Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (3): 431-442.doi: 10.3864/j.issn.0578-1752.2025.03.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Association Study of Husk Traits in Maize

ZHOU GuangFei1(), MA Liang1, MA Lu1, ZHANG ShuYu1, ZHANG HuiMin1, SONG XuDong1, ZHANG ZhenLiang1, LU HuHua1, HAO DeRong1, MAO YuXiang1, XUE Lin1,2, CHEN GuoQing1,2()   

  1. 1 Jiangsu Yanjiang Institute of Agricultural Science, Nantong 226012, Jiangsu
    2 Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing 210095
  • Received:2024-07-05 Accepted:2024-08-19 Online:2025-02-01 Published:2025-02-11
  • Contact: CHEN GuoQing

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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

Table 1

Statistical analysis of maize husk traits"

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

Fig. 1

Frequency distribution of maize husk traits"

Table 2

Correlation analysis of maize husk traits and kernel moisture content"

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

Table 3

Analysis of variance and broad-sense heritability of maize husk traits"

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

Fig. 2

Manhattan (left) and QQ (right) plots of genome-wide association study for maize husk traits A, B and C were Manhattan and QQ plots of genome-wide association study for husk number, length and coverage, respectively"

Fig. 3

Allelic effect analysis of five stable SNPs for maize husk traits *, ** and *** represented significant at P<0.05, P<0.01 and P<0.001 level"

Table 4

The screened gene based on five stable SNPs"

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
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

Fig. 4

The regression analysis between expression of nine genes and husk traits in 17 maize inbred lines Expression level for each gene from B73 was set at 1"

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