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作物学报

作物学报 ›› 2026, Vol. 52 ›› Issue (5): 1573-1590.doi: 10.3724/SP.J.1006.2026.53065

• 研究简报 • 上一篇    

玉米穗上叶片数全基因组关联分析和全基因组选择

杨欣雨(), 崔文涛, 迪力尼格尔·阿力木, 汪凯翔, 吴鹏昊, 任姣姣*()   

  1. 新疆农业大学农学院, 新疆乌鲁木齐 830052
  • 收稿日期:2025-08-21 接受日期:2026-01-22 出版日期:2026-05-12 网络出版日期:2026-02-10
  • 通讯作者: *任姣姣, E-mail: renjiaojiao789@sina.com
  • 作者简介:E-mail: yangxinyutop@163.com
  • 基金资助:
    自治区天山英才项目(2022TSYCJU0003);自治区自然科学基金重点项目(2022D01D34);自治区重点研发计划项目(2024B02008-1);自治区重大专项(2022A02003-4);国家自然科学基金项目(32360491);新疆玉米产业技术体系项目(XJARS-02)

Genome-wide association and genomic selection analysis of the number of leaves above the ear in maize

Yang Xin-Yu(), Cui Wen-Tao, Dilinigeer Alimu, Wang Kai-Xiang, Wu Peng-Hao, Ren Jiao-Jiao*()   

  1. College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
  • Received:2025-08-21 Accepted:2026-01-22 Published:2026-05-12 Published online:2026-02-10
  • Contact: *Ren Jiao-Jiao, E-mail: renjiaojiao789@sina.com
  • Supported by:
    Autonomous Region Tianshan Elite Program(2022TSYCJU0003);Key Project of the Autonomous Region Natural Science Foundation(2022D01D34);Key R&D Program of the Autonomous Region(2024B02008-1);Major Special Project of the Autonomous Region(2022A02003-4);National Natural Science Foundation of China(32360491);Xinjiang Maize Industrial Technology System Project(XJARS-02)

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摘要：

穗上叶片数是影响玉米株型的重要性状之一, 采用遗传定位方法能鉴定到与玉米穗上叶片数显著关联的单核苷酸多态性(SNP)位点, 并进一步筛选出调控该性状的候选基因, 为玉米理想株型定向选育及籽粒产量的高效提升奠定基础。利用291个玉米自交系组成的自然群体进行多个环境试验, 采用测序手段进行基因分型, 对穗上叶片数(LNAE)进行全基因组关联分析(GWAS)和全基因组选择(GS)。穗上叶片数受基因型(G)、环境(E)及基因型与环境互作(G×E)影响极显著(P < 0.001), 广义遗传力为81.23%; 穗上叶片数在环境间以及在与产量相关性状间均呈显著正相关。MLMM模型检测到15个与穗上叶片数显著相关的SNP位点, 单个SNP解释的表型贡献率为1.12%~22.43%。FarmCPU模型检测到了37个显著相关的SNP, 单个SNP解释的表型贡献率为0.02%~18.23%。2种不同的模型共检测到11个共定位位点, 分别位于第2、4、5、6、7和9染色体上。其中, 位于5号染色体的5_93495559既是环境稳定位点, 又是模型共定位位点, 与前期研究相比, 该SNP是新的遗传位点。结合关联图谱、共定位分析和候选基因表达预测分析发现, 在11个共定位位点的15个候选基因中, 基因Zm00001eb315650、Zm00001eb315660和Zm00001eb089980在特定的叶片生长阶段呈现高水平表达。全基因选择结果显示, 70%的训练群体规模和3000个SNP可以获得较高的预测准确度。总之, 本研究通过全基因组关联分析定位到52个与穗上叶片数显著相关的SNP位点, 11个共定位位点确定了15个候选基因, 其中, Zm00001eb315650、Zm00001eb315660和Zm00001eb089980为本研究的3个关键候选基因; 穗上叶片数全基因组选择结果表明, 70%的训练群体规模和3000个SNP标记组合可获得较高的预测准确度, 该参数可用于穗上叶片数的分子育种选择。

关键词: 玉米, 穗上叶片数, 全基因组关联分析, 候选基因, 全基因组选择

Abstract:

The number of leaves on the ear is an important trait influencing maize plant architecture. Genetic mapping approaches can identify single nucleotide polymorphisms (SNPs) significantly associated with this trait and facilitate the discovery of candidate genes, thereby laying a foundation for targeted breeding of ideal maize plant architecture and efficient enhancement of grain yield. In this study, a natural population of 291 maize inbred lines was evaluated across multiple environments. Genotyping was performed using sequencing technologies, and both genome-wide association studies (GWAS) and genomic selection (GS) were conducted for the leaf number above the ear (LNAE). LNAE was significantly affected by genotype (G), environment (E), and the genotype-by-environment interaction (G × E) (P < 0.001), with a broad-sense heritability of 81.23%. Using the MLMM model, 15 SNPs significantly associated with LNAE were identified, each explaining 1.12% to 22.43% of the phenotypic variation. The FarmCPU model identified 37 significant SNPs, with individual contributions ranging from 0.02% to 18.23%. A total of 11 co-located loci were detected on chromosomes 2, 4, 5, 6, 7, and 9 were detected by two different models. Among them, SNP 5_93495559 on chromosome 5 was identified as both an environmentally stable and model co-located locus. Compared with previous reports, this SNP represents a novel genetic locus. By integrating association mapping, co-location analysis, and candidate gene expression profiling, three genes—Zm00001eb315650, Zm00001eb315660, and Zm00001eb089980—were found to exhibit high expression during key leaf development stages and were identified as likely candidates underlying LNAE. Genomic selection analysis indicated that using 70% of the population as a training set and 3000 SNPs could achieve high prediction accuracy. This parameter can be utilized for molecular breeding selection of the number of leaves above the ear.

Key words: maize, number of leaves on the ear, genome-wide association study, candidate gene, genomic selection

表1

玉米穗上叶片数描述性统计及遗传力"

环境
Environment		 均值
Mean		 最小值
Min.		 最大值
Max.		 偏度
Skewness		 峰度
Kurtosis		 变异系数
CV (%)		 遗传力
H2 (%)
PX23 6.61 5.54 8.01 0.337 -0.271 8.00 81.23
PD23 6.10 4.86 7.38 -0.079 0.133 6.94
PN24 6.04 5.16 7.42 0.179 -0.165 7.68
Combined 6.25 5.26 7.38 0.216 -0.202 6.47

表2

玉米穗上叶片数方差分析"

变异来源
Source		 自由度
DF		 平方和
Sum Sq.		 均方
Mean Sq.		 F值F value P值P-value
基因型Genotype (G) 290 420.65 1.45 10.36 ***
环境Environment (E) 2 104.53 52.27 373.33 ***
基因型与环境互作G×E 541 152.52 0.28 2.01 ***
误差Error 797 111.58 0.14 — —

图1

玉米穗上叶片数环境间相关性分析(A)及与产量性状的相关性分析(B) PX23为新疆奇台环境; PD23为奇台西地环境; PN24为海南乐东环境; Combined为联合环境。LNAE为穗上叶片数; GW为单穗粒重; HKW为百粒重。*和***分别代表在0.05和0.001水平上显著相关。"

表3

MLMM模型和FarmCPU模型鉴定到的与穗上叶片数显著相关的SNP"

模型Model 环境Environment SNP 区间Bin MAF P值P-value PVE (%)
MLMM PD23 2_120634825 2.05 0.06 1.43×10-6 2.50
PD23 2_168025488 2.06 0.49 2.55×10-6 3.98
PN24 3_225158062 3.09 0.08 5.19×10-7 4.81
Combined 4_157618103 4.06 0.07 1.64×10-6 9.53
PD23 4_205497294 4.08 0.07 7.58×10-7 8.62
PX23 5_161426166 5.04 0.28 1.33×10-6 3.38
Combined 5_28589012 5.03 0.08 4.80×10-7 1.87
PD23 5_93495559 5.04 0.09 1.58×10-6 4.34
Combined 5_93495559 5.04 0.09 5.22×10-7 1.80
PN24 6_151035576 6.05 0.10 8.23×10-10 22.43
MLMM PX23 6_92586565 6.01 0.05 1.16×10-6 9.86
PX23 7_134339386 7.03 0.12 1.64×10-6 1.35
PN24 7_26144877 7.02 0.22 7.56×10-7 1.12
PD23 9_47509326 9.03 0.08 5.11×10-7 5.43
PD23 10_135626210 10.05 0.13 1.75×10-6 3.37
FarmCPU PN24 1_111517760 1.05 0.06 1.06×10-6 1.95
PN24 1_258669737 1.09 0.35 1.81×10-11 1.57
PN24 1_30205600 1.03 0.09 2.53×10-8 3.20
Combined 1_35793348 1.03 0.08 1.02×10-6 2.29
PN24 1_41061523 1.03 0.45 4.23×10-8 1.31
PD23 1_96687462 1.05 0.05 2.07×10-6 7.45
PD23 2_120634825 2.05 0.06 2.83×10-6 5.61
PN24 2_41387828 2.04 0.07 1.40×10-6 6.16
PN24 3_107497527 3.04 0.06 2.31×10-11 7.62
PN24 3_131795894 3.05 0.49 2.71×10-6 1.36
Combined 3_186294797 3.06 0.05 8.47×10-7 0.02
PN24 3_199745851 3.07 0.05 5.19×10-17 10.62
PX23 4_134561575 4.05 0.06 1.75×10-6 1.92
Combined 4_157618103 4.06 0.07 8.10×10-7 15.46
PN24 4_175173380 4.06 0.05 2.89×10-6 4.32
PD23 4_205497294 4.08 0.07 9.99×10-7 5.70
PX23 4_210561941 4.08 0.07 1.23×10-6 6.23
PX23 4_230408762 4.09 0.07 2.44×10-6 0.03
Combined 4_230408762 4.09 0.07 2.50×10-7 4.50
PX23 5_161426166 5.04 0.28 1.68×10-6 2.88
Combined 5_28589012 5.03 0.08 2.44×10-7 2.89
PX23 5_71843763 5.03 0.26 5.14×10-7 4.27
PD23 5_93495559 5.04 0.09 2.59×10-6 5.75
Combined 5_93495559 5.04 0.09 1.44×10-7 3.88
PN24 6_115959165 6.04 0.07 1.39×10-7 3.14
PN24 6_143596272 6.05 0.05 2.55×10-10 9.22
PN24 6_151035576 6.05 0.10 2.25×10-7 9.68
PX23 6_92586565 6.01 0.05 1.96×10-7 18.23
PN24 7_132786846 7.02 0.08 4.82×10-10 8.85
PX23 7_134339386 7.03 0.12 8.23×10-7 2.24
Combined 7_134339386 7.03 0.12 9.90×10-7 4.67
PN24 7_173598659 7.04 0.09 2.53×10-8 4.65
PN24 8_176458605 8.08 0.15 1.51×10-6 0.99
Combined 8_22982115 8.03 0.10 1.75×10-6 4.19
PD23 9_148731042 9.06 0.07 2.05×10-6 10.75
PD23 9_47509326 9.03 0.08 2.89×10-6 4.22
PN24 10_67379697 10.03 0.08 6.98×10-7 2.77

图2

MLMM模型下穗上叶片数的曼哈顿和Q-Q图 PX23为新疆奇台环境; PD23为奇台西地环境; PN24为海南乐东环境; Combined为联合环境。"

图3

FarmCPU模型下穗上叶片数的曼哈顿和Q-Q图 PX23为新疆奇台环境; PD23为奇台西地环境; PN24为海南乐东环境; Combined为联合环境。"

表4

11个稳定SNP的具体信息"

定位条件
Positioning condition		 SNP 候选基因
Candidate gene		 区间
Bin
PD23-MLMM, PD23-FarmCPU 2_120634825 Zm00001eb089980 2.05
Combined-MLMM, Combined-FarmCPU 4_157618103 — 4.06
PD23-MLMM, PD23-FarmCPU 4_205497294 Zm00001eb199890 4.08
PX23-FarmCPU, Combined-FarmCPU 4_230408762 Zm00001eb203860 4.09
Combined-MLMM, Combined-FarmCPU 5_28589012 Zm00001eb221520 5.03
Zm00001eb221530 5.03
PD23-FarmCPU, Combined-FarmCPU, PD23-MLMM, Combined-MLMM 5_93495559 Zm00001eb233990 5.04
PX23-MLMM, PX23-FarmCPU 5_161426166 Zm00001eb240510 5.04
Zm00001eb240520 5.04
Zm00001eb240530 5.04
Zm00001eb240540 5.04
PX23-MLMM, PX23-FarmCPU 6_92586565 Zm00001eb272100 6.01
PN24-MLMM, PN24-FarmCPU 6_151035576 Zm00001eb286080 6.05
PX23-FarmCPU, Combined-FarmCPU, PX23-MLMM 7_134339386 Zm00001eb315650 7.03
Zm00001eb315660 7.03
PD23-MLMM, PD23-FarmCPU 9_47509326 Zm00001eb381590 9.03

图4

稳定SNP等位变异对表型的影响 A-K分别为11个稳定SNP在3个环境和联合环境中等位变异对应的穗上叶片数表型值差异。PX23为新疆奇台环境; PD23为奇台西地环境; PN24为海南乐东环境; Combined为联合环境。P为显著性差异, *代表P < 0.05, **代表P < 0.01, ***代表P < 0.001。"

表5

玉米穗上叶片数推定候选基因"

SNP 候选基因
Candidate gene		 功能注释
Function annotation
4_134561575 Zm00001eb183540 蛋白质毛状体双折射样蛋白33 Protein trichome birefringence-like 33
Zm00001eb183550 未表征的LOC103653699 Uncharacterized LOC103653699
4_210561941 Zm00001eb200840 核酸结合蛋白(C2H2样锌指蛋白) Nucleic acid binding protein (C2H2-like zinc finger protein)
Zm00001eb200860 甘油醛氧化酶Glyoxal oxidase
5_71843763 Zm00001eb230020 —
1_96687462 — —
9_148731042 Zm00001eb398600 IRK相互作用蛋白IRK-interacting protein
1_30205600 Zm00001eb009640 亮氨酸富含重复序列受体样丝氨酸/苏氨酸蛋白激酶BAM2
Leucine-rich repeat receptor-like serine/threonine-protein kinase BAM2
1_41061523 Zm00001eb012470 热休克同源蛋白70 kD蛋白2 Heat shock cognate 70 kD protein 2
Zm00001eb012480 PHM2177
Zm00001eb012490 线粒体磷酸盐载体蛋白3 Mitochondrial phosphate carrier protein 3, mitochondrial
1_111517760 Zm00001eb025660 —
1_258669737 — —
2_41387828 Zm00001eb080140 ABC转运蛋白G家族成员51 ABC transporter G family member 51
3_107497527 — —
3_131795894 Zm00001eb137220 腺嘌呤核苷酸α水解酶样超家族蛋白Adenine nucleotide alpha hydrolase-like superfamily protein
3_199745851 Zm00001eb152260 蓝铜蛋白Blue copper protein
Zm00001eb152270 DUF155家族蛋白DUF155 family protein
Zm00001eb152280 未表征的蛋白质Uncharacterized protein
4_175173380 Zm00001eb190970 U-box结构域含蛋白33 U-box domain-containing protein 33
6_115959165 Zm00001eb277790 与Shaggy相关的蛋白激酶iota Shaggy-related protein kinase iota
Zm00001eb277800 含UmuC结构域的蛋白质UmuC domain-containing protein
Zm00001eb277810 果胶裂解酶样超家族蛋白Pectin lyase-like superfamily protein
6_143596272 Zm00001eb284230 花粉特异性蛋白SF21 Pollen-specific protein SF21
Zm00001eb284240 丝氨酸合成酶1叶绿体Threonine synthase 1 chloroplastic
Zm00001eb284250 含锌指CCCH结构域蛋白35 Zinc finger CCCH domain-containing protein 35
7_132786846 — —
7_173598659 Zm00001eb327060 EAL2
Zm00001eb327080 蛋白质蛋装置-1 Protein EGG APPARATUS-1
Zm00001eb327090 未表征的蛋白质Uncharacterized protein
8_176458605 Zm00001eb368560 AT富集元件结合因子3 AT-rich element binding factor 3
10_67379697 Zm00001eb414020 丝氨酸/苏氨酸蛋白激酶STY13 Serine/threonine-protein kinase STY13
Zm00001eb414030 YTH结构域含蛋白ECT2 YTH domain-containing protein ECT2
1_35793348 Zm00001eb011120 PGG结构域含蛋白质PGG domain-containing protein
3_186294797 Zm00001eb148440 未表征的蛋白质Uncharacterized protein
4_230408762 Zm00001eb203860 F-box/Kelch家族蛋白F-box/Kelch-repeat protein
8_22982115 Zm00001eb337930 酪蛋白激酶1样蛋白HD16 Casein kinase 1-like protein HD16
5_161426166 Zm00001eb240510 UDP-糖基转移酶73D1 UDP-glycosyltransferase 73D1
Zm00001eb240520 UDP-糖基转移酶73C5 UDP-glycosyltransferase 73C5
Zm00001eb240530 —
Zm00001eb240540 —
6_92586565 Zm00001eb272100 ATP依赖性锌金属蛋白酶FTSH 5叶绿体
ATP-dependent zinc metalloprotease FTSH 5 chloroplastic
7_134339386 Zm00001eb315650 蓝铜蛋白Blue copper protein
Zm00001eb315660 转录调控蛋白AlgP Transcriptional regulatory protein AlgP
2_120634825 Zm00001eb089980 60 kD茉莉酸盐诱导蛋白60 kD jasmonate-induced protein
2_168025488 Zm00001eb095640 蛋白质长叶素2 Protein LONGIFOLIA 2
Zm00001eb095650 未表征的蛋白质Uncharacterized protein
4_205497294 Zm00001eb199890 未表征的蛋白质Uncharacterized protein
9_47509326 Zm00001eb381590 羧基端加工蛋白酶Carboxyl-terminal-processing protease
10_135626210 Zm00001eb427460 β-果糖苷酶1样蛋白Beta-fructofuranosidase 1-like
3_225158062 Zm00001eb160130 未表征的蛋白质Uncharacterized protein
6_151035576 Zm00001eb286080 FAM91A1样蛋白FAM91A1-like protein
7_26144877 — —
4_157618103 — —
5_28589012 Zm00001eb221520 浮游蛋白样蛋白2 Flotillin-like protein 2
Zm00001eb221530 未表征的蛋白质Uncharacterized protein
5_93495559 Zm00001eb233990 未表征的LOC111589340 Uncharacterized LOC111589340

图5

与穗上叶片数相关的15个候选基因在28种叶片相关组织中的表达量热图 图例中数字为候选基因的表达值, 即log2 (FPKM+1)。"

图6

不同训练群体大小对预测准确性的影响"

图7

不同标记数量对穗上叶片数预测准确性的影响"

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