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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (12): 3261-3276.doi: 10.3724/SP.J.1006.2023.33010

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

Mining maize flowering traits related candidate genes based on GWAS and WGCNA data

QIAN Fu1(), ZHANG Zhan-Qin2, CHEN Shu-Bin2, DING Yong-Fu2, SANG Zhi-Qin2,*(), LI Wei-Hua1,*()   

  1. 1College of Agriculture, Shihezi University / Key Laboratory of Oasis Eco-Agriculture, Shihezi 832000, Xinjiang, China
    2Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, Xinjiang, China
  • Received:2023-02-22 Accepted:2023-05-24 Online:2023-12-12 Published:2023-08-28
  • Contact: * E-mail: lwh_agr@shzu.edu.cn; E-mail: sangzhiqin@126.com
  • Supported by:
    Tackling Key Scientific and Technological Problems in Key Areas of Xinjiang Production and Construction Corps(2019AB021);Science and Technology Innovation Talent Plan of Xinjiang Production and Construction Corps(2021CB038);Chinese Academy of Sciences “Western Young Scholar”

Abstract:

The flowering time is one of the important traits in maize. It is of great significance to analyze the genetic basis and to mine the key core genes in flowering for maize varieties with wide adaptability. A natural population consisting of 580 maize inbred lines were planted for three years, to determine the three flowering traits (including days to anthesis, days to silking, and anthesis silking interval). Genome-wide association analysis was conducted using 31,826 SNPs distributed throughout the whole genome. Combined with transcriptome data of 14 different developmental stages of inbred line B73, weighted gene co-expression network analysis was performed to select tissue specific modules and key genes related to maize flowering time. A total of 14 SNPs for four flower traits under multiple environments and 10 potential candidate genes were mined by GWAS, WGCNA was used to mine 17 potential candidate genes in flowering time, three candidate genes were jointly mined by both approaches. Zm00001d052180 encodes a MADS box transcription factor 19, Zm00001d016814 encodes the NAC transcription factor 133, Zm00001d048082 encodes MADS box transcription factor 8, mainly involved in regulating inflorescence growth and development, which has certain research value and significance. These results provide a reference for the genetic basis and molecular mechanisms of flowering time related traits in maize.

Key words: maize, flowering time related traits, GWAS, WGCNA, candidate gene

Table 1

Statistical analysis of flowering time related traits in different years"

性状
Trait
年份
Year
范围
Range
均值
Mean
标准差
SD
变异系数
CV (%)
偏度
Skewness
峰度
Kurtosis
遗传力
H2 (%)
散粉期
DTA
2019 59.00-86.00 73.46 5.78 7.86 -0.23 -0.66 96.18
2020 53.00-83.00 65.22 6.22 9.54 0.14 -0.61
2021 48.00-75.00 60.72 5.66 9.31 -0.09 -0.67
BLUE 53.43-81.00 66.52 5.73 8.61 -0.07 -0.65
吐丝期
DTS
2019 60.67-89.00 76.12 5.98 7.86 -0.30 -0.56 95.54
2020 55.00-84.50 68.06 6.49 9.53 0.11 -0.68
2021 50.50-75.50 62.51 5.37 8.59 0.07 -0.48
BLUE 55.53-83.68 68.97 5.79 8.40 -0.07 -0.58
散粉吐丝间隔期ASI 2019 0.33-6.67 2.67 1.11 41.59 0.72 0.40 56.50
2020 0-6.50 2.72 1.20 44.23 0.47 -0.07
2021 0-5.00 1.69 1.05 61.87 0.48 -0.18
BLUE 0.67-6.16 2.39 0.86 35.88 0.68 0.94

Table 2

Variance analysis of flowering time related traits"

性状
Trait
变异来源
Source
自由度
DF
均方
MS
散粉期DTA 基因型 Genotype 579 208***
年份 Year 2 55,678***
基因型×年份 Genotype×Year 1149 8***
残差 Residual 2109 4
吐丝期DTS 基因型 Genotype 579 210***
年份 Year 2 62,735***
基因型×年份 Genotype×Year 1149 9***
残差 Residual 2105 4
散粉吐丝间隔期ASI 基因型 Genotype 579 4.7***
年份 Year 2 387.5***
基因型×年份 Genotype×Year 1144 1.9***
残差 Residual 2067 1.3

Fig. 1

Correlation of flowering time related traits ** and *** indicate significant in the 0.01 and 0.001 probability levels, respectively. Abbreviations are the same as those given in Table 1."

Fig. 2

Manhattan plot and quantile-quantile plot of flowering time related traits BLUE Abbreviations are the same as those given in Table 1."

Fig. S1

Manhattan plot and quantile-quantile plot of flowering time related traits DTA: days to anthesis; DTS: days to silking; ASI: anthesis silking interval."

Table S1

Significant SNPs for flowering time related traits in four environments"

性状
Trait
年份
Years
标记
SNPs
染色体
Chr.
物理位置
Position (bp)
P
P-value
次等位基因频率
MAF
DTS 2019 8_159342177 8 159,342,177 6.89E-11 0.34103
DTS 2019 5_48863489 5 48,863,489 1.63E-09 0.386323
DTS 2019 5_176849292 5 176,849,292 1.68E-09 0.23357
DTS 2019 5_147435514 5 147,435,514 4.75E-08 0.487567
DTS 2019 3_170291855 3 170,291,855 1.91E-07 0.493783
DTS 2019 8_160072522 8 160,072,522 2.90E-07 0.332149
DTS 2019 5_30789224 5 30,789,224 5.54E-07 0.37389
DTA 2019 10_69098512 10 69,098,512 8.51E-10 0.179262
DTA 2019 5_176849292 5 176,849,292 1.05E-09 0.232865
DTA 2019 10_10799643 10 10,799,643 1.80E-08 0.395431
DTA 2019 2_1359194 2 1,359,194 2.70E-08 0.260984
DTA 2019 6_128386990 6 128,386,990 3.07E-08 0.230228
DTA 2019 5_72656332 5 72,656,332 3.81E-08 0.44464
DTA 2019 7_109239367 7 109,239,367 7.89E-08 0.463972
DTA 2019 5_145997443 5 145,997,443 2.14E-07 0.329525
DTA 2019 8_160072522 8 160,072,522 2.97E-07 0.332162
DTA 2019 8_159342177 8 159,342,177 3.18E-07 0.341828
DTA 2019 8_134443746 8 134,443,746 3.78E-07 0.355888
DTA 2019 3_138802769 3 138,802,769 5.32E-07 0.132689
DTA 2019 4_135184025 4 135,184,025 7.44E-07 0.393673
DTA 2020 2_83703979 2 83,703,979 5.11E-12 0.243007
DTA 2020 8_130284569 8 130,284,569 9.81E-11 0.368881
DTA 2020 3_135182164 3 135,182,164 1.23E-10 0.190559
DTA 2020 7_157639029 7 157,639,029 5.63E-09 0.356643
DTA 2020 5_87683979 5 87,683,979 2.14E-08 0.252622
DTA 2020 7_109239367 7 109,239,367 3.45E-08 0.465909
DTA 2020 4_182045481 4 182,045,481 1.09E-07 0.403846
DTA 2020 9_15913145 9 15,913,145 2.29E-07 0.449301
DTA 2020 6_63992603 6 63,992,603 6.89E-07 0.318182
DTA 2020 8_159342177 8 159,342,177 9.73E-07 0.340035
DTA 2020 6_128386990 6 128,386,990 1.56E-06 0.230769
DTA 2021 3_135182164 3 135,182,164 1.56E-12 0.191413
DTA 2021 3_206999249 3 206,999,249 3.81E-11 0.476744
DTA 2021 8_130282760 8 130,282,760 2.11E-10 0.199463
DTA 2021 7_168431448 7 168,431,448 4.93E-10 0.388193
DTA 2021 9_154601150 9 154,601,150 3.07E-09 0.232558
DTA 2021 7_109239367 7 109,239,367 4.45E-08 0.466011
DTA 2021 3_6928983 3 6,928,983 7.33E-08 0.34347
DTA 2021 3_33440636 3 33,440,636 1.34E-07 0.308587
DTA 2021 4_146577795 4 146,577,795 2.31E-07 0.127907
DTA 2021 4_182045481 4 182,045,481 5.73E-07 0.407871
DTA 2021 8_159342177 8 159,342,177 6.13E-07 0.342576
DTA 2021 2_80389048 2 80,389,048 1.56E-06 0.390877
DTA BLUE 8_130284569 8 130,284,569 1.90E-11 0.365517
DTA BLUE 5_71931331 5 71,931,331 4.00E-10 0.493103
DTA BLUE 6_128386990 6 128,386,990 1.30E-09 0.232759
DTA BLUE 2_80271281 2 80,271,281 1.60E-09 0.39569
DTA BLUE 7_165890330 7 165,890,330 2.23E-09 0.369828
DTA BLUE 3_6928983 3 6,928,983 2.06E-08 0.341379
DTA BLUE 3_135182164 3 135,182,164 6.12E-08 0.191379
DTA BLUE 1_175994724 1 175,994,724 6.29E-08 0.194828
DTA BLUE 4_182045481 4 182,045,481 2.09E-07 0.406897
DTA BLUE 1_8218880 1 8,218,880 2.24E-07 0.228448
DTA BLUE 5_176849292 5 176,849,292 3.71E-07 0.230172
DTA BLUE 8_159342177 8 159,342,177 4.79E-07 0.343966
DTA BLUE 5_213317177 5 213,317,177 9.59E-07 0.334483
DTA BLUE 5_87683979 5 87,683,979 1.15E-06 0.253448
DTS 2020 8_130284569 8 130,284,569 3.09E-15 0.367596
DTS 2020 8_159342177 8 159,342,177 5.61E-09 0.342334
DTS 2020 3_135182164 3 135,182,164 6.72E-09 0.189895
DTS 2020 4_36061401 4 36,061,401 5.58E-08 0.461672
DTS 2020 4_182045481 4 182,045,481 1.16E-07 0.402439
DTS 2020 2_80271281 2 80,271,281 2.70E-07 0.39547
DTS 2020 5_71931331 5 71,931,331 2.75E-07 0.490418
DTS 2020 10_27456815 10 27,456,815 8.62E-07 0.402439
DTS 2020 1_8218880 1 8,218,880 1.23E-06 0.229094
DTS 2021 8_130282760 8 130,282,760 2.06E-10 0.199463
DTS 2021 8_159342177 8 159,342,177 2.80E-09 0.342576
DTS 2021 6_65919084 6 65,919,084 1.25E-08 0.347943
DTS 2021 3_206999249 3 206,999,249 2.14E-08 0.476744
DTS 2021 5_73163352 5 73,163,352 2.90E-08 0.120751
DTS 2021 9_149761626 9 149,761,626 1.48E-07 0.13059
DTS 2021 2_61511737 2 61,511,737 1.70E-07 0.363148
DTS 2021 5_87683979 5 87,683,979 3.98E-07 0.253131
DTS BLUE 8_130284569 8 130,284,569 1.75E-11 0.365517
DTS BLUE 3_6928983 3 6,928,983 5.95E-09 0.341379
DTS BLUE 2_80271281 2 80,271,281 6.90E-09 0.39569
DTS BLUE 5_176849292 5 176,849,292 7.82E-09 0.230172
DTS BLUE 7_165890330 7 165,890,330 3.42E-08 0.369828
DTS BLUE 7_168431448 7 168,431,448 1.47E-07 0.392241
DTS BLUE 1_8218880 1 8,218,880 1.79E-07 0.228448
DTS BLUE 9_149761626 9 149,761,626 2.08E-07 0.131034
DTS BLUE 3_135182164 3 135,182,164 3.03E-07 0.191379
DTS BLUE 3_170291855 3 170,291,855 3.73E-07 0.496552
DTS BLUE 7_109239367 7 109,239,367 4.01E-07 0.467241
DTS BLUE 1_175994724 1 175,994,724 5.31E-07 0.194828
DTS BLUE 4_132936409 4 132,936,409 1.12E-06 0.15
DTS BLUE 8_125053113 8 125,053,113 1.17E-06 0.421552
DTS BLUE 6_128386990 6 128,386,990 1.50E-06 0.232759
ASI 2020 1_282472600 1 282,472,600 6.18E-11 0.417553
ASI 2020 4_121588214 4 121,588,214 1.24E-06 0.298759
ASI 2020 7_1680665 7 1,680,665 1.26E-06 0.405142
ASI 2020 6_129660777 6 129,660,777 1.35E-06 0.496454
ASI BLUE 3_213737451 3 213,737,451 2.39E-08 0.374138
ASI BLUE 4_121588214 4 121,588,214 3.84E-07 0.300862

Table 3

Significant colocalization of SNPs for flowering time related traits"

性状
Trait
标记
SNPs
染色体
Chromosome
物理位置
Position (bp)
P-value
2019 2020 2021 BLUE
散粉期
DTA
3_6928983 3 6,928,983 7.33E-08 2.06E-08
3_135182164 3 135,182,164 1.23E-10 1.56E-12 6.12E-08
4_182045481 4 182,045,481 1.09E-07 5.73E-07 2.09E-07
5_87683979 5 87,683,979 2.14E-08 1.15E-06
5_176849292 5 176,849,292 1.05E-09 3.71E-07
6_128386990 6 128,386,990 3.07E-08 1.56E-06 1.30E-09
7_109239367 7 109,239,367 7.89E-08 3.45E-08 4.45E-08
8_130284569 8 130,284,569 9.81E-11 1.90E-11
8_159342177 8 159,342,177 3.18E-07 9.73E-07 6.13E-07 4.79E-07
吐丝期
DTS
1_8218880 1 8,218,880 1.23E-06 1.79E-07
2_80271281 2 80,271,281 2.70E-07 6.90E-09
3_135182164 3 135,182,164 6.72E-09 3.03E-07
3_170291855 3 170,291,855 1.91E-07 3.73E-07
5_176849292 5 176,849,292 1.68E-09 7.82E-09
8_130284569 8 130,284,569 3.09E-15 1.75E-11
8_159342177 8 159,342,177 6.89E-11 9.73E-07 2.80E-09
9_149761626 9 149,761,626 1.48E-07 2.08E-07
散粉吐丝间隔期
ASI
4_121588214 4 121,588,214 1.24E-06 3.84E-07

Fig. 3

Number of significant colocalization of SNPs for flowering time related traits Abbreviations are the same as those given in Table 1."

Fig. 4

Analysis of allelic effects of colocalized SNPs for flowering time related traits *** indicates significant difference in the 0.001 probability level. Abbreviations are the same as those given in Table 1."

Fig. S2

Analysis of allelic effects of colocalized SNPs for flowering time related traits Abbreviations are the same as those given in Fig. S1."

Fig. 5

Result of gene co-expression network construction A: the clustering dendrogram of samples and tissue correspondence; B: the determination of soft threshold; C: gene clustering and module construction; D: correlation between traits and modules (Red color of each box represents the positive correlation between module and trait. Green color of each box represents the negative relationships between module and trait. The values inside and outside the brackets in the figure are P-values and correlation coefficients, respectively); E: enrichment pathway of flowering time."

Table 4

GWAS candidate genes"

性状
Trait
标记
SNPs
基因
Gene
功能注释
Annotation
DTA 4_182045481 Zm00001d052180* Tunicate 1
DTA, DTS 8_159342177 Zm00001d011703 WD-repeat protein RBAP 1
DTA 3_6928983 zma-MIR156b Corngrass 1
DTA 5_87683979 Zm00001d015385 Chlorophyll a-b binding protein, chloroplastic
DTA 7_109239367 Zm00001d020361 PHD-transcription factor 30
DTA 6_128386990 Zm00001d037532 6-phosphofructo-2-kinase/fructose-26-bisphosphatase
DTA, DTS 5_176849292 Zm00001d016814* NAC-transcription factor 133
DTS 1_8218880 Zm00001d027554 LYR family of Fe/S cluster biogenesis protein
DTS 9_149761626 Zm00001d048082* MADS 8
ASI 4_121588214 Zm00001d050768 Cytokinin response regulator 7

Fig. 6

Local regulation network of gene co-expression of key modules The green node is the flowering time genes reported, the red nodes are flowering time candidate genes."

Table 5

WGCNA candidate genes"

模块
Moudle
基因
Gene
功能注释
Annotation
Blue Zm00001d014863 MYB-related-transcription factor 96
Zm00001d012395 Mannose-1-phosphate guanylyltransferase 2
Brown Zm00001d041685 RALF
Zm00001d022469 Putative histone-arginine methyltransferase 1.4
Zm00001d053880 CO CO-LIKE TIMING OF CAB1 protein domain 24
Green Zm00001d037182 12-oxo-phytodienoic acid reductase 3
Zm00001d023424 bZIP-transcription factor 109
Zm00001d016814* NAC-transcription factor 133
Purple Zm00001d020970 Dihydroflavonoid reductase 1
Black Zm00001d030656 Rotten ear 1
Zm00001d013964 ALG2-interacting protein X
Zm00001d048082* MADS 8
Zm00001d033976 Aux/IAA-transcription factor 4
Royalblue Zm00001d042985 BAG family molecular chaperone regulator 4
Grey60 Zm00001d012719 bZIP-transcription factor 20
Lightcyan Zm00001d035629 Actin-depolymerizing factor 4
Zm00001d052180* Tunicate 1
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[3] YANG Jian-Chang;ZHANG Jian-Hua;WANG Zhi-Qin;ZH0U Qing-Sen. Changes in Contents of Polyamines in the Flag Leaf and Their Relationship with Drought-resistance of Rice Cultivars under Water Deficiency Stress[J]. Acta Agron Sin, 2004, 30(11): 1069 -1075 .
[4] Yan Mei;Yang Guangsheng;Fu Tingdong;Yan Hongyan. Studies on the Ecotypical Male Sterile-fertile Line of Brassica napus L.Ⅲ. Sensitivity to Temperature of 8-8112AB and Its Inheritance[J]. Acta Agron Sin, 2003, 29(03): 330 -335 .
[5] Wang Yongsheng;Wang Jing;Duan Jingya;Wang Jinfa;Liu Liangshi. Isolation and Genetic Research of a Dwarf Tiilering Mutant Rice[J]. Acta Agron Sin, 2002, 28(02): 235 -239 .
[6] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[7] TIAN Meng-Liang;HUNAG Yu-Bi;TAN Gong-Xie;LIU Yong-Jian;RONG Ting-Zhao. Sequence Polymorphism of waxy Genes in Landraces of Waxy Maize from Southwest China[J]. Acta Agron Sin, 2008, 34(05): 729 -736 .
[8] HU Xi-Yuan;LI Jian-Ping;SONG Xi-Fang. Efficiency of Spatial Statistical Analysis in Superior Genotype Selection of Plant Breeding[J]. Acta Agron Sin, 2008, 34(03): 412 -417 .
[9] WANG Yan;QIU Li-Ming;XIE Wen-Juan;HUANG Wei;YE Feng;ZHANG Fu-Chun;MA Ji. Cold Tolerance of Transgenic Tobacco Carrying Gene Encoding Insect Antifreeze Protein[J]. Acta Agron Sin, 2008, 34(03): 397 -402 .
[10] ZHENG Xi;WU Jian-Guo;LOU Xiang-Yang;XU Hai-Ming;SHI Chun-Hai. Mapping and Analysis of QTLs on Maternal and Endosperm Genomes for Histidine and Arginine in Rice (Oryza sativa L.) across Environments[J]. Acta Agron Sin, 2008, 34(03): 369 -375 .