Prediction of Gene Regulating Protein Content Involved in Super Sweet Corn Stalk Based on GWAS

doi:10.7668/hbnxb.20195953

Abstract

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

CLC Number:

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.

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Figures/Tables 9

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

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

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

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).

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.

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.

Fig.6 Dynamic expression heat map of candidate genes

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

Fig.7 Protein interaction network analysis

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