019	3.59E-06/8.91E-07	0.72/0.69	0.31
	PZE-106115356	6	165,632,631	2019	2.94E-05	0.52	0.41
	PZE-107055553	7	110,762,862	2020	6.93E-07	1.23	0.35
	PZE-107116723	7	169,607,175	BLUP/2019/2020	7.09E-11/5.74E-09/4.43E-08	4.32/3.40/3.79	0.23
	PZE-108005561	8	5,864,518	2019	9.98E-05	0.01	0.48
	PZE-108080140	8	140,264,937	2019	9.53E-07	2.80	0.47
	PZA03608.2	8	146,863,745	BLUP/2020	1.01E-06/5.53E-06	2.05/2.47	0.44
	PZE-109037923	9	76,271,588	2019	9.78E-08	1.39	0.31
	PZE-109061922	9	107,147,924	BLUP	5.78E-05	0.37	0.45
	SYN20545	10	88,765,819	2019	7.29E-05	0.18	0.48
穗长 EL	PZE-101162306	1	208,334,343	BLUP/2019	2.91E-06/5.22E-05	2.88/1.86	0.35
	PZE-102065179	2	45,039,241	BLUP	1.80E-05	3.15	0.46
	SYN27033	2	227,085,703	2019	9.34E-05	2.92	0.32
	PZE-104073430	4	148,150,704	2019	2.33E-05	2.56	0.40
	PZE-104113905	4	193,372,982	BLUP/2019	4.72E-05/3.35E-06	0.01/0.33	0.38
	PZE-104140854	4	234,265,598	2019	4.80E-05	0.99	0.16
	PZE-105039536	5	25,111,571	2019	5.52E-05	0.57	0.20
	PZE-105105086	5	163,308,887	BLUP	4.51E-06	1.73	0.30
	SYN6220	6	151,019,477	2019	7.16E-05	1.81	0.26
	SYN35928	8	93,549,629	2019	5.51E-05	2.56	0.38
	PZE-108059570	8	108,903,711	BLUP	3.11E-05	1.56	0.40
	PZE-108106737	8	165,505,598	2019	6.36E-05	0.01	0.41
	PZE-108133100	8	178,781,276	2020	8.87E-05	5.34	0.45
穗粗 ED	PZB02058.1	1	28,614,062	BLUP	1.65E-05	0.31	0.39
	PZE-102047851	2	27,664,781	2020	4.19E-05	2.97	0.12
	PUT-163a-60393963-2893	2	32,965,430	2019	7.21E-05	0.98	0.44
	PZE-102120444	2	168,965,413	2019	5.10E-05	0.07	0.49
	PZE-103087199	3	145,604,315	2019	1.09E-05	4.34	0.28
	SYN8382	4	45,460,142	BLUP	2.70E-05	2.20	0.45
	PZE-104041818	4	59,704,298	2020	1.99E-07	3.02	0.36
	PZE-104045413	4	69,980,490	2020	7.70E-05	1.17	0.44
	PZE-104093153	4	172,487,553	BLUP/2020	2.92E-05/2.26E-05	1.62/1.87	0.32
	PZE-104093898	4	173,802,472	BLUP	1.14E-05	1.54	0.19
	PZE-104126211	4	208,732,552	BLUP/2020	1.00E-05/7.50E-05	0.19/0.66	0.47
	SYN22663	5	3,212,673	2019	1.33E-05	0.92	0.47
	PZE-105032165	5	18,159,660	2019	4.21E-06	0.34	0.49
	PZE-105080632	5	95,622,206	2019	1.27E-06	2.06	0.36
	SYN32729	5	200,052,824	BLUP/2019	5.19E-05/2.98E-05	4.00/3.84	0.49
	SYN4194	6	162,814,863	BLUP/2019	2.89E-09/8.17E-07	2.56/2.66	0.31
	PZE-107055553	7	110,762,862	2020	1.90E-07	2.79	0.35
	SYN13511	7	125,838,654	2019	6.35E-05	1.00	0.48
	PZE-107070986	7	131,255,494	2019	3.75E-05	0.07	0.44
	PZE-108036722	8	57,892,012	2019	1.02E-05	2.88	0.43
	PZE-109003046	9	3,291,982	BLUP/2020	1.21E-07/2.08E-10	3.90/4.01	0.26
	PZB00235.1	9	36,013,505	2019	1.96E-05	2.80	0.48
	PZE-109061922	9	107,147,924	BLUP	5.99E-05	0.07	0.45
	PZE-110043433	10	82,662,170	BLUP	1.31E-05	1.37	0.46

Table S1

Table 3

High confidence SNPs and candidate genes for KRN, EL, and ED traits"

性状 Trait	标记名称 Marker name	染色体 Chr.	位置 Position (bp)	最小等位基因频率 MAF	环境 Environment	表型变异解释率 PVE (%)	候选基因 Candidate gene	基因注释 Gene annotation
穗行数 KRN	PZE-103149597	3	206,991,538	0.21	BLUP 2019	1.46	Zm00001d043674	Cytidine deaminase
							Zm00001d043675	Reversion-to-ethylene sensitivity1 like2
							Zm00001d043681	Amino_oxidase domain-containing protein
	PZE-104041818	4	59,704,298	0.36	BLUP 2020	6.44	Zm00001d050016	bHLH transcription factor
	PZE-104126211	4	208,732,552	0.47	BLUP 2020	7.08	Zm00001d053006	C2H2-like zinc finger protein
							Zm00001d053004	Auxin transporter-like protein
							Zm00001d053003	ARM repeat superfamily protein
							Zm00001d053011	Putative DUF869 domain containing family protein
	SYN4194	6	162,814,863	0.31	BLUP 2019	0.72	Zm00001d038699	O-methyltransferase ZRP4
							Zm00001d038698	Auxin response factor
							Zm00001d038695	Gibberellin 2-oxidase7
							Zm00001d038690	Non-specific serine/threonine protein kinase
							Zm00001d038693	C2C2-DOF transcription factor
	PZE-107116723	7	169,607,175	0.23	BLUP 2019 2020	4.32	Zm00001d022077	Probable 6-phosphogluconolactonase
							Zm00001d022071	Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain
							Zm00001d022075	Cytochrome P-450 17
	PZA03608.2	8	146,863,745	0.44	BLUP 2020	2.47	Zm00001d011329	DNA methyl transferase
							Zm00001d011323	Agamous-like MADS-box protein AGL62
							Zm00001d011326	Plant Tudor-like RNA-binding protein
							Zm00001d011327	Plant Tudor-like RNA-binding protein
							Zm00001d011328	GTP-binding nuclear protein
穗长 EL	PZE-101162306	1	208,334,343	0.35	BLUP 2019	2.88	Zm00001d031973	Phosphatidylinositol-3-phosphatase myotubularin-1
	PZE-101162306	1	208,334,343	0.35	BLUP 2019	2.88	Zm00001d031981	Evolutionarily conserved C-terminal region 5
	PZE-104113905	4	193,372,982	0.38	BLUP 2019	0.33	Zm00001d052570	Cation-chloride cotransporter 1
							Zm00001d052561	mRNA-decapping enzyme-like protein
							Zm00001d052564	Putative NAC domain transcription factor superfamily protein
							Zm00001d052578	Putative F-box protein
							Zm00001d052584	Protein kinase domain containing protein expressed
穗粗 ED	PZE-104093153	4	172,487,553	0.32	BLUP 2020	1.87	Zm00001d051856	O-fucosyltransferase family protein
	PZE-104093153	4	172,487,553	0.32		1.87	Zm00001d051861	AT-hook motif nuclear-localized protein
	PZE-104126211	4	208,732,552	0.47	BLUP 2020	0.66	Zm00001d053006	C2H2-like zinc finger protein
							Zm00001d053004	Auxin transporter-like protein
							Zm00001d053003	ARM repeat superfamily protein
							Zm00001d053011	Putative DUF869 domain containing family protein
	SYN32729	5	200,052,824	0.49	BLUP 2019	4.00	Zm00001d017573	Transcription factor bHLH157
	SYN32729	5	200,052,824	0.49	BLUP 2019	4.00	Zm00001d017575	Dof zinc finger protein DOF2.5
	SYN4194	6	162,814,863	0.31	BLUP 2019	2.66	Zm00001d038699	O-methyltransferase ZRP4
							Zm00001d038698	Auxin response factor
							Zm00001d038695	Gibberellin 2-oxidase7
							Zm00001d038690	Non-specific serine/threonine protein kinase
							Zm00001d038693	C2C2-DOF transcription factor
	PZE-109003046	9	3,291,982	0.26	BLUP 2020	4.01	Zm00001d044812	Auxin efflux carrier component

Table 3

Fig. 4

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性状 Trait	环境 Environment	平均值 Mean (cm)	最大值 Maximum (cm)	最小值 Minimum (cm)	范围 Range (cm)	标准差 Standard deviation	偏度 Skewness	峰度 Kurtosis	遗传力 h²
穗行数KRN	2019	13.80	21.33	8.00	13.33	1.93	0.632	0.810	0.80
	2020	14.89	24.40	8.40	16.00	2.17	0.607	0.755
穗长EL	2019	13.11	21.83	6.78	15.04	1.95	0.293	0.798	0.65
	2020	14.45	21.03	8.34	12.69	1.98	0.012	0.221
穗粗ED	2019	4.25	5.67	3.11	2.56	0.34	0.151	0.872	0.79
	2020	4.44	5.83	3.09	2.73	0.36	0.073	0.998

性状 Trait	变异来源 Source	均方 Mean of square	F值 F-value	P值 P-value
穗行数KRN	基因型Genotype	22.271	13.694	<0.001
	环境Environment	1273.476	783.028	<0.001
	基因型与环境互作Genotype and environment interaction	4.392	2.701	<0.001
穗长EL	基因型Genotype	19.133	24.162	<0.001
	环境Environment	1916.165	2419.761	<0.001
	基因型与环境互作Genotype and environment interaction	6.260	7.905	<0.001
穗粗ED	基因型Genotype	0.649	23.762	<0.001
	环境Environment	39.665	1451.942	<0.001
	基因型与环境互作Genotype and environment interaction	0.124	4.546	<0.001

Genome-wide association study and candidate genes predication of yield related ear traits in maize

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