基于GWAS预测调控超甜玉米秸秆蛋白质含量基因

doi:10.7668/hbnxb.20195953

摘要/Abstract

摘要：

为深入解析调控超甜玉米秸秆蛋白质含量的遗传基础,基于玉米56K基因芯片,采用BLINK模型定位控制超甜玉米秸秆蛋白质含量的主要SNP位点及预测候选基因。结果表明:在超甜玉米收获期,其秸秆蛋白质含量为12.63~30.29 g/kg,平均值为20.76 g/kg,呈正态分布;GWAS共关联定位到调控超甜玉米秸秆蛋白质含量6个显著SNP位点,这些位点分布于第1,4和6号染色体上,其贡献率为10.07%~18.17%,其中位于6号染色体的Affx-115330268的贡献率最高。在显著关联位点上下游200 kb的置信区间内,共检测到184个候选基因,其中已注释基因34个,占比为18.48%;通过GO功能注释和KEGG通路富集分析,候选基因主要参与生物调节、细胞过程、催化活性等生物过程,并富集于类固醇生物合成、色氨酸代谢、光合作用-天线蛋白等通路。基于文献查找比对发现,6个(GRMZM2G141473、GRMZM2G007854、GRMZM2G111319、 GRMZM2G121024、 GRMZM2G010353、 GRMZM2G049547)调控超甜玉米秸秆蛋白质的关键基因,其主要参与蛋白质和酶合成等途径。

关键词: 超甜玉米, 秸秆蛋白质, 全基因组关联分析, 候选基因

Abstract:

In order to further analyze the genetic basis regulating the protein content of super sweet corn stalk,this study used the BLINK model to locate the major SNP loci and predict candidate genes controlling the trait,based on the maize 56K gene chip.The results showed that during the harvest period of super sweet corn,the protein content of stalk ranged from 12.63 to 30.29 g/kg,with an average of 20.76 g/kg,showing a normal distribution.Six significant SNP loci regulating the protein content of super sweet corn stalk were identified by GWAS.These loci were distributed on chromosomes 1,4 and 6,and their contribution rates ranged from 10.07% to 18.17%.Among them,Affx-115330268 on chromosome 6 had the highest contribution rate.A total of 184 candidate genes were detected in the 200 kb confidence interval between the upstream and downstream of the significant association sites,of which 34 were annotated genes,accounting for 18.48%.Through GO functional annotation and KEGG pathway enrichment analysis,candidate genes were mainly involved in biological processes such as biological regulation,cellular processes,and catalytic activity,and were enriched in steroid biosynthesis,tryptophan metabolism,photosynthesis-antenna protein and other pathways.Based on the literature search and comparison,it was found that six key genes (GRMZM2G141473, GRMZM2G007854, GRMZM2G111319, GRMZM2G121024, GRMZM2G010353, GRMZM2G049547) that regulate the protein content of super sweet corn stalk,which are mainly involved in protein and enzyme synthesis.

Key words: Super sweet corn, Stalk protein, Genome-wide association analysis, Candidate gene

中图分类号:

文伟祺, 余育林, 郁灵隽, 邓召, 崔妮妮, 余海兵, 程昕昕. 基于GWAS预测调控超甜玉米秸秆蛋白质含量基因[J]. 华北农学报, 2026, 41(3): 17-24. doi: 10.7668/hbnxb.20195953.

WEN Weiqi, YU Yulin, YU Lingjun, DENG Zhao, CUI Nini, YU Haibing, CHENG Xinxin. Prediction of Gene Regulating Protein Content Involved in Super Sweet Corn Stalk Based on GWAS[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(3): 17-24. doi: 10.7668/hbnxb.20195953.

http://www.hbnxb.net/CN/Y2026/V41/I3/17

图/表 9

图1 100 份超甜玉米秸秆蛋白含量的频率分布

Fig.1 Frequency distribution of protein content in 100 samples of sweet corn stalks

图2 调控秸秆蛋白质含量全基因组关联分析 A.Manhattan;B.QQ-plot.

Fig.2 Genome-wide association analysis of regulated stalk protein content

表1 秸秆蛋白质含量候选 SNP 鉴定结果

Tab.1 Identification results of candidate SNPs for stalk protein content

序号 Index	SNP位点 SNP Marker	染色体 Chromosomes	位置/bp Position	P值 P-value	贡献率/% Contribution rate
1	Affx-90514859	1	286 629 521	3.93E-05	10.07
2	Affx-90162720	4	228 440 300	6.65E-05	15.10
3	Affx-90747382	4	237 340 914	2.04E-04	10.35
4	Affx-90901362	6	14 050 061	2.17E-04	16.24
5	Affx-90684850	1	286 620 104	2.41E-04	15.08
6	Affx-115330268	6	84 281 632	2.43E-04	18.17

图3 显著SNP位点的连锁不平衡(LD)热图及等位基因变异效应分析 A.连锁不平衡分析:*.关联位点所在位置;B.等位变异效应分析:不同大写字母表示基因型间差异极显著(P<0.01)。

Fig.3 Linkage disequilibrium(LD)heatmap and allelic variant effect analysis of significant SNP loci A.Linkage disequilibrium analysis:*.The location of the associated loci;B.Allelic variation effect analysis:different uppercase letters indicated extremely significant differences among genotypes (P<0.01).

图4 GO功能注释 1.细胞过程;2.对刺激的反应;3.生物调节;4.发育过程;5.多细胞生物过程;6.生物中的种间相互作用过程;7.繁殖过程;8.生长;9.解毒;10.体内稳态过程;11.免疫系统过程;12.定位;13.细胞解剖结构;14.含蛋白复合物;15.催化活性;16.结合;17.转录调控活性;18.分子传导活性;19.抗氧化活性。

Fig.4 GO function annotation 1.Cellular process;2.Response to stimulus;3.Biological regulation;4.Developmental process;5.Multicellular organismal process;6.Interspecies interaction processes in biology;7.Reproductive process;8.Growth;9.Detoxification;10.Homeostatic process;11.Immune system process;12.Localization;13.Cellular anatomical structure;14.Protein containing complex;15.Catalytic activity;16.Binding;17.Transcription regulator activity;18.Molecular transducer activity;19.Antioxidant activity.

图5 KEGG富集分析 1.核糖体;2.植物激素信号转导;3.苯丙烷类生物合成;4.RNA 转运;5.RNA 降解;6.次生代谢物的生物合成;7.代谢通路;8.核苷酸切除修复;9.DNA 复制;10.错配修复;11.光合作用-天线蛋白;12.色氨酸代谢;13.类固醇生物合成。

Fig.5 KEGG enrichment analysis 1.Ribosome;2.Plant hormone signal transduction;3.Phenylpropanoid biosynthesis;4.RNA transport;5.RNA degradation;6.Biosynthesis of secondary metabolites;7.Metabolic pathways;8.Nucleotide excision repair;9.DNA replication;10.Mismatch repair;11.Photosynthesis-antenna proteins;12.Tryptophan metabolism;13.Steroid biosynthesis.

图6 候选基因的动态表达热图

Fig.6 Dynamic expression heat map of candidate genes

表2 超甜玉米秸秆蛋白质含量显著SNP位点的候选基因及功能注释

Tab.2 Candidate genes and functional annotation of SNP loci with significant protein content in super sweet corn stalk

SNP标记 SNP Marker	染色体 Chromosome	位置/bp Position	候选基因 Candidate gene	功能注释 Description
Affx-90514859	1	286 577 038	GRMZM2G141473	醛氧化酶
Affx-90162720	4	228 239 151	GRMZM2G007854	蛋白激酶超家族蛋白
Affx-90747382	4	237 502 083	GRMZM2G111319	蛋白激酶超家族蛋白
Affx-90901362	6	13 918 932	GRMZM2G121024	胆碱激酶
Affx-90684850	1	286 390 345	GRMZM2G010353	谷氨酸羧肽酶
		286 781 681	GRMZM2G049547	锌金属蛋白酶 EGY1

图7 蛋白质互作网络分析

Fig.7 Protein interaction network analysis

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