玉米株高和穗位高性状全基因组关联分析

doi:10.3724/SP.J.1006.2023.23023

作物学报 ›› 2023, Vol. 49 ›› Issue (3): 647-661.doi: 10.3724/SP.J.1006.2023.23023

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

玉米株高和穗位高性状全基因组关联分析

马雅杰¹(), 鲍建喜¹(), 高悦欣¹, 李雅楠¹, 秦文萱¹, 王彦博¹, 龙艳¹, 李金萍², 董振营¹^,²^,^*(), 万向元¹^,²^,^*()

¹北京科技大学生物与农业研究中心 / 化学与生物工程学院 / 顺德研究生院 / 北京中智生物农业国际研究院, 北京 100083
²北京首佳利华科技有限公司 / 主要作物生物育种北京市工程实验室 / 生物育种北京市国际科技合作基地, 北京 100192

收稿日期:2022-03-03 接受日期:2022-05-05 出版日期:2023-03-12 网络出版日期:2022-05-19
通讯作者: 董振营,万向元
作者简介:马雅杰, E-mail: 13292097686@163.com
鲍建喜, E-mail: bjx1232003@126.com第一联系人：^**同等贡献
基金资助:
国家重点研发计划项目“农业生物种质资源挖掘与创新利用”重点专项(2021YFD1200700)

Genome-wide association analysis of plant height and ear height related traits in maize

MA Ya-Jie¹(), BAO Jian-Xi¹(), GAO Yue-Xin¹, LI Ya-Nan¹, QIN Wen-Xuan¹, WANG Yan-Bo¹, LONG Yan¹, LI Jin-Ping², DONG Zhen-Ying¹^,²^,^*(), WAN Xiang-Yuan¹^,²^,^*()

¹Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, School of Chemistry and Biological Engineering, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100083, China
²Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China

Received:2022-03-03 Accepted:2022-05-05 Published:2023-03-12 Published online:2022-05-19
Contact: DONG Zhen-Ying,WAN Xiang-Yuan
About author:First author contact:^**Contributed equally to this work
Supported by:
National Key Research and Development Program of China(2021YFD1200700)

摘要/Abstract

摘要：

适宜的株高和穗位高可提高植株的养分利用效率及抗倒伏性, 对玉米增产和稳产具有重要意义。为揭示玉米株高和穗位高遗传机制, 本研究以854份玉米自交系为关联群体, 利用均匀分布于玉米10条染色体的2795个SNP标记对4个环境下玉米株高、穗位高以及穗位系数进行全基因组关联分析(genome-wide association study, GWAS)。共定位到81个显著关联SNP位点(P<0.0001), 其中与株高显著关联的SNP为35个, 单个位点表型解释率为0.02%~6.23%; 与穗位高显著关联SNP为31个, 单个位点表型变异解释率为0.03%~3.06%; 与穗位系数显著关联的SNP位点为24个, 单个位点表型变异解释率为0.03%~6.64%。进一步鉴定出15个可在2个及以上环境共定位的稳定SNP, 其中6个为本研究首次发现, 9个位于前人定位QTL区间或/和关联SNP位点2 Mb范围内。在15个稳定SNP位点上下游各200 kb的置信区间共发现83个功能注释基因, 结合文献分析筛选出了每个位点最有可能的候选基因, 这些候选基因主要参与激素合成与信号转导、糖类代谢、细胞分裂调控等途径。鉴定出6个主效SNP位点, 并发现1个可同时调控株高、穗位高和穗位系数的一因多效位点。本研究可为分子标记辅助选择育种提供有效遗传位点, 为精细定位和克隆株高与穗位高相关性状基因提供参考。

关键词: 玉米, 株高, 穗位高, 全基因组关联分析, 候选基因

Abstract:

Suitable plant height (PH) and ear height (EH) can improve the efficiency of nutrient utilization and lodging resistance, which is of great significance for stable and high yield in maize. In this study, an association panel including 854 maize inbred lines used to analyze the PH, EH, and the ratio of EH to PH (EH/PH) in four environments, and genome-wide association study (GWAS) was then conducted using 2795 single nucleotide polymorphism (SNP) markers distributed uniformly throughout maize genome. A total of 81 SNP loci (P < 0.0001) were identified by using FarmCPU model, among which 35 SNPs were significantly associated with PH, with phenotypic variation explained (PVE) ranging from 0.020% to 6.225%; 31 SNPs were significantly associated with ear height, and PVE was from 0.026% to 3.060%; 24 SNPs were significantly associated with EH/PH, and the PVE ranged from 0.032% to 6.636%. 15 stable SNPs that were repeatedly detected in multiple environments for specific trait were further identified, among which six loci were reported for the first time in this study, and the remaining nine loci located in the previously identified quantitative trait loci (QTLs) or/and no more than 2 Mb with the known SNPs related with PH and EH traits. A total of 83 genes were annotated in the confidence intervals of the 15 stable SNPs, and the most likely candidate genes were further predicted according to the gene functional annotations and comparison with previous reports. The candidate genes were mainly involved in hormone synthesis and signal transduction, carbohydrate metabolism, cell division regulation and so on. Finally, six major SNP loci and one locus that affected PH, EH, and EH/PH simultaneously were identified. This study can provide genetic loci for molecular marker-assisted selection in maize breeding and provide valuable information for fine mapping and cloning of PH and EH related genes.

Key words: maize, plant height, ear height, genome-wide association analysis, candidate gene

马雅杰, 鲍建喜, 高悦欣, 李雅楠, 秦文萱, 王彦博, 龙艳, 李金萍, 董振营, 万向元. 玉米株高和穗位高性状全基因组关联分析[J]. 作物学报, 2023, 49(3): 647-661.

MA Ya-Jie, BAO Jian-Xi, GAO Yue-Xin, LI Ya-Nan, QIN Wen-Xuan, WANG Yan-Bo, LONG Yan, LI Jin-Ping, DONG Zhen-Ying, WAN Xiang-Yuan. Genome-wide association analysis of plant height and ear height related traits in maize[J]. Acta Agronomica Sinica, 2023, 49(3): 647-661.

图/表 8

表1

图1

表2

附图1

附表1

不同环境下株高、穗位高、穗位系数显著关联SNP位点汇总"

性状 Trait	环境 Environment		SNP位点 SNP marker	染色体 Chr.		位置 Locus (bp)	P值 P-value	表型变异率 PVE (%)
株高 PH	21PG		PZE-101024808	1		15,068,364	2.47E-08	4.13
	21ZC		PZE-101029689	1		18,044,029	1.81E-05	4.96
	20PG/BLUP		PZE-101058322	1		42,289,643	2.46E-05	1.90
	20PG		PZE-101105515	1		110,116,696	4.70E-07	6.23
	21PG		PZE-101108837	1		117,679,240	3.43E-08	0.47
	21ZC/BLUP		PZE-101109358	1		118,829,520	2.72E-05	3.71
	20PG		PZE-101113278	1		128,845,856	4.58E-05	1.00
	20PG/21ZC/BLUP		PZE-101256370	1		305,347,287	2.66E-05	5.19
	20ZC/21PG		PZE-102097841	2		117,120,291	4.31E-05	1.52
	20ZC		PZE-102116677	2		159,754,465	9.78E-05	0.79
	21ZC		SYN31434	3		66,376,933	2.48E-05	2.53
	21ZC		SYN28063	3		212,353,001	1.31E-05	0.22
	20ZC		PZE-104022504	4		26,481,392	7.36E-05	0.02
	21PG		PZE-104026267	4		32,890,533	2.10E-05	3.77
	21ZC/BLUP		PZE-104088728	4		166,718,467	5.98E-06	2.26
	20ZC/BLUP		PZE-104102768	4		181,859,161	5.59E-06	3.22
	21PG		PZE-104118502	4		199,488,030	1.59E-05	3.39
	20ZC		PZE-104122415	4		203,858,809	8.62E-05	0.07
	BLUP		PZE-104123974	4		205,691,345	7.57E-06	3.30
	20ZC		PZE-104130351	4		214,564,236	4.33E-05	0.41
	21ZC		PZA01570.1	5		3,612,315	3.52E-06	0.23
	21PG		SYN31840	5		23,268,618	8.86E-05	1.22
	20PG/BLUP		PZE-105047805	5		38,631,014	2.52E-05	2.65
	20ZC/21PG/21ZC/BLUP		PZE-105102182	5		157,723,585	7.14E-06	1.64
	21PG		PZE-105128589	5		190,328,323	8.50E-05	3.79
	20ZC		PZE-105158980	5		212,371,623	8.74E-07	2.36
	20ZC		SYN26885	6		58,235,167	3.58E-06	2.46
	21PG		SYN11451	6		171,556,727	2.15E-05	0.04
	21ZC		PZE-107086184	7		146,560,786	1.34E-07	5.02
	21ZC		PZE-108079027	8		139,020,108	1.91E-05	0.32
	20PG		PZE-108079422	8		139,545,943	1.82E-05	0.48
	20ZC		PZE-109024796	9		24,932,017	5.16E-05	0.67
	20ZC		PZE-109061773	9		38,609	7.40E-05	0.22
	BLUP		SYN20545	10		88,765,819	9.09E-05	1.95
	21ZC		PZE-110084754	10		137,929,862	9.32E-05	0.09
性状 Trait	环境 Environment	SNP位点 SNP marker		染色体 Chr.	位置 Locus (bp)	P值 P-value		表型变异率 PVE (%)
穗位高 EH	20PG/BLUP	PZE-101024808		1	15,068,364	1.37E-05		2.47
	21ZC	PZE-101029689		1	18,044,029	1.99E-07		1.65
	20PG	PZE-101098535		1	92,004,604	7.45E-05		0.87
	20PG/20ZC/BLUP	PZE-101105515		1	110,116,696	1.34E-05		2.32
	21PG	PZE-101108837		1	117,679,240	2.52E-06		2.35
	BLUP	PZE-101161396		1	206,925,042	2.30E-05		0.03
	BLUP	PZE-101173330		1	220,307,491	5.12E-05		1.88
	21ZC	PZE-101182552		1	230,566,972	2.85E-06		2.95
	BLUP	ZM013367-0314		1	243,024,263	3.73E-05		0.29
	21ZC	PZE-102076989		2	61,180,066	1.49E-05		2.74
	20ZC	PZE-102100073		2	122,534,230	6.54E-08		0.37
	BLUP	PZE-103067949		3	111,511,559	1.44E-05		3.06
	BLUP	PZE-103083718		3	139,354,703	2.27E-06		0.54
	20PG	SYN15468		3	149,897,051	6.46E-08		1.69
	20ZC	SYN20322		3	162,506,292	1.39E-06		1.11
	21PG	PZE-104112784		4	192,219,121	5.58E-05		1.71
	21PG	SYN27455		4	234,425,224	9.78E-06		0.97
	21PG	PZE-105043361		5	31,731,809	1.90E-05		0.06
	20ZC	PZE-105047974		5	39,072,734	8.05E-08		1.07
	20ZC/21PG/21ZC	PZE-105098019		5	147,968,605	1.20E-05		3.00
	BLUP	SYN7363		5	180,154,411	5.63E-05		0.73
	20PG	SYN32728		5	200,050,570	8.42E-06		1.94
	21PG	PZE-105149244		5	206,545,681	3.46E-05		1.88
	21ZC	PZE-106043310		6	95,865,051	7.48E-06		0.23
	21PG	PZE-106078719		6	138,545,114	6.09E-05		0.11
	20PG	PZE-107028964		7	36,379,816	1.20E-05		0.27
	20ZC	PZE-107106841		7	164,177,644	1.22E-05		0.40
	20PG	PZE-108059088		8	107,623,992	8.95E-05		0.04
	20PG/21PG	PZE-108069615		8	125,245,658	2.92E-05		2.86
	20PG	PZE-108079422		8	139,545,943	4.78E-05		0.98
	BLUP	PZE-109003046		9	3,291,982	1.44E-05		0.60
穗位系数 EH/PH	20PG	SYN5056		1	16,011,707	2.43E-05		3.89
	BLUP	PZE-101075097		1	59,163,811	4.46E-05		5.30
	21ZC	PZE-101130082		1	168,091,438	3.70E-05		3.30
	21ZC	SYN13128		1	182,826,264	1.45E-06		4.00
	21ZC	PZE-101182552		1	230,566,972	2.42E-07		4.23
	21ZC/BLUP	PZE-103075978		3	126,523,695	2.96E-05		5.58
	21ZC/BLUP	PZE-103083718		3	139,354,703	2.08E-05		0.74
	BLUP	SYN16519		3	149,050,783	5.42E-05		0.36
	21PG	SYN23245		3	187,679,537	4.38E-05		1.53
	21PG	PZE-104051877		4	85,020,190	5.63E-05		0.32
	21ZC	PZE-104079748		4	157,609,086	3.29E-05		1.05
	BLUP	PZE-104082879		4	160,500,101	7.30E-05		0.03
	20ZC	PZE-105102393		5	158,090,068	8.57E-07		4.87
	21ZC	SYN7363		5	180,154,411	6.25E-06		1.57
	21ZC	PZE-106016519		6	40,855,166	5.66E-05		0.32
	20ZC	PZE-106038001		6	89,033,009	2.28E-07		1.55
	21ZC	SYN2958		6	95,987,816	5.31E-05		4.91
	21ZC/BLUP	PZE-108039693		8	64,911,909	2.72E-05		1.80
	20PG/BLUP	PZE-108069615		8	125,245,658	3.04E-07		6.64
	20ZC	PZE-108074750		8	134,120,027	2.59E-05		0.54
	21PG	PZE-108102648		8	162,806,745	2.25E-05		2.93
	BLUP	PZE-108102684		8	162,917,082	5.83E-07		4.09
	BLUP	PZE-109051855		9	92,960,428	7.50E-05		3.31
	BLUP	PZE-110002415		10	2,028,528	5.41E-05		1.91

附表1

图2

表3

图3

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性状 Trait	环境 Environment	均值±标准差^a Mean ± SD ^a	变异系数 CV (%)	变异范围^a Range ^a	偏度 Skewness	峰度 Kurtosis	遗传力 H²
株高 PH	20PG	209.58±27.36	13.05	118.20-284.00	-0.084	0.053	0.81
	20ZC	193.97±25.70	13.25	79.00-282.80	-0.175	0.557
	21PG	209.99±28.14	13.40	83.60-291.00	-0.150	0.503
	21ZC	179.73±23.49	13.07	81.00-247.00	-0.186	0.660
穗位高 EH	20PG	79.23±16.70	21.08	35.60-137.20	0.248	0.148	0.78
	20ZC	75.21±14.97	19.90	27.60-124.20	0.071	0.036
	21PG	79.53±17.57	22.09	30.20-139.40	0.186	0.016
	21ZC	58.91±13.10	22.24	19.50-100.40	0.210	0.134
穗位系数EH/PH	20PG	0.38±0.06	15.79	0.19-0.55	0.017	-0.057	0.74
	20ZC	0.39±0.05	12.82	0.22-0.59	-0.081	-0.043
	21PG	0.38±0.06	15.79	0.19-0.55	-0.108	0.052
	21ZC	0.33±0.05	15.15	0.18-0.49	0.054	-0.009

性状 Trait	PH- 20PG	PH- 20ZC	PH- 21PG	PH- 21ZC	EH- 20PG	EH- 20ZC	EH- 21PG	EH- 21ZC	EH/PH- 20PG	EH/PH- 20ZC	EH/PH- 21PG
PH-20ZC	0.716^**
PH-21PG	0.847^**	0.753^**
PH-21ZC	0.766^**	0.747^**	0.770^**
EH-20PG	0.652^**	0.424^**	0.579^**	0.472^**
EH-20ZC	0.472^**	0.685^**	0.551^**	0.495^**	0.699^**
EH-21PG	0.541^**	0.473^**	0.706^**	0.475^**	0.799^**	0.746^**
EH-21ZC	0.447^**	0.476^**	0.523^**	0.647^**	0.699^**	0.729^**	0.705^**
EH/PH-20PG	0.031	-0.027	0.064	-0.007	0.770^**	0.522^**	0.592^**	0.548^**
EH/PH-20ZC	-0.003	0.027	0.066	-0.007	0.570^**	0.741^**	0.583^**	0.562^**	0.744^**
EH/PH-21PG	0.069^*	0.048	0.165	0.039	0.648^**	0.587^**	0.809^**	0.562^**	0.788^**	0.760^**
EH/PH-21ZC	0.001	0.055	0.092	0.085^*	0.553^**	0.572^**	0.553^**	0.808^**	0.731^**	0.742^**	0.711^**

玉米株高和穗位高性状全基因组关联分析

Genome-wide association analysis of plant height and ear height related traits in maize

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性状 Trait	SNP标记 SNP Marker	P值 P-value	表型变异率¹ PVE ¹ (%)	环境 Environment	染色体 Chr.	位置 Locus (bp)	候选基因 Candidate gene	基因功能注释 Gene annotation
株高 Plant height (PH)	PZE-101058322	2.46E-05	1.90	BLUP/20PG	1	42,289,643	Zm00001d028671	ABC transporter B family member 6
	PZE-101109358	2.72E-05	3.71	BLUP/21ZC	1	118,829,520	Zm00001d030282	Alpha-mannosidase
	PZE-101256370	2.66E-05	5.19	BLUP/20PG/21ZC	1	305,347,287	Zm00001d034914	Protein EXPORTIN 1A
	PZE-102097841	4.31E-05	1.52	20ZC/21PG	2	117,120,291	Zm00001d004541	Zinc finger CCCH domain-containing protein 24
	PZE-104088728	5.98E-06	2.26	BLUP/21ZC	4	166,718,467	Zm00001d051685	ADP, ATP carrier protein 2, mitochondrial
	PZE-104102768	5.59E-06	3.22	BLUP/20ZC	4	181,859,161	Zm00001d052174	Cyclin-dependent kinase inhibitor 1
	PZE-105047805	2.52E-05	2.65	BLUP/20PG	5	38,631,014	Zm00001d014271	Caltractin
	PZE-105102182	7.14E-06	1.64	BLUP/20ZC/21PG/21ZC	5	157,723,585	Zm00001d016332	Protein-serine/threonine phosphatase
穗位高 Ear height (EH)	PZE-101024808	1.37E-05	2.47	BLUP/20PG	1	15,068,364	Zm00001d027842	O-fucosyltransferase family protein
	PZE-101105515	4.70E-07	2.32	BLUP/20PG/20ZC	1	110,116,696	Zm00001d030166	Glycosyltransferase-like KOBITO 1
	PZE-105098019	1.20E-05	3.00	20ZC/21PG/21ZC	5	147,968,605	Zm00001d016162	RING/U-box superfamily protein
	PZE-108069615	3.04E-07	2.36	20PG/21PG	8	125,245,658	Zm00001d010713	CPP-transcription factor 8
穗位系数 EH/PH	PZE-103075978	2.96E-05	5.58	BLUP/21ZC	3	126,523,695	Zm00001d041549	Dof zinc finger protein DOF2.2
	PZE-103083718	2.27E-06	0.74	BLUP/21ZC	3	139,354,703	Zm00001d041823	O-fucosyltransferase family protein
	PZE-108039693	2.72E-05	1.80	BLUP/21ZC	8	64,911,909	Zm00001d009448	ABC transporter B family member 9
	PZE-108069615	2.92E-05	6.64	BLUP/20PG	8	125,245,658	Zm00001d010713	CPP-transcription factor 8

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