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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (05): 672-685.doi: 10.3724/SP.J.1006.2018.00672

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

Genome-wide Association Studies of Seed Germination Related Traits in Maize

Run-Miao TIAN1,**(), Xue-Hai ZHANG1,**, Ji-Hua TANG1, Guang-Hong BAI2, Zhi-Yuan FU1,*()   

  1. 1 College of Agronomy, Henan Agricultural University, Zhengzhou 450002, Henan, China
    2 Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
  • Received:2017-11-02 Accepted:2018-03-15 Online:2018-05-20 Published:2018-03-16
  • Contact: Run-Miao TIAN,Xue-Hai ZHANG,Zhi-Yuan FU E-mail:tianrunmiao@foxmail.com;fuzhiyuan2004@163.com
  • Supported by:
    This study was supported by the Regional Science Foundation of National Natural Science Foundation of China (31760389).

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Abstract:

Germination is important for seed emergence, which has significant impact on maize yield. To reveal the genetic mechanism of maize seed germination, we investigated six traits related to seed germination using 467 diverse inbred lines. The genome-wide association studies (GWAS) between the six traits and 1.25M SNPs were implemented in three different models (Q model, K model, and Q+K model). The K model was much better than the other two models for weight before imbibition, volume before imbibition, weight after imbibition, volume after imbibition and volume of imbibition. While weight of imbibition trait could be well evaluated by Q+K model. In total, 15 SNPs were significantly associated with the six traits by the optimal model. These SNPs correspond to six QTLs, including five QTLs co-located in different biological replications. The six QTLs were located on chromosomes 3, 6, 7, and 10. The single SNP could explain 5.09%-7.85% variation of phenotype. Genes within or nearby most significant SNP were selected as candidates, and six candidate genes were identified for seed germination related traits in the six loci. Among these genes, GRMZM2G148411 encoding a TLD-domain calcium ion binding protein according to the annotations associated with weight after imbibition, volume after imbibition and volume of imbibition might be a signal molecule regulating seed germination and dormancy. The QTLs identified in this study are useful for developing functional markers and elucidating the genetic basis of seed germination.

Key words: maize, seed germination, genome-wide association study, candidate gene

Fig. 1

Frequency distribution of seed emergence traits Name of each trait is given in Table 1."

Table 1

Statistical analysis of seed germination traits"

性状
Trait		 平均值±标准差
Mean± SD		 变幅
Range		 变异系数
CV (%)		 峰度
Skewness		 偏度
Kurtosis
W1 (g) 4.92±0.92 1.63-7.40 18.77 0.22 0.07
V1 (mL) 4.43±0.77 2.57-6.47 17.35 0.42 -0.03
W2 (g) 6.52±1.19 2.02-9.86 18.29 0.25 0.23
V2 (mL) 5.87±1.06 1.93-9.20 18.06 0.43 0.33
W3 (g) 1.61±0.35 0.38-2.72 21.77 0.55 0.54
V3 (mL) 1.44±0.41 0.35-2.76 28.41 0.25 -0.13

Table 2

ANOVA of seed germination traits"

性状
Trait		 变异来源
Variation source		 自由度
df		 均方
MS		 F值
F-value
W1 材料Variety 475 2.56 52.99**
重复Repeat 2 0.11 2.27
误差Error 940 0.05
V1 材料Variety 475 1.77 14.50**
重复Repeat 2 0.96 7.85**
误差Error 941 0.12
W2 材料Variety 475 4.24 32.12**
重复Repeat 2 4.31 32.68**
误差Error 940 0.13
V2 材料Variety 475 3.35 19.35**
重复Repeat 2 0.33 1.93
误差Error 93 0.17
W3 材料Variety 475 0.36 8.28**
重复Repeat 2 4.02 92.23**
误差Error 934 0.04
V3 材料Variety 475 0.50 2.62**
重复Repeat 2 1.32 6.96**
误差Error 932 0.19

Table 3

Pearson correlation analysis of seed germination traits"

性状 Trait W1 V1 W2 V2 W3
V1 0.955**
W2 0.976** 0.956**
V2 0.935** 0.942** 0.966**
W3 0.675** 0.725** 0.821** 0.811**
V3 0.606** 0.543** 0.682** 0.793** 0.724**

Fig. 2

Quantile-quantile plots (QQ plots) of estimated -lg(P) from association analysis using three methods for seed emergence traits Detailed name of each trait was given in Table 1. The horizontal axis shows -lg transformed expected P-values, and the vertical axis shows -lg transformed observed P-values."

Fig. 3

Manhattan of GWAS for seed germination traits Name of each trait is given in Table 1. Black dotted line indicates the genome-wide significance threshold."

Fig 4

Manhattan of GWAS for seed germination traits (single round) Name of each trait is given in Table 1. R1: the first biological repeat; R2: the second biological repeat; R3: the third biological repeat. Black dotted line indicates the genome-wide significance threshold."

Table 4

Candidate genes and their anmotations of seed germination traits"

Table 5

SNPs associated with seed germination traits"

性状
Trait		 重复
Repeat		 候选位点
Locus		 SNP 染色体
Chr.		 物理位置
Position		 P值
P-value		 贡献率
R2 (%)
W1 1 Chr4: 2865435-2865435? Chr4.S_2925435 4 2925435 7.76×10-7 8.33
Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 1.48×10-6 5.58
2 Chr10: 139810517-139870517 Chr10.S_139840517 10 139840517 1.87×10-6 9.60
W1 Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 4.34×10-7 6.10
Chr7.S_4828028 7 4828028 7.66×10-7 5.84
W2 1 Chr10: 6343038-6403038 Chr10.S_6373105 10 6373105 1.81×10-6 5.16
Chr10: 117510861-117630861 Chr10.S_117570861 10 117570861 1.16×10-6 5.21
Chr4: 2865435-2865435 Chr4.S_2925435 4 2925435 3.83×10-7 8.73
Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 1.57×10-6 5.54
2 Chr10: 6343038-6403038 Chr10.S_6373105 10 6373105 1.86×10-6 5.14
Chr3: 209027864-209147864 Chr3.S_209087864 3 209087864 1.58×10-6 9.50
Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.75×10-6 5.25
Chr10.S_6373105 10 6373105 1.50×10-6 5.27
Chr9: 144257637-144377637 Chr9.S_144308026 9 144308026 1.77×10-6 5.08
Chr9.S_144308098 9 144308098 2.01×10-6 5.05
Chr9.S_144309854 9 144309854 1.77×10-6 5.08
Chr9.S_144309860 9 144309860 3.69×10-7 5.77
W2 Chr9.S_144317637 9 144317637 2.21×10-7 6.56
Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.86×10-6 5.17
Chr10.S_6373105 10 6373105 1.16×10-6 5.34
W3 1 Chr1: 206063394-206183394 Chr1.S_206123394 1 206123394 1.55×10-6 5.31
3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.01×10-7 5.92
Chr10.S_6373105 10 6373105 1.75×10-8 6.60
Chr2: 152687771-152807771 Chr2.S_205719834 2 205719834 6.26×10-7 7.05
Chr2.S_205770041 2 205770041 5.71×10-7 5.02
Chr2.S_205771072 2 205771072 5.71×10-7 5.02
Chr2.S_205771170 2 205771170 5.71×10-7 5.02
Chr2.S_205771560 2 205771560 5.71×10-7 5.02
Chr2.S_205771697 2 205771697 5.71×10-7 5.02
Chr2.S_205772111 2 205772111 5.71×10-7 5.02
Chr2.S_205773201 2 205773201 5.71×10-7 5.02
Chr2.S_205774142 2 205774142 5.71×10-7 5.02
Chr5:152687771-152807771 Chr5.S_152747771 5 152747771 4.70×10-7 8.78
Chr6: 95574386-95634386 Chr6.S_98573207 6 98573207 4.22×10-7 5.78
Chr9: 26957278-27077278 Chr9.S_27017278 9 27017278 1.47×10-6 5.13
W3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 3.22×10-9 8.06
Chr10.S_6373105 10 6373105 5.75×10-9 7.73
V1 1 Chr4: 2865435- 2865435? Chr4.S_2925435 4 2925435 8.89×10-7 8.44
Chr6: 6778454-6838454 Chr6.S_6808454 6 6808454 1.38×10-6 8.07
2 Chr10: 139780517-139900517 Chr10.S_139840517 10 139840517 3.47×10-7 10.56
Chr9: 144257637- 144377637 Chr9.S_144309860 9 144309860 1.60×10-6 5.12
3 Chr6: 95574386-95634386 Chr6.S_95604386 6 95604386 8.22×10-7 5.32
Chr6.S_95604517 6 95604517 1.42×10-6 5.08
Chr6.S_95604625 6 95604625 1.42×10-6 5.08
性状
Trait		 重复
Repeat		 候选位点
Locus		 SNP 染色体
Chr.		 物理位置
Position		 P值
P-value		 贡献率
R2 (%)
Chr6.S_95604950 6 95604950 1.11×10-6 5.20
Chr6.S_95605307 6 95605307 1.21×10-6 5.14
Chr6.S_95605330 6 95605330 1.10×10-6 5.22
Chr6.S_95605331 6 95605331 1.95×10-6 5.04
Chr6.S_95605458 6 95605458 1.21×10-6 5.14
Chr6.S_95605541 6 95605541 1.21×10-6 5.14
Chr8: 14037401-14157401 Chr8.S_14097401 8 14097401 1.93×10-6 5.71
V1 Chr6: 6778454-6838454 Chr6.S_6808454 6 6808454 2.01×10-6 7.85
Chr6: 95574386-95634386 Chr6.S_95604386 6 95604386 8.76×10-7 5.28
Chr6.S_95604517 6 95604517 1.31×10-6 5.10
Chr6.S_95604625 6 95604625 1.31×10-6 5.10
Chr6.S_95604950 6 95604950 1.08×10-6 5.19
Chr6.S_95605307 6 95605307 1.14×10-6 5.16
Chr6.S_95605330 6 95605330 1.03×10-6 5.23
Chr6.S_95605331 6 95605331 1.67×10-6 5.09
Chr6.S_95605458 6 95605458 1.14×10-6 5.16
Chr6.S_95605541 6 95605541 1.14×10-6 5.16
V2 1 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 5.73×10-7 5.73
Chr4: 2865435-2865435 Chr4.S_2925435 4 2925435 1.49×10-6 7.54
Chr4: 185676597-185796597 Chr4.S_185736597 4 185736597 5.59×10-7 7.89
2 Chr10: 6147016-6267016 Chr10.S_6207016 10 6207016 1.14×10-6 8.84
V3 1 Chr2: 182455178-182575178 Chr2.S_182515178 2 182515178 9.03×10-7 5.98
Chr7: 145940024-146000024 Chr7.S_145970024 7 145970024 4.26×10-7 5.75
2 Chr1: 262661257-262781257 Chr1.S_262721257 1 262721257 1.59×10-6 5.55
Chr5: 213497149-213617149 Chr5.S_213557149 5 213557149 8.90×10-7 5.68
3 Chr7: 95428593-95548593 Chr7.S_95488593 7 95488593 1.05×10-6 7.48
Chr7.S_95488613 7 95488613 1.43×10-6 6.80
V3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.60×10-6 5.21
Chr3: 197628474-197688474 Chr3.S_197658474 3 197658474 1.72×10-6 5.93
Chr7: 145940024-146000024 Chr7.S_145970024 7 145970024 1.70×10-6 5.13
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