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作物学报

作物学报 ›› 2026, Vol. 52 ›› Issue (6): 1604-1617.doi: 10.3724/SP.J.1006.2026.51092

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

小麦籽粒铜含量的全基因组关联分析及候选基因预测

习千辉(), 徐梓瑗, 刘梦梦, 王宏艺, 郎凯琳, 井震海, 陈锋, 赵磊*()   

  1. 河南农业大学农学院 / 小麦玉米两熟高效生产全国重点实验室 / 河南粮食作物协同创新中心, 河南郑州 450046
  • 收稿日期:2025-11-10 接受日期:2026-03-04 出版日期:2026-06-12 网络出版日期:2026-03-06
  • 通讯作者: * 赵磊, E-mail: leizhao2016@163.com
  • 作者简介:习千辉, E-mail: 18238632602@163.com
  • 基金资助:
    河南省科技研发计划联合基金项目(242301420132);河南省高等学校重点科研项目(25A210020)

Genome-wide association study and candidate gene prediction of grain copper content in wheat

Xi Qian-Hui(), Xu Zi-Yuan, Liu Meng-Meng, Wang Hong-Yi, Lang Kai-Lin, Jing Zhen-Hai, Chen Feng, Zhao Lei*()   

  1. College of Agronomy, Henan Agricultural University / State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping / Collaborative Innovation Center of Henan Grain Crops, Zhengzhou 450046, Henan, China
  • Received:2025-11-10 Accepted:2026-03-04 Published:2026-06-12 Published online:2026-03-06
  • Contact: * Zhao Lei, E-mail: leizhao2016@163.com
  • Supported by:
    Henan Provincial Science and Technology Research and Development Program Joint Fund(242301420132);Key Scientific Research Projects of Higher Education Institutions in Henan Province(25A210020)

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摘要：

铜是人体必需的微量矿物质, 缺乏铜会威胁人体健康。小麦为全球重要的口粮作物, 借助生物强化提高小麦籽粒铜含量, 是解决人体铜元素缺乏的最经济有效的措施。然而, 目前小麦籽粒铜含量的遗传调控机制尚不清晰。本研究对349份小麦品系的籽粒铜含量进行测定, 结合小麦660K高密度SNP芯片进行全基因组关联分析(GWAS)。结果显示, 共检测到775个显著性SNPs, 主要分布在1B、4A和7A染色体上, 其中56个SNPs可以在4个及以上重复中被检测到; 单倍型分析表明, GCuC_Hap_1B和GCuC_Hap_4A可能是调控籽粒铜含量的重要基因位点, 且二者具有明显的聚合效应; 借助生物信息学分析和单倍型分析, 推测TraesCS1B03G1265400和TraesCS4A03G0093900基因可能是调控小麦籽粒铜含量的候选基因。本研究解析了小麦籽粒铜含量的遗传机制, 并为小麦品质改良育种中培育高籽粒铜含量种质资源提供重要的参考信息。

关键词: 小麦, 籽粒铜含量, 全基因组关联分析, 候选基因分析, 品质改良

Abstract:

Copper is an essential trace element in humans, and copper deficiency can compromise health. Wheat is a major staple crop worldwide, and biofortification of wheat grain with copper is a cost-effective strategy to help alleviate dietary copper deficiency. However, the genetic basis of grain copper content in wheat remains poorly understood. Here grain copper content was evaluated in 349 wheat accessions, and a genome-wide association study (GWAS) was performed using the Wheat 660K SNP array. In total, 775 significant SNPs were identified, mainly on chromosomes 1B, 4A, and 7A; among these, 56 SNPs were consistently detected in four or more replicates. Haplotype analysis indicated that GCuC_Hap_1B and GCuC_Hap_4A are key loci associated with grain copper content and show a significant pyramiding effect. Based on bioinformatics and haplotype analysis, TraesCS1B03G1265400 and TraesCS4A03G0093900 were proposed as candidate genes for regulating grain copper content. These results clarify the genetic architecture of grain copper content in wheat and provide a valuable foundation for developing germplasm with elevated grain copper content for wheat quality improvement breeding.

Key words: wheat, grain copper content, genome-wide association study, candidate gene analysis, quality improvement

表1

供试群体籽粒铜含量的统计分析"

重复
Repeat		 平均值
Mean		 最大值
Maximum		 最小值
Minimum		 标准差
Standard deviation		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis		 均方
Mean square		 F值
F value		 P值
P value		 遗传力
H2
22R1 5.29 8.30 3.27 0.91 17.42 0.56 0.65 0.85 3.11 < 2e-16 0.83
22R2 5.36 9.73 2.35 1.01 18.81 0.83 1.91 1.02 3.24 < 2e-16
24R1 5.23 9.64 2.52 0.99 19.02 0.53 1.69 0.99 5.83 < 2e-16
24R2 5.30 8.30 3.17 0.90 16.96 0.60 0.72 0.81 5.69 < 2e-16
BLUP 5.29 8.30 3.18 0.90 17.02 0.60 0.71 0.81 5.69 < 2e-16

图1

供试群体籽粒铜含量表型分布 22R1和22R2: 参试群体2021-2022生长季的重复1和重复2; 24R1和24R2: 参试群体2023-2024生长季的重复1和重复2; BLUP: 最佳线性无偏预测值; GCuC: 籽粒铜含量。"

图2

供试群体籽粒铜含量的全基因组关联分析 22R1和22R2: 参试群体2021-2022生长季的重复1和重复2; 24R1和24R2: 参试群体2023-2024生长季的重复1和重复2; BLUP: 最佳线性无偏预测值。"

图3

显著性SNP的染色体分布"

表2

3次及以上重复下均可被检测到的显著性SNP"

SNP名称
SNP name		 染色体
Chromosome		 物理位置
Position (bp)		 P值
P value		 SNP名称
SNP name		 染色体
Chromosome		 物理位置
Position (bp)		 P值
P value
AX-94530450 1A 1172700 4.46E-04 AX-109324297 4A 39552040 5.64E-04
AX-109815310 1A 575418400 1.66E-04 AX-111756571 4A 39552479 7.66E-04
AX-94867479 1A 596660896 5.38E-04 AX-110516271 4A 39599332 7.66E-04
AX-110628468 1B 20966905 3.72E-04 AX-110930637 4A 39668476 8.27E-04
AX-109487530 1B 22088843 4.08E-04 AX-109826845 4A 39711461 8.52E-04
AX-108801693 1B 661932705 4.60E-04 AX-111089903 4A 39773639 6.08E-04
AX-89398876 1B 688113518 5.02E-04 AX-109328742 4A 39789366 7.66E-04
AX-110362942 1B 690612026 3.04E-04 AX-111543194 4A 39852555 8.52E-04
AX-109945625 1B 690641229 7.36E-04 AX-111662290 4A 39926548 8.52E-04
AX-110942991 1B 690794812 9.44E-04 AX-111065981 4A 40043703 7.66E-04
AX-110428571 1B 690811782 5.60E-04 AX-109415937 4A 40045486 7.85E-04
AX-110969986 1B 691375326 8.65E-04 AX-111803627 4A 40050601 7.69E-04
AX-109460254 1B 691379744 6.03E-04 AX-111676988 4A 40141173 7.66E-04
AX-110580333 1B 691509817 7.30E-04 AX-109397344 4A 40148212 9.06E-04
AX-110990325 1B 691510616 3.23E-04 AX-109900077 4A 40160130 8.52E-04
AX-111825384 1B 691511006 3.07E-04 AX-111090142 4A 40166034 7.66E-04
AX-111083811 1B 691558516 4.24E-04 AX-109036722 4A 40166473 7.85E-04
AX-111469178 1B 691657810 4.60E-04 AX-109078962 4A 40166812 9.16E-04
AX-111480990 1B 691658252 5.53E-04 AX-110529317 4A 575487148 1.21E-04
AX-110736943 1B 691663501 2.30E-04 AX-110403576 4B 636261336 1.44E-04
AX-111213346 1B 691727313 2.94E-04 AX-109306021 4D 3420471 5.51E-04
AX-111014627 1B 691750748 2.01E-04 AX-109929578 4D 3422357 2.32E-04
AX-110058996 1B 691751963 2.62E-04 AX-86178487 4D 3423247 6.37E-04
AX-110737103 1B 691754211 2.11E-04 AX-110487570 4D 3423300 4.70E-04
AX-109366507 1B 691764513 5.72E-04 AX-110519606 4D 3423484 2.82E-04
AX-108978821 1B 691828131 3.59E-04 AX-110580022 4D 3425334 3.94E-04
AX-110186568 1B 691865887 5.54E-04 AX-109422741 4D 3425521 4.57E-04
AX-110508317 1B 691890614 8.70E-04 AX-109011458 4D 3425613 4.56E-04
AX-110612250 1B 692134751 6.27E-04 AX-109288826 5A 472835597 8.07E-04
AX-110015226 1B 692135681 5.66E-04 AX-111494447 5A 605561508 8.98E-04
AX-110036472 1B 692203795 4.82E-04 AX-95009846 5A 628107525 2.60E-04
AX-109276851 1B 692290725 5.31E-04 AX-109999595 5B 313052848 9.06E-04
AX-109272807 1B 692291177 5.38E-04 AX-111280385 5B 403526765 4.69E-04
AX-111045500 1B 692293990 7.04E-04 AX-111747852 6A 4469179 2.58E-04
AX-109383458 1B 692304919 4.87E-04 AX-111479539 6A 11393962 9.87E-04
AX-111503414 1B 692364177 5.42E-04 AX-109527641 6D 479487752 7.11E-04
AX-108824506 1B 692406053 3.05E-04 AX-109580146 7A 146892032 2.59E-04
AX-89763438 1B 692406499 7.38E-04 AX-111579292 7A 148811277 1.00E-04
AX-111944457 1D 30205757 7.83E-04 AX-108767249 7A 153069407 2.49E-04
AX-111445091 1D 30310087 6.03E-04 AX-111452183 7A 154754618 6.77E-04
AX-111087795 1D 31251979 8.65E-04 AX-110487497 7A 167698634 5.91E-04
AX-94552269 1D 487770871 8.34E-04 AX-110168752 7A 173782280 1.45E-04
AX-110079220 1D 488163611 5.81E-04 AX-111638724 7A 175962991 1.24E-04
AX-94776977 1D 490213596 6.53E-04 AX-110447016 7A 585004815 8.08E-04
AX-110717464 1D 491481451 9.87E-04 AX-111786094 7A 585038693 5.68E-04
AX-108850784 1D 494164059 3.33E-04 AX-110596125 7A 585039306 9.80E-04
AX-109381336 2A 717986825 4.08E-04 AX-111560413 7A 585042652 4.27E-04
AX-89453541 2B 28521755 9.84E-04 AX-109593525 7A 585090173 8.66E-04
AX-109070149 2B 33321629 9.12E-04 AX-111628955 7A 585247575 4.31E-04
AX-94647778 3B 132303578 9.87E-04 AX-109981888 7A 585249385 3.46E-04
AX-109852738 3D 550964736 2.39E-04 AX-94909500 7B 739858437 8.23E-04
AX-109549813 4A 39501339 9.68E-04 AX-109346029 7B 740409395 7.66E-04
AX-110651557 4A 39503118 7.66E-04 AX-110460303 7B 740443058 8.54E-04
AX-111609188 4A 39504605 7.85E-04 AX-110606855 7B 744827003 7.06E-04
AX-109589613 4A 39505200 7.66E-04 AX-94861112 7D 142849690 8.32E-04
AX-111781572 4A 39541915 7.66E-04

表3

部分重要SNP籽粒铜含量的Student’s t检验"

SNP名称
SNP name		 染色体
Chromosome		 物理位置
Position (bp)		 等位基因型
Alleles		 品种数量
Variety number		 籽粒铜含量
GCuC (mg kg-1)		 t检验下的P值 P value for t-test
22R1 22R2 24R1 24R2 BLUP
AX-94530450 1A 1172700 GG AA 261 76 5.27 5.40 0.235 0.017 0.379 0.125 0.129
AX-109815310 1A 575418400 AA GG 330 9 5.32 4.59 0.022 0.043 0.055 0.028 0.028
AX-94867479 1A 596660896 GG AA 168 141 5.012 5.575 0.000 0.000 0.000 0.000 0.000
AX-110628468 1B 20966905 TT CC 277 37 5.32 4.95 0.004 0.044 0.014 0.010 0.010
AX-108801693 1B 661932705 CC TT 336 6 5.26 6.61 0.000 0.010 0.000 0.000 0.000
AX-110942991 1B 690794812 CC TT 281 44 5.22 5.78 0.000 0.002 0.000 0.000 0.000
AX-110969986 1B 691375326 CC AA 284 42 5.22 5.81 0.000 0.001 0.000 0.000 0.000
AX-109460254 1B 691379744 CC TT 281 42 5.22 5.81 0.000 0.001 0.000 0.000 0.000
AX-110580333 1B 691509817 CC TT 282 44 5.22 5.79 0.000 0.001 0.000 0.000 0.000
AX-110990325 1B 691510616 TT GG 290 41 5.22 5.81 0.000 0.001 0.000 0.000 0.000
AX-111825384 1B 691511006 GG AA 279 43 5.21 5.78 0.000 0.001 0.000 0.000 0.000
AX-111083811 1B 691558516 GG AA 296 41 5.22 5.83 0.000 0.001 0.000 0.000 0.000
AX-111469178 1B 691657810 CC TT 283 30 5.22 5.87 0.000 0.005 0.000 0.000 0.000
AX-111480990 1B 691658252 AA GG 288 28 5.22 5.83 0.000 0.005 0.000 0.000 0.000
AX-110736943 1B 691663501 CC TT 297 29 5.22 5.88 0.000 0.004 0.000 0.000 0.000
AX-111213346 1B 691727313 TT GG 276 29 5.21 5.88 0.000 0.005 0.000 0.000 0.000
AX-111014627 1B 691750748 CC TT 303 26 5.22 5.94 0.000 0.003 0.000 0.000 0.000
AX-110058996 1B 691751963 TT CC 192 53 5.19 5.71 0.000 0.002 0.000 0.000 0.000
AX-110737103 1B 691754211 TT GG 299 29 5.22 5.89 0.000 0.006 0.000 0.000 0.000
AX-109366507 1B 691764513 CC GG 291 28 5.22 5.88 0.000 0.004 0.000 0.000 0.000
AX-108978821 1B 691828131 GG AA 289 28 5.22 5.88 0.000 0.004 0.000 0.000 0.000
AX-110186568 1B 691865887 GG AA 290 51 5.21 5.70 0.000 0.003 0.000 0.000 0.000
AX-110508317 1B 691890614 AA GG 280 42 5.22 5.80 0.000 0.001 0.000 0.000 0.000
AX-110036472 1B 692203795 CC GG 297 43 5.22 5.80 0.000 0.001 0.000 0.000 0.000
AX-109276851 1B 692290725 CC TT 302 39 5.22 5.77 0.000 0.002 0.000 0.000 0.000
AX-109272807 1B 692291177 GG TT 304 39 5.22 5.77 0.000 0.002 0.000 0.000 0.000
AX-111045500 1B 692293990 CC TT 302 39 5.22 5.77 0.000 0.002 0.000 0.000 0.000
AX-108824506 1B 692406053 TT GG 298 44 5.22 5.79 0.000 0.001 0.000 0.000 0.000
AX-111445091 1D 30310087 CC TT 333 12 5.32 4.66 0.008 0.013 0.012 0.006 0.006
AX-94776977 1D 490213596 GG AA 228 105 5.48 4.87 0.000 0.000 0.000 0.000 0.000
AX-108850784 1D 494164059 CC GG 196 133 5.16 5.52 0.000 0.003 0.000 0.000 0.000
AX-109549813 4A 39501339 TT CC 340 6 5.31 4.14 0.003 0.002 0.001 0.001 0.001
AX-110529317 4A 575487148 AA GG 321 27 5.22 6.14 0.000 0.000 0.000 0.000 0.000
AX-111609188 4A 39504605 TT CC 341 7 5.32 4.31 0.006 0.002 0.003 0.001 0.002
AX-109415937 4A 40045486 GG AA 341 7 5.32 4.31 0.006 0.002 0.003 0.001 0.002
AX-109036722 4A 40166473 AA CC 341 7 5.32 4.31 0.006 0.002 0.003 0.001 0.002
AX-109078962 4A 40166812 GG AA 340 6 5.31 4.15 0.004 0.001 0.002 0.001 0.001
AX-109929578 4D 3422357 GG AA 330 12 5.25 6.32 0.000 0.008 0.000 0.000 0.000
AX-86178487 4D 3423247 TT CC 333 12 5.25 6.32 0.000 0.010 0.000 0.000 0.000
AX-110487570 4D 3423300 AA GG 328 13 5.25 6.21 0.000 0.011 0.000 0.000 0.000
AX-110519606 4D 3423484 TT GG 332 6 5.25 6.47 0.001 0.012 0.000 0.000 0.000
AX-110580022 4D 3425334 TT CC 331 13 5.25 6.21 0.000 0.011 0.000 0.000 0.000
AX-109422741 4D 3425521 CC TT 331 12 5.25 6.32 0.000 0.009 0.000 0.000 0.000
AX-109011458 4D 3425613 TT CC 330 13 5.25 6.21 0.000 0.011 0.000 0.000 0.000
AX-111494447 5A 605561508 GG AA 184 147 5.52 5.02 0.000 0.000 0.000 0.000 0.000
AX-95009846 5A 628107525 AA GG 243 105 5.14 5.67 0.000 0.000 0.000 0.000 0.000
AX-111280385 5B 403526765 CC GG 309 27 5.25 5.75 0.002 0.003 0.013 0.002 0.003
AX-109527641 6D 479487752 CC TT 318 25 5.23 5.95 0.000 0.003 0.000 0.000 0.000
AX-110447016 7A 585004815 TT CC 314 28 5.24 5.82 0.002 0.005 0.000 0.000 0.001
AX-110596125 7A 585039306 GG AA 301 38 5.24 5.79 0.001 0.002 0.000 0.000 0.000
AX-109593525 7A 585090173 CC TT 300 40 5.23 5.72 0.001 0.005 0.000 0.001 0.001
AX-111628955 7A 585247575 AA GG 304 39 5.23 5.77 0.001 0.002 0.000 0.000 0.000
AX-109981888 7A 585249385 GG AA 300 37 5.23 5.81 0.000 0.001 0.000 0.000 0.000
AX-94909500 7B 739858437 TT CC 263 81 5.30 5.30 0.430 0.122 0.179 0.498 0.494
AX-110460303 7B 740443058 GG CC 301 41 5.21 5.92 0.000 0.000 0.000 0.000 0.000
AX-110606855 7B 744827003 AA GG 261 48 5.17 5.87 0.000 0.000 0.000 0.000 0.000

图4

1B和4A染色体显著性SNP的单倍型分析 A1、B1: 1B和4A染色体显著性SNP的LD热图; A2、B2: 1B和4A位点不同单倍型间的籽粒铜含量; A3、B3: 1B和4A连锁区段不同单倍型间的籽粒铜含量比较; C1、C2: 1B和4A 2个位点的聚合效应分析。22R1和22R2: 参试群体2021-2022生长季的重复1和重复2; 24R1和24R2: 参试群体2023-2024生长季的重复1和重复2; BLUP: 最佳线性无偏预测值; GCuC: 籽粒铜含量。**表示Student’s t检验在P < 0.01水平差异显著。"

表4

定位区段内基因注释信息"

基因名称
Gene name		 染色体
Chromosome		 注释信息
Annotation information
TraesCS1B03G1265300 1B 延长因子1-α Elongation factor 1-alpha
TraesCS1B03G1265400 1B 同源框亮氨酸拉链蛋白 Homeobox leucine zipper protein
TraesCS4A03G0093900 4A 巯基氧化酶 Sulfhydryl oxidase
TraesCS4A03G0094100 4A 羧基末端肽酶(DUF239) Carboxyl-terminal peptidase (DUF239)

图5

定位区段注释基因组织表达模式分析 SS_SG: 幼苗期地上部; SS_RT: 幼苗期根部; JS_LF: 拔节期叶片; JS_BPST: 拔节期茎基部; JS_RT: 拔节期根; BS_LF: 孕穗期叶片; BS_SP: 孕穗期幼穗; BS_RT: 孕穗期根; HS_FLLF: 抽穗期旗叶; HS_SH: 抽穗期叶鞘; HS_SL: 抽穗期茎; HS_SP: 抽穗期穗子; HS_RT: 抽穗期根; FS_RT: 灌浆期根; FS_14 d_SD: 开花后14 d籽粒; FS_28 d_SD: 开花后28 d籽粒; FS_35 d_SD: 开花后35 d籽粒。"

图6

定位区段注释基因单倍型分析 A1、A2: TraesCS1B03G1265300基因单倍型分析; B1、B2: TraesCS1B03G1265400基因单倍型分析; C1、C2: TraesCS4A03G0093900基因单倍型分析; D1、D2: TraesCS4A03G0094100基因单倍型分析。22R1和22R2: 参试群体2021-2022生长季的重复1和重复2; 24R1和24R2: 参试群体2023-2024生长季的重复1和重复2; BLUP: 最佳线性无偏预测值; GCuC: 籽粒铜含量。*和**分别表示Student’s t检验在P < 0.05和P < 0.01水平差异显著; ns: 差异不显著。"

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