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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (3): 647-661.doi: 10.3724/SP.J.1006.2023.23023

所属专题： 玉米：遗传育种·种质资源·分子遗传学

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米株高和穗位高性状全基因组关联分析

马雅杰1(), 鲍建喜1(), 高悦欣1, 李雅楠1, 秦文萱1, 王彦博1, 龙艳1, 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:2022-03-03 接受日期:2022-05-05 出版日期:2023-03-12 网络出版日期:2022-05-19
  • 通讯作者: 董振营,万向元
  • 作者简介:马雅杰, E-mail: 13292097686@163.com
    鲍建喜, E-mail: bjx1232003@126.com第一联系人：**同等贡献
  • 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 analysis of plant height and ear height related traits in maize

MA Ya-Jie1(), BAO Jian-Xi1(), GAO Yue-Xin1, LI Ya-Nan1, QIN Wen-Xuan1, WANG Yan-Bo1, LONG Yan1, 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:2022-03-03 Accepted:2022-05-05 Published:2023-03-12 Published online:2022-05-19
  • Contact: DONG Zhen-Ying,WAN Xiang-Yuan
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Key Research and Development Program of China(2021YFD1200700)

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摘要：

适宜的株高和穗位高可提高植株的养分利用效率及抗倒伏性, 对玉米增产和稳产具有重要意义。为揭示玉米株高和穗位高遗传机制, 本研究以854份玉米自交系为关联群体, 利用均匀分布于玉米10条染色体的2795个SNP标记对4个环境下玉米株高、穗位高以及穗位系数进行全基因组关联分析(genome-wide association study, GWAS)。共定位到81个显著关联SNP位点(P<0.0001), 其中与株高显著关联的SNP为35个, 单个位点表型解释率为0.02%~6.23%; 与穗位高显著关联SNP为31个, 单个位点表型变异解释率为0.03%~3.06%; 与穗位系数显著关联的SNP位点为24个, 单个位点表型变异解释率为0.03%~6.64%。进一步鉴定出15个可在2个及以上环境共定位的稳定SNP, 其中6个为本研究首次发现, 9个位于前人定位QTL区间或/和关联SNP位点2 Mb范围内。在15个稳定SNP位点上下游各200 kb的置信区间共发现83个功能注释基因, 结合文献分析筛选出了每个位点最有可能的候选基因, 这些候选基因主要参与激素合成与信号转导、糖类代谢、细胞分裂调控等途径。鉴定出6个主效SNP位点, 并发现1个可同时调控株高、穗位高和穗位系数的一因多效位点。本研究可为分子标记辅助选择育种提供有效遗传位点, 为精细定位和克隆株高与穗位高相关性状基因提供参考。

关键词: 玉米, 株高, 穗位高, 全基因组关联分析, 候选基因

Abstract:

Suitable plant height (PH) and ear height (EH) can improve the efficiency of nutrient utilization and lodging resistance, which is of great significance for stable and high yield in maize. In this study, an association panel including 854 maize inbred lines used to analyze the PH, EH, and the ratio of EH to PH (EH/PH) in four environments, and genome-wide association study (GWAS) was then conducted using 2795 single nucleotide polymorphism (SNP) markers distributed uniformly throughout maize genome. A total of 81 SNP loci (P < 0.0001) were identified by using FarmCPU model, among which 35 SNPs were significantly associated with PH, with phenotypic variation explained (PVE) ranging from 0.020% to 6.225%; 31 SNPs were significantly associated with ear height, and PVE was from 0.026% to 3.060%; 24 SNPs were significantly associated with EH/PH, and the PVE ranged from 0.032% to 6.636%. 15 stable SNPs that were repeatedly detected in multiple environments for specific trait were further identified, among which six loci were reported for the first time in this study, and the remaining nine loci located in the previously identified quantitative trait loci (QTLs) or/and no more than 2 Mb with the known SNPs related with PH and EH traits. A total of 83 genes were annotated in the confidence intervals of the 15 stable SNPs, and the most likely candidate genes were further predicted according to the gene functional annotations and comparison with previous reports. The candidate genes were mainly involved in hormone synthesis and signal transduction, carbohydrate metabolism, cell division regulation and so on. Finally, six major SNP loci and one locus that affected PH, EH, and EH/PH simultaneously were identified. This study can provide genetic loci for molecular marker-assisted selection in maize breeding and provide valuable information for fine mapping and cloning of PH and EH related genes.

Key words: maize, plant height, ear height, genome-wide association analysis, candidate gene

表1

株高、穗位高和穗位系数表型数据统计分析"

性状
Trait		 环境
Environment		 均值±标准差a
Mean ± SD a		 变异系数
CV (%)		 变异范围a
Range a		 偏度
Skewness		 峰度
Kurtosis		 遗传力
H2
株高
PH		 20PG 209.58±27.36 13.05 118.20-284.00 -0.084 0.053 0.81
20ZC 193.97±25.70 13.25 79.00-282.80 -0.175 0.557
21PG 209.99±28.14 13.40 83.60-291.00 -0.150 0.503
21ZC 179.73±23.49 13.07 81.00-247.00 -0.186 0.660
穗位高
EH		 20PG 79.23±16.70 21.08 35.60-137.20 0.248 0.148 0.78
20ZC 75.21±14.97 19.90 27.60-124.20 0.071 0.036
21PG 79.53±17.57 22.09 30.20-139.40 0.186 0.016
21ZC 58.91±13.10 22.24 19.50-100.40 0.210 0.134
穗位系数EH/PH 20PG 0.38±0.06 15.79 0.19-0.55 0.017 -0.057 0.74
20ZC 0.39±0.05 12.82 0.22-0.59 -0.081 -0.043
21PG 0.38±0.06 15.79 0.19-0.55 -0.108 0.052
21ZC 0.33±0.05 15.15 0.18-0.49 0.054 -0.009

图1

不同环境玉米株高、穗位高和穗位系数频率分布图 处理缩写同表1。"

表2

不同环境间PH、EH和EH/PH性状相关性分析"

性状
Trait		 PH-
20PG		 PH-
20ZC		 PH-
21PG		 PH-
21ZC		 EH-
20PG		 EH-
20ZC		 EH-
21PG		 EH-
21ZC		 EH/PH-
20PG		 EH/PH-
20ZC		 EH/PH-
21PG
PH-20ZC 0.716**
PH-21PG 0.847** 0.753**
PH-21ZC 0.766** 0.747** 0.770**
EH-20PG 0.652** 0.424** 0.579** 0.472**
EH-20ZC 0.472** 0.685** 0.551** 0.495** 0.699**
EH-21PG 0.541** 0.473** 0.706** 0.475** 0.799** 0.746**
EH-21ZC 0.447** 0.476** 0.523** 0.647** 0.699** 0.729** 0.705**
EH/PH-20PG 0.031 -0.027 0.064 -0.007 0.770** 0.522** 0.592** 0.548**
EH/PH-20ZC -0.003 0.027 0.066 -0.007 0.570** 0.741** 0.583** 0.562** 0.744**
EH/PH-21PG 0.069* 0.048 0.165 0.039 0.648** 0.587** 0.809** 0.562** 0.788** 0.760**
EH/PH-21ZC 0.001 0.055 0.092 0.085* 0.553** 0.572** 0.553** 0.808** 0.731** 0.742** 0.711**

附图1

关联分析群体系统进化树"

附表1

不同环境下株高、穗位高、穗位系数显著关联SNP位点汇总"

性状
Trait		 环境
Environment		 SNP位点
SNP marker		 染色体
Chr.		 位置
Locus (bp)		 P值
P-value		 表型变异率
PVE (%)
株高
PH		 21PG PZE-101024808 1 15,068,364 2.47E-08 4.13
21ZC PZE-101029689 1 18,044,029 1.81E-05 4.96
20PG/BLUP PZE-101058322 1 42,289,643 2.46E-05 1.90
20PG PZE-101105515 1 110,116,696 4.70E-07 6.23
21PG PZE-101108837 1 117,679,240 3.43E-08 0.47
21ZC/BLUP PZE-101109358 1 118,829,520 2.72E-05 3.71
20PG PZE-101113278 1 128,845,856 4.58E-05 1.00
20PG/21ZC/BLUP PZE-101256370 1 305,347,287 2.66E-05 5.19
20ZC/21PG PZE-102097841 2 117,120,291 4.31E-05 1.52
20ZC PZE-102116677 2 159,754,465 9.78E-05 0.79
21ZC SYN31434 3 66,376,933 2.48E-05 2.53
21ZC SYN28063 3 212,353,001 1.31E-05 0.22
20ZC PZE-104022504 4 26,481,392 7.36E-05 0.02
21PG PZE-104026267 4 32,890,533 2.10E-05 3.77
21ZC/BLUP PZE-104088728 4 166,718,467 5.98E-06 2.26
20ZC/BLUP PZE-104102768 4 181,859,161 5.59E-06 3.22
21PG PZE-104118502 4 199,488,030 1.59E-05 3.39
20ZC PZE-104122415 4 203,858,809 8.62E-05 0.07
BLUP PZE-104123974 4 205,691,345 7.57E-06 3.30
20ZC PZE-104130351 4 214,564,236 4.33E-05 0.41
21ZC PZA01570.1 5 3,612,315 3.52E-06 0.23
21PG SYN31840 5 23,268,618 8.86E-05 1.22
20PG/BLUP PZE-105047805 5 38,631,014 2.52E-05 2.65
20ZC/21PG/21ZC/BLUP PZE-105102182 5 157,723,585 7.14E-06 1.64
21PG PZE-105128589 5 190,328,323 8.50E-05 3.79
20ZC PZE-105158980 5 212,371,623 8.74E-07 2.36
20ZC SYN26885 6 58,235,167 3.58E-06 2.46
21PG SYN11451 6 171,556,727 2.15E-05 0.04
21ZC PZE-107086184 7 146,560,786 1.34E-07 5.02
21ZC PZE-108079027 8 139,020,108 1.91E-05 0.32
20PG PZE-108079422 8 139,545,943 1.82E-05 0.48
20ZC PZE-109024796 9 24,932,017 5.16E-05 0.67
20ZC PZE-109061773 9 38,609 7.40E-05 0.22
BLUP SYN20545 10 88,765,819 9.09E-05 1.95
21ZC PZE-110084754 10 137,929,862 9.32E-05 0.09
性状
Trait		 环境
Environment		 SNP位点
SNP marker		 染色体
Chr.		 位置
Locus (bp)		 P值
P-value		 表型变异率
PVE (%)
穗位高
EH		 20PG/BLUP PZE-101024808 1 15,068,364 1.37E-05 2.47
21ZC PZE-101029689 1 18,044,029 1.99E-07 1.65
20PG PZE-101098535 1 92,004,604 7.45E-05 0.87
20PG/20ZC/BLUP PZE-101105515 1 110,116,696 1.34E-05 2.32
21PG PZE-101108837 1 117,679,240 2.52E-06 2.35
BLUP PZE-101161396 1 206,925,042 2.30E-05 0.03
BLUP PZE-101173330 1 220,307,491 5.12E-05 1.88
21ZC PZE-101182552 1 230,566,972 2.85E-06 2.95
BLUP ZM013367-0314 1 243,024,263 3.73E-05 0.29
21ZC PZE-102076989 2 61,180,066 1.49E-05 2.74
20ZC PZE-102100073 2 122,534,230 6.54E-08 0.37
BLUP PZE-103067949 3 111,511,559 1.44E-05 3.06
BLUP PZE-103083718 3 139,354,703 2.27E-06 0.54
20PG SYN15468 3 149,897,051 6.46E-08 1.69
20ZC SYN20322 3 162,506,292 1.39E-06 1.11
21PG PZE-104112784 4 192,219,121 5.58E-05 1.71
21PG SYN27455 4 234,425,224 9.78E-06 0.97
21PG PZE-105043361 5 31,731,809 1.90E-05 0.06
20ZC PZE-105047974 5 39,072,734 8.05E-08 1.07
20ZC/21PG/21ZC PZE-105098019 5 147,968,605 1.20E-05 3.00
BLUP SYN7363 5 180,154,411 5.63E-05 0.73
20PG SYN32728 5 200,050,570 8.42E-06 1.94
21PG PZE-105149244 5 206,545,681 3.46E-05 1.88
21ZC PZE-106043310 6 95,865,051 7.48E-06 0.23
21PG PZE-106078719 6 138,545,114 6.09E-05 0.11
20PG PZE-107028964 7 36,379,816 1.20E-05 0.27
20ZC PZE-107106841 7 164,177,644 1.22E-05 0.40
20PG PZE-108059088 8 107,623,992 8.95E-05 0.04
20PG/21PG PZE-108069615 8 125,245,658 2.92E-05 2.86
20PG PZE-108079422 8 139,545,943 4.78E-05 0.98
BLUP PZE-109003046 9 3,291,982 1.44E-05 0.60
穗位系数
EH/PH		 20PG SYN5056 1 16,011,707 2.43E-05 3.89
BLUP PZE-101075097 1 59,163,811 4.46E-05 5.30
21ZC PZE-101130082 1 168,091,438 3.70E-05 3.30
21ZC SYN13128 1 182,826,264 1.45E-06 4.00
21ZC PZE-101182552 1 230,566,972 2.42E-07 4.23
21ZC/BLUP PZE-103075978 3 126,523,695 2.96E-05 5.58
21ZC/BLUP PZE-103083718 3 139,354,703 2.08E-05 0.74
BLUP SYN16519 3 149,050,783 5.42E-05 0.36
21PG SYN23245 3 187,679,537 4.38E-05 1.53
21PG PZE-104051877 4 85,020,190 5.63E-05 0.32
21ZC PZE-104079748 4 157,609,086 3.29E-05 1.05
BLUP PZE-104082879 4 160,500,101 7.30E-05 0.03
20ZC PZE-105102393 5 158,090,068 8.57E-07 4.87
21ZC SYN7363 5 180,154,411 6.25E-06 1.57
21ZC PZE-106016519 6 40,855,166 5.66E-05 0.32
20ZC PZE-106038001 6 89,033,009 2.28E-07 1.55
21ZC SYN2958 6 95,987,816 5.31E-05 4.91
21ZC/BLUP PZE-108039693 8 64,911,909 2.72E-05 1.80
20PG/BLUP PZE-108069615 8 125,245,658 3.04E-07 6.64
20ZC PZE-108074750 8 134,120,027 2.59E-05 0.54
21PG PZE-108102648 8 162,806,745 2.25E-05 2.93
BLUP PZE-108102684 8 162,917,082 5.83E-07 4.09
BLUP PZE-109051855 9 92,960,428 7.50E-05 3.31
BLUP PZE-110002415 10 2,028,528 5.41E-05 1.91

图2

玉米株高、穗位高和穗位系数GWAS分析结果 A、B、C分别为株高、穗位高、穗位系数性状关联分析的曼哈顿图; D、E、F分别为株高、穗位高、穗位系数性状关联分析的QQ图。BLUP表示最佳线性无偏预测值。其他处理缩写同表1。"

表3

不同性状稳定SNP标记及候选基因"

性状
Trait		 SNP标记
SNP Marker		 P值
P-value		 表型变异率1
PVE 1 (%)		 环境
Environment		 染色体
Chr.		 位置
Locus (bp)		 候选基因
Candidate gene		 基因功能注释
Gene annotation
株高
Plant height (PH)
 PZE-101058322 2.46E-05 1.90 BLUP/20PG 1 42,289,643 Zm00001d028671 ABC transporter B family member 6
PZE-101109358 2.72E-05 3.71 BLUP/21ZC 1 118,829,520 Zm00001d030282 Alpha-mannosidase
PZE-101256370 2.66E-05 5.19 BLUP/20PG/21ZC 1 305,347,287 Zm00001d034914 Protein EXPORTIN 1A
PZE-102097841 4.31E-05 1.52 20ZC/21PG 2 117,120,291 Zm00001d004541 Zinc finger CCCH domain-containing protein 24
PZE-104088728 5.98E-06 2.26 BLUP/21ZC 4 166,718,467 Zm00001d051685 ADP, ATP carrier protein 2, mitochondrial
PZE-104102768 5.59E-06 3.22 BLUP/20ZC 4 181,859,161 Zm00001d052174 Cyclin-dependent kinase inhibitor 1
PZE-105047805 2.52E-05 2.65 BLUP/20PG 5 38,631,014 Zm00001d014271 Caltractin
PZE-105102182 7.14E-06 1.64 BLUP/20ZC/21PG/21ZC 5 157,723,585 Zm00001d016332 Protein-serine/threonine phosphatase
穗位高
Ear height (EH)
 PZE-101024808 1.37E-05 2.47 BLUP/20PG 1 15,068,364 Zm00001d027842 O-fucosyltransferase family protein
PZE-101105515 4.70E-07 2.32 BLUP/20PG/20ZC 1 110,116,696 Zm00001d030166 Glycosyltransferase-like KOBITO 1
PZE-105098019 1.20E-05 3.00 20ZC/21PG/21ZC 5 147,968,605 Zm00001d016162 RING/U-box superfamily protein
PZE-108069615 3.04E-07 2.36 20PG/21PG 8 125,245,658 Zm00001d010713 CPP-transcription factor 8
穗位系数
EH/PH
 PZE-103075978 2.96E-05 5.58 BLUP/21ZC 3 126,523,695 Zm00001d041549 Dof zinc finger protein DOF2.2
PZE-103083718 2.27E-06 0.74 BLUP/21ZC 3 139,354,703 Zm00001d041823 O-fucosyltransferase family protein
PZE-108039693 2.72E-05 1.80 BLUP/21ZC 8 64,911,909 Zm00001d009448 ABC transporter B family member 9
PZE-108069615 2.92E-05 6.64 BLUP/20PG 8 125,245,658 Zm00001d010713 CPP-transcription factor 8

图3

株高、穗位高和穗位系数相关重要SNP位点等位变异效应分析 A: 株高、穗位高、穗位系数主效SNP位点等位变异效应分析; B: PZE-105102182位点对不同性状的等位效应分析。*: 在P < 0.05水平上显著相关; **: 在P < 0.01水平上显著相关。处理缩写同表1。"

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