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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (3): 647-661.doi: 10.3724/SP.J.1006.2023.23023

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

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 Online:2023-03-12 Published:2022-05-19
  • Contact: DONG Zhen-Ying,WAN Xiang-Yuan E-mail:13292097686@163.com;bjx1232003@126.com;zydong@ustb.edu.cn;wanxiangyuan@ustb.edu.cn
  • 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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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

Table 1

Statistical analysis of plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) traits"

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

Fig. 1

Frequency distribution of plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) traits in different environments Abbreviations are the same as those given in Table 1."

Table 2

Correlation analysis of plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) traits in different environments"

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**

Fig. S1

Phylogenetic tree of the association analysis population"

Table S1

Summary of the SNPs significantly associated with plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) in different environments"

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

Fig. 2

GWAS analysis of plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) traits in maize A, B, and C were Manhattan plots for GWAS of PH, EH, and EH/PH, respectively. D, E, and F were QQ plots for GWAS of PH, EH, and EH/PH, respectively. BLUP represents best linear unbiased prediction. Other abbreviations are the same as those given in Table 1."

Table 3

Stable SNP loci and the candidate genes identified in this study"

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

Fig. 3

Allelic effects of the SNPs associated with plant height (PH), ear height (EH), and the ratio of EH/PH (EH/PH) traits A: the allelic effect of dominant SNP locus in plant height, ear height, and the ratio of EH to PH; B: the allelic effect of PZE-105102182 locus on different traits. *: significance correlation at P < 0.05; **: significant correlation at P < 0.01. Abbreviations are the same as those given in Table 1."

[1] Prasanna B M. Diversity in global maize germplasm: characterization and utilization. J Biosci, 2012, 37: 843-855.
doi: 10.1007/s12038-012-9227-1
[2] Tang J H, Teng W T, Yan J B, Ma X Q, Meng Y J, Dai J R, Li J S. Genetic dissection of plant height by molecular markers using a population of recombinant inbred lines in maize. Euphytica, 2007, 155: 117-124.
doi: 10.1007/s10681-006-9312-3
[3] 徐田军, 张勇, 赵久然, 王荣焕, 吕天放, 刘月娥, 蔡万涛, 刘宏伟, 陈传永, 王元东. 宜机收籽粒玉米品种冠层结构、光合及灌浆脱水特性. 作物学报, 2022, 48: 1526-1536.
doi: 10.3724/SP.J.1006.2022.13036
Xu T J, Zhang Y, Zhao J R, Wang R H, Lyu T F, Liu Y E, Cai W T, Liu H W, Chen C Y, Wang Y D. Canopy structure, photosynthesis, grain filling, and dehydration characteristics of maize varieties suitable for grain mechanical harvesting. Acta Agron Sin, 2022, 48: 1526-1536. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2022.13036
[4] 崔爱民, 张久刚, 张虎, 单皓, 陈伟. 我国玉米生产现状及发展变革. 中国农业科技导报, 2020, 22(7): 10-19.
doi: doi:10.13304/j.nykjdb.2019.0508
Cui A M, Zhang J G, Zhang H, Shan H, Chen W. Preliminary exploration on current situation and development of maize production in China. J Agric Sci Technol, 2020, 22(7): 10-19. (in Chinese with English abstract)
[5] 宋振伟, 齐华, 张振平, 钱春荣, 郭金瑞, 邓艾兴, 张卫建. 春玉米中单909农艺性状和产量对密植的响应及其在东北不同区域的差异. 作物学报, 2012, 38: 2267-2277.
doi: 10.3724/SP.J.1006.2012.02267
Song Z W, Qi H, Zhang Z P, Qian C R, Guo J R, Deng A X, Zhang W J. Effects of plant density on agronomic traits and yield in spring maize Zhongdan 909 and their regional differences in northeast China. Acta Agron Sin, 2012, 38: 2267-2277. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2012.02267
[6] Khush G S. Green revolution: the way forward. Nat Rev Genet, 2001, 2: 815-822.
doi: 10.1038/35093585 pmid: 11584298
[7] Donald C M. The breeding of crop ideotypes. Euphytica, 1968, 17: 385-403.
doi: 10.1007/BF00056241
[8] Salas Fernandez M G, Becraft P W, Yin Y H, Lübberstedt T. From dwarves to giants? Plant height manipulation for biomass yield. Trends Plant Sci, 2009, 14: 454-461.
doi: 10.1016/j.tplants.2009.06.005 pmid: 19616467
[9] 郑德波, 杨小红, 李建生, 严建兵, 张士龙, 贺正华, 黄益勤. 基于SNP标记的玉米株高及穗位高QTL定位. 作物学报, 2013, 39: 549-556.
doi: 10.3724/SP.J.1006.2013.00549
Zheng D B, Yang X H, Li J S, Yan J B, Zhang S L, He Z H, Huang Y Q. QTL identification for plant height and ear height based on SNP mapping in maize (Zea mays L.). Acta Agron Sin, 2013, 39: 549-556. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2013.00549
[10] 薛军, 王克如, 谢瑞芝, 勾玲, 张旺锋, 明博, 侯鹏, 李少昆. 玉米生长后期倒伏研究进展. 中国农业科学, 2018, 51: 1845-1854.
Xue J, Wang K R, Xie R Z, Gou L, Zhang W F, Ming B, Hou P, Li S K. Research progress of maize lodging during late stage. Sci Agric Sin, 2018, 51: 1845-1854 (in Chinese with English abstract).
[11] 刘忠祥, 杨梅, 殷鹏程, 周玉乾, 何海军, 邱法展. 玉米株高主效QTL qPH3.2精细定位及遗传效应分析. 作物学报, 2018, 44: 1357-1366.
Liu Z X, Yang M, Yin P C, Zhou Y Q, He H J, Qiu F Z. Fine mapping and genetic effect analysis of a major QTL qPH3.2 associated with plant height in maize (Zea mays L.). Acta Agron Sin, 2018, 44: 1357-1366. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2018.01357
[12] 刘磊, 詹为民, 丁武思, 刘通, 崔连花, 姜良良, 张艳培, 杨建平. 玉米矮化突变体gad39的遗传分析与分子鉴定. 作物学报, 2022, 48: 886-895.
doi: 10.3724/SP.J.1006.2022.13026
Liu L, Zhan W M, Ding W S, Liu T, Cui L H, Jiang L L, Zhang Y P, Yang J P. Genetic analysis and molecular characterization of dwarf mutant gad39 in maize. Acta Agron Sin, 2022, 48: 886-895. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2022.13026
[13] 于芮苏, 田小康, 刘斌斌, 段迎新, 李婷, 张秀英, 张兴华, 郝引川, 李勤, 薛吉全, 徐淑兔. 玉米抗倒伏相关性状QTL的关联和连锁分析. 作物学报, 2022, 48: 138-150.
Yu R S, Tian X K, Liu B B, Duan Y X, Li T, Zhang X Y, Zhang X H, Hao Y C, Li Q, Xue J Q, Xu S T. Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize. Acta Agron Sin, 2022, 48: 138-150. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2022.03072
[14] Beavis W D, Grant D, Albertsen M, Fincher R. Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci. Theor Appl Genet, 1991, 83: 141-145.
doi: 10.1007/BF00226242 pmid: 24202349
[15] Yan J B, Tang H, Huang Y Q, Shi Y G, Li J S, Zheng Y L. Dynamic analysis of QTL for plant height at different developmental stages in maize (Zea mays L.). Chin Sci Bull, 2003, 48: 2601-2607.
doi: 10.1360/03wc0044
[16] Weng J F, Xie C X, Hao Z F, Wang J J, Liu C L, Li M S, Zhang D G, Bai L, Zhang S H, Li X H. Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS One, 2011, 6: e29229.
doi: 10.1371/journal.pone.0029229
[17] Bai W, Zhang H, Zhang Z, Teng F, Wang L, Tao Y, Zheng Y. The evidence for non-additive effect as the main genetic component of plant height and ear height in maize using introgression line populations. Plant Breed, 2009, 129: 376-384.
[18] Vanous A, Gardner C, Blanco M, Blanco M, Schwarze A M, Lipka A E, Garcia S F, Bohn M, Edward J, Lübberstedt T. Association mapping of flowering and height traits in germplasm enhancement of maize doubled haploid (GEM-DH) lines. Plant Genome, 2018, 11: 170083.
doi: 10.3835/plantgenome2017.09.0083
[19] Wang B B, Liu H, Liu Z P, Dong X M, Guo J J, Li W, Chen J, Gao C, Zhu Y B, Zheng X M, Chen Z L, Chen J, Song W B, Hauck A, Lai J S. Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays). BMC Plant Biol, 2018, 18: 17.
doi: 10.1186/s12870-018-1233-5 pmid: 29347909
[20] 刘坤, 张雪海, 孙高阳, 闫鹏帅, 郭海平, 陈思远, 薛亚东, 郭战勇, 谢惠玲, 汤继华, 李卫华. 玉米株型相关性状的全基因组关联分析. 中国农业科学, 2018, 51: 821-834.
Liu K, Zhang X H, Sun G Y, Yan P S, Guo H P, Chen S Y, Xue Y D, Guo Z Y, Xie H L, Tang J H, Li W H. Genome-wide association studies of plant type traits in maize. Sci Agric Sin, 2018, 51: 821-834. (in Chinese with English abstract)
[21] Knapp S J, Stroup W W, Ross W M. Exact confidence intervals for heritability on a progeny mean basis. Crop Sci, 1985, 25: 192-194.
doi: 10.2135/cropsci1985.0011183X002500010046x
[22] Chen D H, Ronald P C. A rapid DNA minipreparation method suitable for AFLP and other PCR application. Plant Mol Biol Rep, 1999, 17: 53-57.
doi: 10.1023/A:1007585532036
[23] Tian H L, Wang F G, Zhao J R, Yi H M, Wang L, Wang R. Yang Y, Song W. Development of maize SNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. Mol Breed, 2015, 35: 136.
doi: 10.1007/s11032-015-0335-0
[24] Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000, 155: 945-959.
doi: 10.1093/genetics/155.2.945 pmid: 10835412
[25] Liu X L, Huang M, Fan B, Buckler E S, Zhang Z W. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet, 2016, 12: e1005767.
[26] Wang M, Yan J B, Zhao J R, Song W, Zhang X B, Xiao Y N, Zheng Y L. Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Sci, 2012, 196: 125-131.
doi: 10.1016/j.plantsci.2012.08.004 pmid: 23017907
[27] 贺建波, 刘方东, 邢光南, 王吴彬, 赵团结, 管荣展, 盖钧镒. 限制性两阶段多位点全基因组关联分析方法的特点与计算程序. 作物学报, 2018, 44: 1274-1289.
He J B, Liu F D, Xing G N, Wang W B, Zhao T J, Guan R Z, Gai J Y. Characterization and analytical programs of the restricted two-stage multi-locus genome-wide association analysis. Acta Agron Sin, 2018, 44: 1274-1289 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2018.01274
[28] Li X P, Zhou Z J, Ding J Q, Wu Y B, Zhou B, Wang R X, Ma J L, Wang S W, Zhang X C, Xia Z L, Chen J F, Wu J Y. Combined linkage and association mapping reveals QTL and candidate genes for plant and ear height in maize. Front Plant Sci, 2016, 7: 833.
doi: 10.3389/fpls.2016.00833 pmid: 27379126
[29] 李博, 张焕欣, 杨小艳, 吕颖颖, 江培顺, 郝转芳, 吕香玲, 王宏伟, 翁建峰. 玉米穗位高全基因组关联分析及其候选基因预测. 作物杂志, 2013, (2): 27-32.
Li B, Zhang H X, Yang X Y, Lyu Y Y, Jiang P S, Hao Z F, Lyu X L, Wang H W, Weng J F. Genome-wide association study and candidate gene prediction of ear height in maize (Zea mays L.). Crops, 2013, (2): 27-32. (in Chinese with English abstract)
[30] 张焕欣, 翁建峰, 张晓聪, 刘昌林, 雍洪军, 郝转芳, 李新海. 玉米穗行数全基因组关联分析. 作物学报, 2014, 40: 1-6.
doi: 10.3724/SP.J.1006.2014.00001
Zhang H X, Weng J F, Zhang X C, Liu C L, Yong H J, Hao Z F, Li X H. Genome-wide association analysis of kernel row number in maize. Acta Agron Sin, 2014, 40: 1-6. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2014.00001
[31] Pandis N. Linear regression. Am J Orthod Dentofac, 2016, 149: 431-434.
doi: 10.1016/j.ajodo.2015.11.019 pmid: 26926032
[32] 袁亮, 孟鑫, 汪亚龙, 廖长见, 李高科, 吕桂华, 宋军, 邱正高, 林海建. 镉胁迫下甜、糯玉米开花期性状的全基因组关联分析. 植物遗传资源学报, 2021, 22: 438-447.
Yuan L, Meng X, Wang Y L, Liao C J, Li G K, Lyu G H, Song J, Qiu Z G, Lin H J. Genome wide association analysis of flowering traits in sweet and waxy maize under cadmium stress. J Plant Genet Resour, 2021, 22: 438-447 (in Chinese with English abstract).
[33] 马雅杰, 高悦欣, 李依萍, 龙艳, 董振营, 万向元. 玉米株高和穗位高的遗传基础与分子机制. 中国生物工程杂志, 2021, 41(12): 61-73.
Ma Y J, Gao Y X, Li Y P, Long Y, Dong Z Y, Wan X Y. Progress on genetic analysis and molecular dissection on maize plant height and ear height. China Biotechnol, 2021, 41(12): 61-73. (in Chinese with English abstract)
[34] Ertiro B T, Labuschagne M, Olsen M, Das B, Prasanna B M, Gowda M. Genetic dissection of nitrogen use efficiency in tropical maize through genome-wide association and genomic prediction. Front Plant Sci, 2020, 11: 474.
doi: 10.3389/fpls.2020.00474 pmid: 32411159
[35] Zhu C, Gore M, Buckler E S, Yu J M. Status and prospects of association mapping in plants. Plant Genome, 2008, 1: 5-20.
[36] An Y X, Chen L, Li Y X, Li C H, Shi Y S, Zhang D F, Li Y, Wang T Y. Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize. BMC Plant Biol, 2020, 20: 490.
doi: 10.1186/s12870-020-02676-x pmid: 33109077
[37] Zhang Y, Wan J Y, He L, Lan H, Li L J. Genome-wide association analysis of plant height using the maize F1 population. Plants (Basel), 2019, 8: 432.
doi: 10.3390/plants8100432
[38] 渠建洲, 冯文豪, 张兴华, 徐淑兔, 薛吉全. 基于全基因组关联分析解析玉米籽粒大小的遗传结构. 作物学报, 2022, 48: 304-319.
doi: 10.3724/SP.J.1006.2022.13002
Qu J Z, Feng W H, Zhang X H, Xu S T, Xue J Q. Dissecting the genetic architecture of maize kernel size based on genome-wide association study. Acta Agron Sin, 2022, 48: 304-319. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2022.13002
[39] Zhao Y, Wang H S, Bo C, Dai W, Zhang X G, Cai R H, Gu L J, Ma Q, Jiang H Y, Zhu J, Cheng B J. Genome-wide association study of maize plant architecture using F1 populations. Plant Mol Biol, 2019, 99: 1-15.
doi: 10.1007/s11103-018-0797-7
[40] Zhou Z Q, Zhang C S, Lu X H, Wang L W, Hao Z F, Li M S, Zhang D G, Yong H J, Zhu H Y, Weng J F, Li X H. Dissecting the genetic basis underlying combining ability of plant height related traits in maize. Front Plant Sci, 2018, 9: 1117.
doi: 10.3389/fpls.2018.01117 pmid: 30116252
[41] 杨晓军, 路明, 张世煌, 周芳, 曲延英, 谢传晓. 玉米株高和穗位高的QTL定位. 遗传, 2008, 30: 1477-1486.
Yang X J, Lu M, Zhang S H, Zhou F, Qu Y Y, Xie C X. QTL mapping of plant height and ear position in maize (Zea mays L.). Hereditas (Beijing), 2008, 30: 1477-1486. (in Chinese with English abstract)
[42] Zhang Z M, Zhao M J, Ding H P, Rong T Z, Pan G T. Quantitative trait loci analysis of plant height and ear height in maize (Zea mays L.). Russ J Genet, 2006, 42: 306-310.
doi: 10.1134/S1022795406030112
[43] Hu S L, Wang C L, Sanchez D L, Lipka A E, Liu P, Yin Y H, Blanco M, Lübberstedt T. Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.). Front Plant Sci, 2017, 8: 1039.
doi: 10.3389/fpls.2017.01039
[44] Tang Z X, Yang Z F, Hu Z Q, Zhang D, Lu X, Jia B, Deng D X, Xu C W. Cytonuclear epistatic quantitative trait locus mapping for plant height and ear height in maize. Mol Breed, 2013, 31: 1-14.
doi: 10.1007/s11032-012-9762-3
[45] Liu H J, Wang X Q, Xiao Y J, Luo J Y, Qiao F, Yang W Y, Zhang R Y, Meng Y J, Sun J M, Yan S J, Peng Y, Niu L Y, Jian L M, Song W, Yan J L, Li C H, Zhao Y X, Liu Y, Warburton M L, Zhao J R, Yan J B. CUBIC: an atlas of genetic architecture promises directed maize improvement. Genome Biol, 2020, 21: 20.
doi: 10.1186/s13059-020-1930-x
[46] Dell’Acqua M, Gatti D M, Pea G, Cattonaro F, Coppens F, Magris G, Hlaing A L, Aung H H, Nelissen H, Baute J, Frascaroli E, Churchill G A, Inzé D, Morgante M, Pè M E. Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. Genome Biol, 2015, 16: 167.
doi: 10.1186/s13059-015-0716-z
[47] Park K J, Sa K J, Kim B W, Koh H J, Lee J K. Genetic mapping and QTL analysis for yield and agronomic traits with an F2:3population derived from a waxy corn × sweet corn cross. Genes Genom, 2014, 36: 179-189.
doi: 10.1007/s13258-013-0157-6
[48] Pan Q C, Xu Y C, Li K, Peng Y, Zhan W, Li W Q, Li L, Yan J B. The genetic basis of plant architecture in 10 maize recombinant inbred line populations. Plant Physiol, 2017, 175: 858-873.
doi: 10.1104/pp.17.00709 pmid: 28838954
[49] Li Y L, Dong Y B, Niu S Z, Cui D Q. The genetic relationship among plant-height traits found using multiple-trait QTL mapping of a dent corn and popcorn cross. Genome, 2007, 50: 357-364.
pmid: 17546094
[50] 李卫华. 玉米多种抗病基因的分子聚合育种. 中国科学院遗传与发育生物学研究所博士学位论文, 北京, 2008.
Li W H. Pyramiding Breeding of Resistance Genes to Maize Diseases with Marker-assisted Selection. PhD Dissertation of Institute of Genetics and Developmental Biology, Chinese Academy of Sciences,Beijing, China, 2008 (in Chinese with English abstract).
[51] Xu X Z, Wan W, Jiang G B, Xi Y, Huang H J, Cai J J, Chang Y N, Duan C G, Mangrauthia S K, Peng X X, Zhu J K, Zhu G H. Nucleocytoplasmic trafficking of the Arabidopsis WD40 repeat protein XIW1 regulates ABI5 stability and abscisic acid responses. Mol Plant, 2019, 12: 1598-1611.
doi: 10.1016/j.molp.2019.07.001
[52] 戚义东, 秦华, 高雅迪, 王芳芳, 黄荣峰, 权瑞党. 脱落酸拮抗赤霉素抑制水稻地上部生长的研究. 生物技术进展, 2019, 9: 483-489.
Qi Y D, Qin H, Gao Y D, Wang F F, Huang R F, Quan R D. Study on antagonizing regulation of shoot growth by abscisic acid and gibberellic acid in rice. Curr Biotech, 2019, 9: 483-489. (in Chinese with English abstract)
[53] Russin W A, Evert R F, Vanderveer P J, Sharkey T D, Briggs S P. Modification of a specific class of plasmodesmata and loss of sucrose export ability in the sucrose export defective1 maize mutant. Plant Cell, 1996, 8: 645-658.
doi: 10.2307/3870341
[54] 覃碧. 泛素蛋白酶体途径及其对植物激素信号转导的调控. 热带农业科学, 2013, 33: 39-45.
Qin B. Ubiquitin-proteasome pathway and its regulation of plant hormone signaling. Chin J Trop Agric, 2013, 33: 39-45. (in Chinese with English abstract)
[55] 冯玥. 棉花岩藻糖基转移酶家族基因(FucT)的发掘和FucT4功能初步分析. 南京农业大学博士学位论文, 江苏南京, 2016.
Feng Y. Genome-wide Identification of Fucosyltransferase (FucT) Gene Family and Functional Analysis of FucT4 in Cotton. PhD Dissertation of Nanjing Agricultural University, Nanjing, Jiangsu, China, 2016. (in Chinese with English abstract)
[56] Skirycz A, Radziejwoski A, Busch W, Hannah M A, Czeszejko J, Kwasniewski M, Zanor M I, Lohmann J U, Veylder L D, Witt I, Roeber B M. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J, 2008, 56: 779-792.
doi: 10.1111/j.1365-313X.2008.03641.x
[57] 王凯. 拟南芥和水稻CPP转录因子家族的生物信息学分析. 生物技术通报, 2010, (2): 76-84.
Wang K. Bioinformatic analysis of the CPP transcription factors family in Arabidopsis and rice. Biotech Bull, 2010, (2): 76-84. (in Chinese with English abstract)
[58] 何亮, 李富华, 沙莉娜, 付凤玲, 李晚忱. 玉米2C型丝氨酸/苏氨酸蛋白磷酸酶(PP2C)活性与耐旱性的关系. 作物学报, 2008, 34: 899-903.
doi: 10.3724/SP.J.1006.2008.00899
He L, Li F H, Sha L N, Fu F L, Li W C. Activity of serine/threonine protein phosphatase type-2C (PP2C) and its relationships to drought tolerance in maize. Acta Agron Sin, 2008, 34: 899-903. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2008.00899
[59] 卫卓赟, 黎家. 受体激酶介导的油菜素内酯信号转导途径. 生命科学, 2011, 23: 1106-1113.
Wei Z Y, Li J. Receptor kinases mediated brassinosteroid signal transduction in plants. Chin Bull Life Sci, 2011, 23: 1106-1113. (in Chinese with English abstract)
[60] Kir G, Ye H X, Nelissen H, Neelakandan A K, Kusnandar A S, Luo A, Inzé D, Sylvester A W, Yin Y H, Becraft P W. RNA interference knockdown of BRASSINOSTEROID INSENSITIVE1 in maize reveals novel functions for brassinosteroid signaling in controlling plant architecture. Plant Physiol, 2015, 169: 826-839.
doi: 10.1104/pp.15.00367
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