基于GWAS和WGCNA分析挖掘玉米花期相关候选基因

doi:10.3724/SP.J.1006.2023.33010

作物学报 ›› 2023, Vol. 49 ›› Issue (12): 3261-3276.doi: 10.3724/SP.J.1006.2023.33010

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于GWAS和WGCNA分析挖掘玉米花期相关候选基因

钱甫¹(), 张占琴², 陈树宾², 丁永福², 桑志勤²^,^*(), 李卫华¹^,^*()

¹石河子大学农学院 / 绿洲生态农业兵团重点实验室, 新疆石河子 832000
²新疆农垦科学院, 新疆石河子832000

收稿日期:2023-02-22 接受日期:2023-05-24 出版日期:2023-12-12 网络出版日期:2023-08-28
通讯作者: * 李卫华, E-mail: lwh_agr@shzu.edu.cn; 桑志勤, E-mail: sangzhiqin@126.com
作者简介:E-mail: 1971194140@qq.com
基金资助:
兵团重点领域科技攻关项目(2019AB021);兵团科技创新人才计划项目(2021CB038);中国科学院“西部青年学者”项目

Mining maize flowering traits related candidate genes based on GWAS and WGCNA data

QIAN Fu¹(), ZHANG Zhan-Qin², CHEN Shu-Bin², DING Yong-Fu², SANG Zhi-Qin²^,^*(), LI Wei-Hua¹^,^*()

¹College of Agriculture, Shihezi University / Key Laboratory of Oasis Eco-Agriculture, Shihezi 832000, Xinjiang, China
²Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, Xinjiang, China

Received:2023-02-22 Accepted:2023-05-24 Published:2023-12-12 Published online:2023-08-28
Contact: * E-mail: lwh_agr@shzu.edu.cn; E-mail: sangzhiqin@126.com
Supported by:
Tackling Key Scientific and Technological Problems in Key Areas of Xinjiang Production and Construction Corps(2019AB021);Science and Technology Innovation Talent Plan of Xinjiang Production and Construction Corps(2021CB038);Chinese Academy of Sciences “Western Young Scholar”

摘要/Abstract

摘要：

花期是玉米重要性状之一, 解析玉米花期的遗传基础, 挖掘玉米花期关键基因, 对于选育广适玉米品种具有重要意义。在580份玉米自交系构成的自然群体中, 3年种植测定散粉期、吐丝期和散粉吐丝间隔期等3个花期性状, 利用分布全基因组的31,826个SNPs (single nucleotide polymorphisms)标记进行全基因组关联分析(genome wide association study, GWAS), 结合自交系B73的14个不同发育阶段的转录组数据进行权重基因共表达网络分析(weighted gene co-expression network analysis, WGCNA), 挑选与玉米开花相关的组织特异性模块和关键基因。GWAS在多环境(2个环境以上)下共定位标记14个, 挖掘到潜在候选基因10个, WGCNA挖掘到花期潜在候选基因17个, 2种方法共同挖掘到候选基因3个。Zm00001d052180编码一个MADS-box转录因子19, Zm00001d016814编码NAC转录因子133, Zm00001d048082编码MADS-box转录因子8, 这些基因主要参与调节花序生长发育。研究结果为解析玉米花期遗传基础及分子机制提供参考。

关键词: 玉米, 花期性状, GWAS, WGCNA, 候选基因

Abstract:

The flowering time is one of the important traits in maize. It is of great significance to analyze the genetic basis and to mine the key core genes in flowering for maize varieties with wide adaptability. A natural population consisting of 580 maize inbred lines were planted for three years, to determine the three flowering traits (including days to anthesis, days to silking, and anthesis silking interval). Genome-wide association analysis was conducted using 31,826 SNPs distributed throughout the whole genome. Combined with transcriptome data of 14 different developmental stages of inbred line B73, weighted gene co-expression network analysis was performed to select tissue specific modules and key genes related to maize flowering time. A total of 14 SNPs for four flower traits under multiple environments and 10 potential candidate genes were mined by GWAS, WGCNA was used to mine 17 potential candidate genes in flowering time, three candidate genes were jointly mined by both approaches. Zm00001d052180 encodes a MADS box transcription factor 19, Zm00001d016814 encodes the NAC transcription factor 133, Zm00001d048082 encodes MADS box transcription factor 8, mainly involved in regulating inflorescence growth and development, which has certain research value and significance. These results provide a reference for the genetic basis and molecular mechanisms of flowering time related traits in maize.

Key words: maize, flowering time related traits, GWAS, WGCNA, candidate gene

钱甫, 张占琴, 陈树宾, 丁永福, 桑志勤, 李卫华. 基于GWAS和WGCNA分析挖掘玉米花期相关候选基因[J]. 作物学报, 2023, 49(12): 3261-3276.

QIAN Fu, ZHANG Zhan-Qin, CHEN Shu-Bin, DING Yong-Fu, SANG Zhi-Qin, LI Wei-Hua. Mining maize flowering traits related candidate genes based on GWAS and WGCNA data[J]. Acta Agronomica Sinica, 2023, 49(12): 3261-3276.

图/表 14

表1

表2

图1

图2

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附表1

4个环境下花期性状显著SNPs标记"

性状 Trait	年份 Years	标记 SNPs	染色体 Chr.	物理位置 Position (bp)	P值 P-value	次等位基因频率 MAF
DTS	2019	8_159342177	8	159,342,177	6.89E-11	0.34103
DTS	2019	5_48863489	5	48,863,489	1.63E-09	0.386323
DTS	2019	5_176849292	5	176,849,292	1.68E-09	0.23357
DTS	2019	5_147435514	5	147,435,514	4.75E-08	0.487567
DTS	2019	3_170291855	3	170,291,855	1.91E-07	0.493783
DTS	2019	8_160072522	8	160,072,522	2.90E-07	0.332149
DTS	2019	5_30789224	5	30,789,224	5.54E-07	0.37389
DTA	2019	10_69098512	10	69,098,512	8.51E-10	0.179262
DTA	2019	5_176849292	5	176,849,292	1.05E-09	0.232865
DTA	2019	10_10799643	10	10,799,643	1.80E-08	0.395431
DTA	2019	2_1359194	2	1,359,194	2.70E-08	0.260984
DTA	2019	6_128386990	6	128,386,990	3.07E-08	0.230228
DTA	2019	5_72656332	5	72,656,332	3.81E-08	0.44464
DTA	2019	7_109239367	7	109,239,367	7.89E-08	0.463972
DTA	2019	5_145997443	5	145,997,443	2.14E-07	0.329525
DTA	2019	8_160072522	8	160,072,522	2.97E-07	0.332162
DTA	2019	8_159342177	8	159,342,177	3.18E-07	0.341828
DTA	2019	8_134443746	8	134,443,746	3.78E-07	0.355888
DTA	2019	3_138802769	3	138,802,769	5.32E-07	0.132689
DTA	2019	4_135184025	4	135,184,025	7.44E-07	0.393673
DTA	2020	2_83703979	2	83,703,979	5.11E-12	0.243007
DTA	2020	8_130284569	8	130,284,569	9.81E-11	0.368881
DTA	2020	3_135182164	3	135,182,164	1.23E-10	0.190559
DTA	2020	7_157639029	7	157,639,029	5.63E-09	0.356643
DTA	2020	5_87683979	5	87,683,979	2.14E-08	0.252622
DTA	2020	7_109239367	7	109,239,367	3.45E-08	0.465909
DTA	2020	4_182045481	4	182,045,481	1.09E-07	0.403846
DTA	2020	9_15913145	9	15,913,145	2.29E-07	0.449301
DTA	2020	6_63992603	6	63,992,603	6.89E-07	0.318182
DTA	2020	8_159342177	8	159,342,177	9.73E-07	0.340035
DTA	2020	6_128386990	6	128,386,990	1.56E-06	0.230769
DTA	2021	3_135182164	3	135,182,164	1.56E-12	0.191413
DTA	2021	3_206999249	3	206,999,249	3.81E-11	0.476744
DTA	2021	8_130282760	8	130,282,760	2.11E-10	0.199463
DTA	2021	7_168431448	7	168,431,448	4.93E-10	0.388193
DTA	2021	9_154601150	9	154,601,150	3.07E-09	0.232558
DTA	2021	7_109239367	7	109,239,367	4.45E-08	0.466011
DTA	2021	3_6928983	3	6,928,983	7.33E-08	0.34347
DTA	2021	3_33440636	3	33,440,636	1.34E-07	0.308587
DTA	2021	4_146577795	4	146,577,795	2.31E-07	0.127907
DTA	2021	4_182045481	4	182,045,481	5.73E-07	0.407871
DTA	2021	8_159342177	8	159,342,177	6.13E-07	0.342576
DTA	2021	2_80389048	2	80,389,048	1.56E-06	0.390877
DTA	BLUE	8_130284569	8	130,284,569	1.90E-11	0.365517
DTA	BLUE	5_71931331	5	71,931,331	4.00E-10	0.493103
DTA	BLUE	6_128386990	6	128,386,990	1.30E-09	0.232759
DTA	BLUE	2_80271281	2	80,271,281	1.60E-09	0.39569
DTA	BLUE	7_165890330	7	165,890,330	2.23E-09	0.369828
DTA	BLUE	3_6928983	3	6,928,983	2.06E-08	0.341379
DTA	BLUE	3_135182164	3	135,182,164	6.12E-08	0.191379
DTA	BLUE	1_175994724	1	175,994,724	6.29E-08	0.194828
DTA	BLUE	4_182045481	4	182,045,481	2.09E-07	0.406897
DTA	BLUE	1_8218880	1	8,218,880	2.24E-07	0.228448
DTA	BLUE	5_176849292	5	176,849,292	3.71E-07	0.230172
DTA	BLUE	8_159342177	8	159,342,177	4.79E-07	0.343966
DTA	BLUE	5_213317177	5	213,317,177	9.59E-07	0.334483
DTA	BLUE	5_87683979	5	87,683,979	1.15E-06	0.253448
DTS	2020	8_130284569	8	130,284,569	3.09E-15	0.367596
DTS	2020	8_159342177	8	159,342,177	5.61E-09	0.342334
DTS	2020	3_135182164	3	135,182,164	6.72E-09	0.189895
DTS	2020	4_36061401	4	36,061,401	5.58E-08	0.461672
DTS	2020	4_182045481	4	182,045,481	1.16E-07	0.402439
DTS	2020	2_80271281	2	80,271,281	2.70E-07	0.39547
DTS	2020	5_71931331	5	71,931,331	2.75E-07	0.490418
DTS	2020	10_27456815	10	27,456,815	8.62E-07	0.402439
DTS	2020	1_8218880	1	8,218,880	1.23E-06	0.229094
DTS	2021	8_130282760	8	130,282,760	2.06E-10	0.199463
DTS	2021	8_159342177	8	159,342,177	2.80E-09	0.342576
DTS	2021	6_65919084	6	65,919,084	1.25E-08	0.347943
DTS	2021	3_206999249	3	206,999,249	2.14E-08	0.476744
DTS	2021	5_73163352	5	73,163,352	2.90E-08	0.120751
DTS	2021	9_149761626	9	149,761,626	1.48E-07	0.13059
DTS	2021	2_61511737	2	61,511,737	1.70E-07	0.363148
DTS	2021	5_87683979	5	87,683,979	3.98E-07	0.253131
DTS	BLUE	8_130284569	8	130,284,569	1.75E-11	0.365517
DTS	BLUE	3_6928983	3	6,928,983	5.95E-09	0.341379
DTS	BLUE	2_80271281	2	80,271,281	6.90E-09	0.39569
DTS	BLUE	5_176849292	5	176,849,292	7.82E-09	0.230172
DTS	BLUE	7_165890330	7	165,890,330	3.42E-08	0.369828
DTS	BLUE	7_168431448	7	168,431,448	1.47E-07	0.392241
DTS	BLUE	1_8218880	1	8,218,880	1.79E-07	0.228448
DTS	BLUE	9_149761626	9	149,761,626	2.08E-07	0.131034
DTS	BLUE	3_135182164	3	135,182,164	3.03E-07	0.191379
DTS	BLUE	3_170291855	3	170,291,855	3.73E-07	0.496552
DTS	BLUE	7_109239367	7	109,239,367	4.01E-07	0.467241
DTS	BLUE	1_175994724	1	175,994,724	5.31E-07	0.194828
DTS	BLUE	4_132936409	4	132,936,409	1.12E-06	0.15
DTS	BLUE	8_125053113	8	125,053,113	1.17E-06	0.421552
DTS	BLUE	6_128386990	6	128,386,990	1.50E-06	0.232759
ASI	2020	1_282472600	1	282,472,600	6.18E-11	0.417553
ASI	2020	4_121588214	4	121,588,214	1.24E-06	0.298759
ASI	2020	7_1680665	7	1,680,665	1.26E-06	0.405142
ASI	2020	6_129660777	6	129,660,777	1.35E-06	0.496454
ASI	BLUE	3_213737451	3	213,737,451	2.39E-08	0.374138
ASI	BLUE	4_121588214	4	121,588,214	3.84E-07	0.300862

附表1

表3

图3

图4

附图2

图5

表4

图6

表5

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性状 Trait	年份 Year	范围 Range	均值 Mean	标准差 SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis	遗传力 H²(%)
散粉期 DTA	2019	59.00-86.00	73.46	5.78	7.86	-0.23	-0.66	96.18
	2020	53.00-83.00	65.22	6.22	9.54	0.14	-0.61
	2021	48.00-75.00	60.72	5.66	9.31	-0.09	-0.67
	BLUE	53.43-81.00	66.52	5.73	8.61	-0.07	-0.65
吐丝期 DTS	2019	60.67-89.00	76.12	5.98	7.86	-0.30	-0.56	95.54
	2020	55.00-84.50	68.06	6.49	9.53	0.11	-0.68
	2021	50.50-75.50	62.51	5.37	8.59	0.07	-0.48
	BLUE	55.53-83.68	68.97	5.79	8.40	-0.07	-0.58
散粉吐丝间隔期ASI	2019	0.33-6.67	2.67	1.11	41.59	0.72	0.40	56.50
	2020	0-6.50	2.72	1.20	44.23	0.47	-0.07
	2021	0-5.00	1.69	1.05	61.87	0.48	-0.18
	BLUE	0.67-6.16	2.39	0.86	35.88	0.68	0.94

性状 Trait	变异来源 Source	自由度 DF	均方 MS
散粉期DTA	基因型 Genotype	579	208^***
	年份 Year	2	55,678^***
	基因型×年份 Genotype×Year	1149	8^***
	残差 Residual	2109	4
吐丝期DTS	基因型 Genotype	579	210^***
	年份 Year	2	62,735^***
	基因型×年份 Genotype×Year	1149	9^***
	残差 Residual	2105	4
散粉吐丝间隔期ASI	基因型 Genotype	579	4.7^***
	年份 Year	2	387.5^***
	基因型×年份 Genotype×Year	1144	1.9^***
	残差 Residual	2067	1.3

性状 Trait	标记 SNPs	基因 Gene	功能注释 Annotation
DTA	4_182045481	Zm00001d052180^*	Tunicate 1
DTA, DTS	8_159342177	Zm00001d011703	WD-repeat protein RBAP 1
DTA	3_6928983	zma-MIR156b	Corngrass 1
DTA	5_87683979	Zm00001d015385	Chlorophyll a-b binding protein, chloroplastic
DTA	7_109239367	Zm00001d020361	PHD-transcription factor 30
DTA	6_128386990	Zm00001d037532	6-phosphofructo-2-kinase/fructose-26-bisphosphatase
DTA, DTS	5_176849292	Zm00001d016814^*	NAC-transcription factor 133
DTS	1_8218880	Zm00001d027554	LYR family of Fe/S cluster biogenesis protein
DTS	9_149761626	Zm00001d048082^*	MADS 8
ASI	4_121588214	Zm00001d050768	Cytokinin response regulator 7

模块 Moudle	基因 Gene	功能注释 Annotation
Blue	Zm00001d014863	MYB-related-transcription factor 96
Blue	Zm00001d012395	Mannose-1-phosphate guanylyltransferase 2
Brown	Zm00001d041685	RALF
	Zm00001d022469	Putative histone-arginine methyltransferase 1.4
	Zm00001d053880	CO CO-LIKE TIMING OF CAB1 protein domain 24
Green	Zm00001d037182	12-oxo-phytodienoic acid reductase 3
	Zm00001d023424	bZIP-transcription factor 109
	Zm00001d016814^*	NAC-transcription factor 133
Purple	Zm00001d020970	Dihydroflavonoid reductase 1
Black	Zm00001d030656	Rotten ear 1
	Zm00001d013964	ALG2-interacting protein X
	Zm00001d048082^*	MADS 8
	Zm00001d033976	Aux/IAA-transcription factor 4
Royalblue	Zm00001d042985	BAG family molecular chaperone regulator 4
Grey60	Zm00001d012719	bZIP-transcription factor 20
Lightcyan	Zm00001d035629	Actin-depolymerizing factor 4
Lightcyan	Zm00001d052180^*	Tunicate 1

基于GWAS和WGCNA分析挖掘玉米花期相关候选基因

Mining maize flowering traits related candidate genes based on GWAS and WGCNA data

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性状 Trait	标记 SNPs	染色体 Chromosome	物理位置 Position (bp)	P-value
性状 Trait	标记 SNPs	染色体 Chromosome	物理位置 Position (bp)	2019	2020	2021	BLUE
散粉期 DTA	3_6928983	3	6,928,983			7.33E-08	2.06E-08
	3_135182164	3	135,182,164		1.23E-10	1.56E-12	6.12E-08
	4_182045481	4	182,045,481		1.09E-07	5.73E-07	2.09E-07
	5_87683979	5	87,683,979		2.14E-08		1.15E-06
	5_176849292	5	176,849,292	1.05E-09			3.71E-07
	6_128386990	6	128,386,990	3.07E-08	1.56E-06		1.30E-09
	7_109239367	7	109,239,367	7.89E-08	3.45E-08	4.45E-08
	8_130284569	8	130,284,569		9.81E-11		1.90E-11
	8_159342177	8	159,342,177	3.18E-07	9.73E-07	6.13E-07	4.79E-07
吐丝期 DTS	1_8218880	1	8,218,880		1.23E-06		1.79E-07
	2_80271281	2	80,271,281		2.70E-07		6.90E-09
	3_135182164	3	135,182,164		6.72E-09		3.03E-07
	3_170291855	3	170,291,855	1.91E-07			3.73E-07
	5_176849292	5	176,849,292	1.68E-09			7.82E-09
	8_130284569	8	130,284,569		3.09E-15		1.75E-11
	8_159342177	8	159,342,177	6.89E-11	9.73E-07	2.80E-09
	9_149761626	9	149,761,626			1.48E-07	2.08E-07
散粉吐丝间隔期 ASI	4_121588214	4	121,588,214		1.24E-06		3.84E-07

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