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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (2): 377-391.doi: 10.3724/SP.J.1006.2023.23021

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米雌穗产量相关性状全基因组关联分析与候选基因鉴定

殷芳冰1(), 李雅楠1, 鲍建喜1, 马雅杰1, 秦文萱1, 王锐璞1, 龙艳1,2, 李金萍2, 董振营1,2,*(), 万向元1,2,*()   

  1. 1北京科技大学生物与农业研究中心 / 化学与生物工程学院 / 顺德研究生院 / 北京中智生物农业国际研究院, 北京 100083
    2北京首佳利华科技有限公司 / 主要作物生物育种北京市工程实验室 / 生物育种北京市国际科技合作基地, 北京 100192
  • 收稿日期:2022-02-27 接受日期:2022-05-05 出版日期:2022-05-26 网络出版日期:2022-05-26
  • 通讯作者: 董振营,万向元
  • 作者简介:E-mail: yinfangbing186@163.com
  • 基金资助:
    国家重点研发计划项目“农业生物种质资源挖掘与创新利用”重点专项(2021YFD1200700)

Genome-wide association study and candidate genes predication of yield related ear traits in maize

YIN Fang-Bing1(), LI Ya-Nan1, BAO Jian-Xi1, MA Ya-Jie1, QIN Wen-Xuan1, WANG Rui-Pu1, LONG Yan1,2, LI Jin-Ping2, DONG Zhen-Ying1,2,*(), WAN Xiang-Yuan1,2,*()   

  1. 1Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, School of Chemistry and Biological Engineering, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100083, China
    2Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
  • Received:2022-02-27 Accepted:2022-05-05 Published:2022-05-26 Published online:2022-05-26
  • Contact: DONG Zhen-Ying,WAN Xiang-Yuan
  • Supported by:
    National Key Research and Development Program of China(2021YFD1200700)

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摘要：

玉米雌穗产量相关性状直接影响玉米最终产量, 解析其遗传机制可为玉米高产提供有益指导。本研究以733份玉米自交系作为关联群体, 在2个环境下随机区组种植, 调查穗行数(KRN)、穗长(EL)和穗粗(ED) 3个产量相关性状, 利用MaizeSNP3072芯片对其进行基因分型, 采用FarmCPU模型进行全基因组关联分析, 分别鉴定出16、13和24个与3个性状显著关联的单核苷酸多态性位点(SNP), 对表型变异的解释率分别为0.01%~7.08%、0.01%~5.34%和0.07%~4.34%。其中, 分别有6、2和5个与3个性状存在显著关联的高可信度(high confidence, HC) SNP, 而且有2个HC-SNP同时与KRN和ED显著相关, 1个KRN HC-SNP和3个ED HC-SNP为本研究首次报道。在所鉴定HC-SNP上下游200 kb范围内筛选出33个重要候选基因, 其中9号染色体SNP标记PZE-109003046所在基因PIN1a为控制生长素极性运输从而调控雌穗性状的已知基因。另一些候选基因编码不同转录因子, 以及参与生长素、赤霉素和乙烯等激素介导的信号转导、DNA甲基化和蛋白磷酸化等翻译后修饰过程的蛋白, 可能从不同方面调控雌穗相关性状。本研究所挖掘的11个HC-SNP与33个候选基因可以为进一步克隆雌穗性状功能基因、揭示相关分子调控机制以及利用分子标记辅助选择育种提供有益指导。

关键词: 玉米, 雌穗产量相关性状, 全基因组关联分析, 候选基因

Abstract:

Ear traits directly affect the final yield of maize, and the analysis of its genetic mechanisms can provide useful guidance for yield enhancement in maize. In this study, 733 maize inbred lines were planted in randomized block designs under two environments, and three yield-related traits, kernel row number (KRN), ear length (EL), and ear diameter (ED), were investigated. Genotyping was performed using MaizeSNP3072 chip and FarmCPU (fixed and random model circulating probability unification) model was used to conduct genome-wide association study (GWAS). 16, 13, and 24 single nucleotide polymorphism (SNP) loci significantly associated with the three traits were identified, and the values of phenotypic variation explained (PVE) for single locus were 0.01%-7.08%, 0.01%-5.34%, and 0.07%-4.34%, respectively. Further, six, two, and five high confidence (HC) SNPs that were repeatedly detected in multiple environments for KRN, EL, and ED were retrieved, among which two SNPs were simultaneously associated with KRN and ED traits, and one KRN HC-SNP and three ED HC-SNPs were firstly reported in this study. By searching 200 kb regions around the 11 HC-SNPs loci, 33 important candidate genes were identified, including a known gene PIN1a regulating ear development via auxin polar transport located in the confidence interval of chromosome 9 SNP marker PZE-109003046. Other candidate genes encoded transcription factors, hormone (such as auxin, gibberellin, and ethylene) pathway related proteins, DNA methylation, and protein phosphorylation related proteins, which might regulate ear traits by different mechanisms. The 11 HC-SNPs and 33 important candidate genes detected in this study can provide valuable information for further cloning of functional genes and reveal the molecular regulatory mechanisms and marker-assisted selection for ear trait in maize.

Key words: maize, yield related ear traits, genome-wide association study (GWAS), candidate gene

表1

穗行数、穗长和穗粗表型数据统计分析"

性状
Trait		 环境
Environment		 平均值
Mean
(cm)		 最大值
Maximum (cm)		 最小值
Minimum (cm)		 范围
Range (cm)		 标准差
Standard deviation		 偏度
Skewness		 峰度
Kurtosis		 遗传力
h2
穗行数KRN 2019 13.80 21.33 8.00 13.33 1.93 0.632 0.810 0.80
2020 14.89 24.40 8.40 16.00 2.17 0.607 0.755
穗长EL 2019 13.11 21.83 6.78 15.04 1.95 0.293 0.798 0.65
2020 14.45 21.03 8.34 12.69 1.98 0.012 0.221
穗粗ED 2019 4.25 5.67 3.11 2.56 0.34 0.151 0.872 0.79
2020 4.44 5.83 3.09 2.73 0.36 0.073 0.998

图1

不同环境间穗行数、穗长和穗粗相关性分析和频率直方图 图中对角线表示穗行数、穗长和穗粗在2019年北京和2020年北京环境的频率直方图, 左下表示穗行数、穗长和穗粗在不同环境下的散点图, 右上表示相关性系数。**、***分别表示在P < 0.01、0.001水平上差异显著。KRN、EL和ED分别表示穗行数、穗长和穗粗。"

表2

穗行数、穗长和穗粗多环境联合方差分析"

性状
Trait		 变异来源
Source		 均方
Mean of square		 F值
F-value		 P值
P-value
穗行数KRN 基因型Genotype 22.271 13.694 <0.001
环境Environment 1273.476 783.028 <0.001
基因型与环境互作Genotype and environment interaction 4.392 2.701 <0.001
穗长EL 基因型Genotype 19.133 24.162 <0.001
环境Environment 1916.165 2419.761 <0.001
基因型与环境互作Genotype and environment interaction 6.260 7.905 <0.001
穗粗ED 基因型Genotype 0.649 23.762 <0.001
环境Environment 39.665 1451.942 <0.001
基因型与环境互作Genotype and environment interaction 0.124 4.546 <0.001

图2

733份玉米自交系主成分分析(a)与亲缘关系分析(b) HZS、NSS和SS分别表示黄早四群体、非坚秆群体和坚秆群体。"

图3

玉米穗行数、穗长、穗粗GWAS曼哈顿图(a, c, e)与QQ-plot图(b, d, f) BLUP表示最佳线性无偏预测值。KRN、EL和ED处理缩写同图1。"

附表1

不同环境下穗行数、穗长、穗粗显著关联SNP位点汇总"

性状
Trait		 标记名称
Maker name		 染色体
Chr.		 物理位置
Position (bp)		 环境
Environment		 P值
P-value		 表型变异解释率
PVE (%)		 最小等位基因频率
MAF
穗行数KRN PZE-103149597 3 206,991,538 BLUP/2019 1.28E-06/1.60E-07 1.13/1.46 0.21
PZE-104041818 4 59,704,298 BLUP/2020 1.58E-06/1.52E-05 6.44/6.18 0.36
PZE-104124173 4 205,899,298 2019 7.02E-08 3.21 0.34
PZE-104126211 4 208,732,552 BLUP/2020 1.46E-10/4.08E-07 7.08/6.74 0.47
PZE-105105740 5 164,510,203 2019 1.90E-05 0.11 0.35
PZE-106038186 6 89,083,642 2020 4.83E-05 0.37 0.44
SYN4194 6 162,814,863 BLUP/2019 3.59E-06/8.91E-07 0.72/0.69 0.31
PZE-106115356 6 165,632,631 2019 2.94E-05 0.52 0.41
PZE-107055553 7 110,762,862 2020 6.93E-07 1.23 0.35
PZE-107116723 7 169,607,175 BLUP/2019/2020 7.09E-11/5.74E-09/4.43E-08 4.32/3.40/3.79 0.23
PZE-108005561 8 5,864,518 2019 9.98E-05 0.01 0.48
PZE-108080140 8 140,264,937 2019 9.53E-07 2.80 0.47
PZA03608.2 8 146,863,745 BLUP/2020 1.01E-06/5.53E-06 2.05/2.47 0.44
PZE-109037923 9 76,271,588 2019 9.78E-08 1.39 0.31
PZE-109061922 9 107,147,924 BLUP 5.78E-05 0.37 0.45
SYN20545 10 88,765,819 2019 7.29E-05 0.18 0.48
穗长
EL		 PZE-101162306 1 208,334,343 BLUP/2019 2.91E-06/5.22E-05 2.88/1.86 0.35
PZE-102065179 2 45,039,241 BLUP 1.80E-05 3.15 0.46
SYN27033 2 227,085,703 2019 9.34E-05 2.92 0.32
PZE-104073430 4 148,150,704 2019 2.33E-05 2.56 0.40
PZE-104113905 4 193,372,982 BLUP/2019 4.72E-05/3.35E-06 0.01/0.33 0.38
PZE-104140854 4 234,265,598 2019 4.80E-05 0.99 0.16
PZE-105039536 5 25,111,571 2019 5.52E-05 0.57 0.20
PZE-105105086 5 163,308,887 BLUP 4.51E-06 1.73 0.30
SYN6220 6 151,019,477 2019 7.16E-05 1.81 0.26
SYN35928 8 93,549,629 2019 5.51E-05 2.56 0.38
PZE-108059570 8 108,903,711 BLUP 3.11E-05 1.56 0.40
PZE-108106737 8 165,505,598 2019 6.36E-05 0.01 0.41
PZE-108133100 8 178,781,276 2020 8.87E-05 5.34 0.45
穗粗
ED		 PZB02058.1 1 28,614,062 BLUP 1.65E-05 0.31 0.39
PZE-102047851 2 27,664,781 2020 4.19E-05 2.97 0.12
PUT-163a-60393963-2893 2 32,965,430 2019 7.21E-05 0.98 0.44
PZE-102120444 2 168,965,413 2019 5.10E-05 0.07 0.49
PZE-103087199 3 145,604,315 2019 1.09E-05 4.34 0.28
SYN8382 4 45,460,142 BLUP 2.70E-05 2.20 0.45
PZE-104041818 4 59,704,298 2020 1.99E-07 3.02 0.36
PZE-104045413 4 69,980,490 2020 7.70E-05 1.17 0.44
PZE-104093153 4 172,487,553 BLUP/2020 2.92E-05/2.26E-05 1.62/1.87 0.32
PZE-104093898 4 173,802,472 BLUP 1.14E-05 1.54 0.19
PZE-104126211 4 208,732,552 BLUP/2020 1.00E-05/7.50E-05 0.19/0.66 0.47
SYN22663 5 3,212,673 2019 1.33E-05 0.92 0.47
PZE-105032165 5 18,159,660 2019 4.21E-06 0.34 0.49
PZE-105080632 5 95,622,206 2019 1.27E-06 2.06 0.36
SYN32729 5 200,052,824 BLUP/2019 5.19E-05/2.98E-05 4.00/3.84 0.49
SYN4194 6 162,814,863 BLUP/2019 2.89E-09/8.17E-07 2.56/2.66 0.31
PZE-107055553 7 110,762,862 2020 1.90E-07 2.79 0.35
SYN13511 7 125,838,654 2019 6.35E-05 1.00 0.48
PZE-107070986 7 131,255,494 2019 3.75E-05 0.07 0.44
PZE-108036722 8 57,892,012 2019 1.02E-05 2.88 0.43
PZE-109003046 9 3,291,982 BLUP/2020 1.21E-07/2.08E-10 3.90/4.01 0.26
PZB00235.1 9 36,013,505 2019 1.96E-05 2.80 0.48
PZE-109061922 9 107,147,924 BLUP 5.99E-05 0.07 0.45
PZE-110043433 10 82,662,170 BLUP 1.31E-05 1.37 0.46

表3

穗行数、穗长和穗粗性状高可信度(high confidence, HC) SNP位点与候选基因"

性状
Trait		 标记名称
Marker name		 染色体
Chr.		 位置
Position (bp)		 最小等位基因频率
MAF		 环境
Environment		 表型变异解释率
PVE (%)		 候选基因
Candidate gene		 基因注释
Gene annotation
穗行数
KRN		 PZE-103149597 3 206,991,538 0.21 BLUP 2019 1.46 Zm00001d043674 Cytidine deaminase
Zm00001d043675 Reversion-to-ethylene sensitivity1 like2
Zm00001d043681 Amino_oxidase domain-containing protein
PZE-104041818 4 59,704,298 0.36 BLUP 2020 6.44 Zm00001d050016 bHLH transcription factor
PZE-104126211 4 208,732,552 0.47 BLUP 2020 7.08 Zm00001d053006 C2H2-like zinc finger protein
Zm00001d053004 Auxin transporter-like protein
Zm00001d053003 ARM repeat superfamily protein
Zm00001d053011 Putative DUF869 domain containing family protein
SYN4194 6 162,814,863 0.31 BLUP 2019 0.72 Zm00001d038699 O-methyltransferase ZRP4
Zm00001d038698 Auxin response factor
Zm00001d038695 Gibberellin 2-oxidase7
Zm00001d038690 Non-specific serine/threonine protein kinase
Zm00001d038693 C2C2-DOF transcription factor
PZE-107116723 7 169,607,175 0.23 BLUP
2019 2020		 4.32 Zm00001d022077 Probable 6-phosphogluconolactonase
Zm00001d022071 Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain
Zm00001d022075 Cytochrome P-450 17
PZA03608.2 8 146,863,745 0.44 BLUP 2020 2.47 Zm00001d011329 DNA methyl transferase
Zm00001d011323 Agamous-like MADS-box protein AGL62
Zm00001d011326 Plant Tudor-like RNA-binding protein
Zm00001d011327 Plant Tudor-like RNA-binding protein
Zm00001d011328 GTP-binding nuclear protein
穗长
EL		 PZE-101162306 1 208,334,343 0.35 BLUP 2019 2.88 Zm00001d031973 Phosphatidylinositol-3-phosphatase myotubularin-1
Zm00001d031981 Evolutionarily conserved C-terminal region 5
PZE-104113905 4 193,372,982 0.38 BLUP 2019 0.33 Zm00001d052570 Cation-chloride cotransporter 1
Zm00001d052561 mRNA-decapping enzyme-like protein
Zm00001d052564 Putative NAC domain transcription factor superfamily protein
Zm00001d052578 Putative F-box protein
Zm00001d052584 Protein kinase domain containing protein expressed
穗粗
ED		 PZE-104093153 4 172,487,553 0.32 BLUP 2020 1.87 Zm00001d051856 O-fucosyltransferase family protein
Zm00001d051861 AT-hook motif nuclear-localized protein
PZE-104126211 4 208,732,552 0.47 BLUP 2020 0.66 Zm00001d053006 C2H2-like zinc finger protein
Zm00001d053004 Auxin transporter-like protein
Zm00001d053003 ARM repeat superfamily protein
Zm00001d053011 Putative DUF869 domain containing family protein
SYN32729 5 200,052,824 0.49 BLUP 2019 4.00 Zm00001d017573 Transcription factor bHLH157
Zm00001d017575 Dof zinc finger protein DOF2.5
SYN4194 6 162,814,863 0.31 BLUP 2019 2.66 Zm00001d038699 O-methyltransferase ZRP4
Zm00001d038698 Auxin response factor
Zm00001d038695 Gibberellin 2-oxidase7
Zm00001d038690 Non-specific serine/threonine protein kinase
Zm00001d038693 C2C2-DOF transcription factor
PZE-109003046 9 3,291,982 0.26 BLUP 2020 4.01 Zm00001d044812 Auxin efflux carrier component

图4

显著关联SNP位点等位变异表型效应分析 NS表示P > 0.05, *、**和***分别表示0.05、0.01和 0.001水平差异显著。KRN、EL和ED处理缩写同图1。"

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