玉米苞叶性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2025.03.003

摘要/Abstract

摘要：

【目的】苞叶是影响玉米机械直收籽粒的重要性状之一，挖掘与玉米苞叶性状显著关联的遗传位点及候选基因，可为玉米苞叶性状的遗传改良提供理论依据。【方法】以251份玉米自交系为试验材料，在2个环境下鉴定玉米苞叶数目、长度和包裹度，借助覆盖全基因组32 853个单核苷酸多态性（single nucleotide polymorphisms，SNP）标记，利用多位SNP随机效应混合线性模型（multi-locus random-SNP-effect mixed linear model，mrMLM）进行全基因组关联分析，检测与3个苞叶性状显著关联的SNP位点，预测候选基因。【结果】3个苞叶性状在群体中表现出广泛的表型变异，变异系数为10.65%—40.60%；各性状在基因型、环境及基因型与环境互作均呈极显著差异，广义遗传率均大于80%。利用2个环境的表型数据及最佳线性无偏预测值，通过全基因组关联分析，共检测到92个与3个玉米苞叶性状显著关联的SNP位点，其中，与苞叶数目显著关联的SNP位点35个，单个SNP位点可解释1.48%—10.53%的表型变异，与苞叶长度显著关联的SNP位点33个，单个SNP位点可解释1.61%—21.79%的表型变异，与苞叶包裹度显著关联的SNP位点24个，单个SNP位点可解释2.17%—20.86%的表型变异。此外，未鉴定到同时与2个性状显著关联的SNP。92个SNP位点中有5个可同时在2个环境和最佳线性无偏预测值下被检测到，被认为是稳定的SNP位点，与前期研究相比，这5个SNP是新的遗传位点。参考关联群体的连锁不平衡衰减距离，利用5个稳定SNP位点，结合17个玉米自交系苞叶组织的qRT-PCR分析，筛选到3个玉米苞叶性状候选基因Zm00001d003850、Zm00001d033706和Zm00001d025612，分别编码BOI相关E3泛素蛋白连接酶、GeBP转录因子和未知功能蛋白。【结论】检测到92个与3个玉米苞叶性状显著关联的SNP位点，其中5个为稳定位点，预测了3个候选基因可能参与玉米苞叶性状的形态建成。

关键词: 玉米, 苞叶性状, 全基因组关联分析, 优异等位变异, 候选基因

Abstract:

【Objective】Husk is an important trait that affects the mechanical harvesting of maize grain, and identification of the genetic loci and candidate genes can provide theoretical basis for genetic improvement of maize husk traits. 【Method】To identify significantly associated single nucleotide polymorphisms (SNPs) and predict candidate genes for three husk traits, 251 maize inbred lines were used as plant materials and evaluated for husk number (HN), length (HL), and coverage (HC) in two environments. The genome-wide association study (GWAS) was conducted by multi-locus random-SNP-effect mixed linear model (mrMLM) with 32 853 SNPs across entire genome. 【Result】The three husk traits exhibited abundant variation among 251 maize inbred lines with 10.65%-40.60% of phenotypic variation coefficients. The variances of genotype, environment, and the genotype×environment interactions were significant at P<0.01 for each trait, and the broad-sense heritability for each trait was more than 80%. A total 92 SNPs significantly associated with three husk traits were identified in two environmental and best linear unbiased predictors (BLUP) across two environments values by GWAS. Among these SNPs, 35 SNPs were significantly associated with HN, and the phenotypic variance explained by single SNP ranged from 1.48% to 10.53%. 33 SNPs were significantly associated with HL, and the phenotypic variance explained by single SNP ranged from 1.61% to 21.69%. 24 SNPs were significantly associated with HC, and the phenotypic variance explained by single SNP ranged from 2.17% to 20.86%. However, none of SNP could be significantly associated with two husk traits. Five of 92 SNPs were stable, as they were repeatedly detected in two environments and BLUP, also they were novel loci for first reported in this study. Based on the five stable SNPs and qRT-PCR analysis for husk tissue of 17 maize inbred lines, three candidate genes (Zm00001d003850, Zm00001d033706 and Zm00001d025612) related to maize husk were screeded out, which encoded BOI-related E3 ubiquitin-protein ligase, GeBP transcription factor, and protein of unknown function, respectively. 【Conclusion】A total of 92 SNPs significantly associated with three husk traits were identified, including five stable SNPs. Three candidate genes were predicted that might be involved in maize husk growth and development.

Key words: maize, husk traits, genome-wide association study, elite allele, candidate gene

周广飞, 马亮, 马璐, 张舒钰, 章慧敏, 宋旭东, 张振良, 陆虎华, 郝德荣, 冒宇翔, 薛林, 陈国清. 玉米苞叶性状全基因组关联分析[J]. 中国农业科学, 2025, 58(3): 431-442.

ZHOU GuangFei, MA Liang, MA Lu, ZHANG ShuYu, ZHANG HuiMin, SONG XuDong, ZHANG ZhenLiang, LU HuHua, HAO DeRong, MAO YuXiang, XUE Lin, CHEN GuoQing. Genome-Wide Association Study of Husk Traits in Maize[J]. Scientia Agricultura Sinica, 2025, 58(3): 431-442.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.03.003

https://www.chinaagrisci.com/CN/Y2025/V58/I3/431

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利用5个稳定SNP位点筛选出的基因"

性状 Trait	标记 Marker	基因 Gene	染色体 Chr.	位置^a Position (bp)	功能注释 Function annotation
苞叶数目 HN	AX-86238852	Zm00001d003850	2	62448255..62449800	BOI相关E3泛素蛋白连接酶 BOI-related E3 ubiquitin-protein ligase
	AX-86238852	Zm00001d003851	2	62503425..62507705	S-核糖核酸酶结合蛋白S-ribonuclease binding protein
	AX-86269638	Zm00001d044686	3	234930037..234930396	脂质转运蛋白Lipid transfer protein
		Zm00001d044689	3	234975746..234982139	PAP/OAS1底物结合结构域超家族 PAP/OAS1 substrate-binding domain superfamily
		Zm00001d044690	3	234987257..234989609	双向氨基酸转运蛋白1 Bidirectional amino acid transporter 1
		Zm00001d044691	3	234992683..234993820	甲基转移酶相关蛋白Methyltransferase-related protein
		Zm00001d044692	3	235008717..235013278	未知蛋白Unknow protein
		Zm00001d044693	3	235061755..235065086	双特异性蛋白磷酸酶家族蛋白 Dual specificity protein phosphatase family protein
		Zm00001d044694	3	235066012..235068964	含Saposin B结构域的蛋白 Saposin B domain-containing protein
苞叶长度 HL	AX-86308176	Zm00001d033704	1	271704791..271710881	FKBP样肽基脯氨酰顺式-反式异构酶家族蛋白 FKBP-like peptidyl-prolyl cis-trans isomerase family protein
		Zm00001d033705	1	271743416..271748692	未知功能蛋白Protein of unknown function
		Zm00001d033706	1	271804516..271808051	GeBP转录因子GeBP transcription factor
		Zm00001d033707	1	271815374..271818063	微粒体谷胱甘肽S转移酶3 Microsomal glutathione S-transferase3
		Zm00001d033708	1	271819145..271823452	mRNA cap甲基转移酶mRNA cap methyltransferase
	AX-86262393	Zm00001d040214	3	32351595..32353238	糖基转移酶家族61蛋白Glycosyltransferase family 61 protein
		Zm00001d040215	3	32388537..32391284	DNAJ-like蛋白DNAJ-like protein
		Zm00001d040216	3	32393165..32395998	核糖体蛋白S8 Ribosomal protein S8
苞叶包裹度 HC	AX-86322933	Zm00001d025611	10	123861237..123862772	ATP依赖的RNA解旋酶ATP-dependent RNA helicase
		Zm00001d025612	10	123896700..123897435	未知功能蛋白Protein of unknown function
		Zm00001d025613	10	123904290..123905104	胱天蛋白酶条膜蛋白2 Casparian strip membrane protein 2
		Zm00001d025614	10	123911243..123912298	具IQ基序的钙调素结合蛋白 IQ motif-containing calmodulin-binding protein
		Zm00001d025615	10	123993115..123994083	未知功能蛋白Protein of unknown function

表4

图4

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性状 Trait	环境 Environment	均值±标准差 Mean±SD	变异范围 Range	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
苞叶数目 HN	NT	8.09±1.57	4.60-14.50	19.38	0.87	1.50
	SY	7.09±1.62	3.50-14.13	22.88	0.98	1.61
	BLUP	7.59±1.19	5.22-12.04	15.69	0.95	1.30
苞叶长度 HL	NT	23.03±2.81	16.83-32.84	12.19	0.35	0.32
	SY	20.42±2.94	12.32-30.17	14.41	0.05	0.36
	BLUP	21.73±2.31	16.12-29.15	10.65	0.29	0.22
苞叶包裹度 HC	NT	3.06±0.10	1.00-5.00	32.33	-0.04	-0.58
	SY	2.51±1.02	1.00-5.00	40.60	0.14	-0.78
	BLUP	2.78±0.28	1.30-4.63	27.71	0.10	-0.68

性状Trait	苞叶数目HN	苞叶长度HL	苞叶包裹度HC	籽粒含水量KMC
苞叶数目HN	1
苞叶长度HL	-0.06	1
苞叶包裹度HC	-0.06	0.70**	1
籽粒含水量KMC	0.26**	0.24**	0.20**	1

方差Variance	苞叶数目HN	苞叶长度HL	苞叶包裹度HC
基因型Genotype (G)	1.74**	6.22**	0.72**
环境Environment (E)	0.50**	3.39**	0.15**
基因型×环境G×E	0.50**	2.38**	0.29**
误差Error	0.61	3.32	0.38
广义遗传率H²(%)	86.72	82.22	81.69