Polymorphisms of Leptin-b Gene Associated with Growth Traits in Orange-Spotted Grouper (Epinephelus coioides)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Single Nucleotide Polymorphisms Identification and Genotyping
2.2. Association Analysis with Growth Traits
SNP | Position | Mutation Type | Sample Size | Genotype Frequencies (%) | Allele Frequencies (%) | H o | H e | p-Value(χ2, HWE) | PIC a | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|
c.14G>A | Exon1 | Missense | 200 | GG | GA | AA | G | A | 0.525 | 0.497 | 0.731 | 0.374 |
Locus14 | R: CGG→Q: CAG | - | 27.5 | 52.5 | 20.0 | 53.75 | 46.25 | - | - | - | - | |
c.93A>G | Exon1 | Synonymous | 200 | AA | AG | GG | A | G | 0.430 | 0.428 | 0.997 | 0.336 |
Locus93 | T: ACA→ACG | - | 47.5 | 43.0 | 9.5 | 69.00 | 31.00 | - | - | - | - | |
c.149G>A | Exon1 | Missense | 200 | GG | GA | AA | G | A | 0.080 | 0.077 | 0.841 | 0.074 |
Locus149 | R: CGG→Q: CAG | - | 92.0 | 8.0 | 0.0 | 96.00 | 4.00 | - | - | - | - | |
c.181A>G | Intron1 | Untranslated | 200 | AA | GA | GG | A | G | 0.060 | 0.068 | 0.287 | 0.065 |
Locus181 | - | - | 93.5 | 6.0 | 0.5 | 96.50 | 3.50 | - | - | - | - | |
c.193G>A | Intron1 | Untranslated | 200 | GG | GA | AA | G | A | 0.400 | 0.416 | 0.863 | 0.329 |
Locus193 | - | - | 50.5 | 40.0 | 9.5 | 70.50 | 29.50 | - | - | - | - | |
c.360C>T | Exon2 | Synonymous | 200 | CC | CT | TT | C | T | 0.495 | 0.467 | 0.707 | 0.358 |
Locus360 | L: CTC→CTT | - | 38.0 | 49.5 | 12.5 | 62.75 | 37.25 | - | - | - | - |
SNP | Genotypes | N | BWT (g) | BWH (cm) | OL (cm) | BL (cm) | TW (cm) | HL (cm) | CPW (cm) | CPL (cm) | SL (cm) | ED (cm) | ID (cm) | K (%) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
c.14G>A | GG | 55 | 87.89 ± 37.17 | 4.66 ± 0.72 | 17.78 ± 2.65 | 14.58 ± 2.22 | 2.72 ± 0.49 | 5.80 ± 0.88 | 1.58 ± 0.23 | 2.42 ± 0.49 | 1.16 ± 0.22 | 0.94 ± 0.08 | 0.92 ± 0.16 | 2.70 ± 0.33 | ||||||||||
GA | 105 | 92.86 ± 45.81 | 4.69 ± 0.72 | 18.07 ± 2.72 | 14.88 ± 2.38 | 2.76 ± 0.55 | 5.84 ± 0.92 | 1.62 ± 0.24 | 2.48 ± 0.50 | 1.20 ± 0.25 | 0.94 ± 0.09 | 0.93 ± 0.16 | 2.66 ± 0.31 | |||||||||||
AA | 40 | 92.60 ± 45.66 | 4.69 ± 0.77 | 17.97 ± 2.87 | 14.75 ± 2.56 | 2.75 ± 0.55 | 5.78 ± 1.01 | 1.59 ± 0.26 | 2.43 ± 0.54 | 1.19 ± 0.20 | 0.95 ± 0.12 | 0.96 ± 0.16 | 2.70 ± 0.32 | |||||||||||
p-value | - | 0.777 | 0.964 | 0.816 | 0.753 | 0.882 | 0.930 | 0.597 | 0.748 | 0.581 | 0.869 | 0.571 | 0.659 | |||||||||||
GG/GA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.895 | 1.000 | 1.000 | 1.000 | |||||||||||
GA/AA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | |||||||||||
AA/GG | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.889 | 1.000 | |||||||||||
c.93A>G | AA | 95 | 93.74 ± 47.82 | 4.70 ± 0.77 | 18.09 ± 2.87 | 14.93 ± 2.52 | 2.78 ± 0.56 | 5.84 ± 0.97 | 1.61 ± 0.25 | 2.47 ± 0.53 | 1.19 ± 0.24 | 0.95 ± 0.10 | 0.95 ± 0.16 | 2.64 ± 0.34 | ||||||||||
AG | 86 | 88.11 ± 40.16 | 4.64 ± 0.72 | 17.74 ± 2.60 | 14.54 ± 2.24 | 2.69 ± 0.53 | 5.76 ± 0.92 | 1.60 ± 0.24 | 2.43 ± 0.49 | 1.18 ± 0.23 | 0.94 ± 0.09 | 0.92 ± 0.17 | 2.70 ± 0.30 | |||||||||||
GG | 19 | 94.95 ± 34.51 | 4.74 ± 0.51 | 18.37 ± 2.53 | 15.03 ± 2.19 | 2.86 ± 0.36 | 5.92 ± 0.75 | 1.62 ± 0.19 | 2.57 ± 0.44 | 1.20 ± 0.18 | 0.94 ± 0.07 | 0.96 ± 0.12 | 2.74 ± 0.30 | |||||||||||
p-value | - | 0.641 | 0.796 | 0.547 | 0.492 | 0.330 | 0.745 | 0.949 | 0.888 | 0.878 | 0.630 | 0.385 | 0.322 | |||||||||||
AA/AG | - | 1.000 | 1.000 | 1.000 | 0.834 | 0.748 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.645 | 0.760 | |||||||||||
AG/GG | - | 1.000 | 1.000 | 1.000 | 1.000 | 0.633 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | |||||||||||
GG/AA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.620 | |||||||||||
c.149G>A | GG | 184 | 93.02 ± 44.09 | 4.71 ± 0.72 a | 18.06 ± 2.73 | 14.86 ± 2.37 | 2.76 ± 0.53 | 5.86 ± 0.93 a | 1.61 ± 0.24 | 2.47 ± 0.50 | 1.19 ± 0.23 | 0.95 ± 0.09 | 0.94 ± 0.16 | 2.68 ± 0.32 | ||||||||||
GA | 16 | 73.25 ± 30.17 | 4.33 ± 0.70 b | 16.88 ± 2.42 | 13.78 ± 2.15 | 2.56 ± 0.51 | 5.36 ± 0.82 b | 1.50 ± 0.22 | 2.23 ± 0.50 | 1.14 ± 0.19 | 0.91 ± 0.09 | 0.89 ± 0.11 | 2.67 ± 0.30 | |||||||||||
p-value | - | 0.081 | 0.041 * | 0.095 | 0.081 | 0.147 | 0.038 * | 0.070 | 0.073 | 0.445 | 0.139 | 0.269 | 0.987 | |||||||||||
c.181A>G | AA | 187 | 91.04 ± 43.05 | 4.68 ± 0.72 | 17.93 ± 2.65 | 14.75 ± 2.29 | 2.75 ± 0.53 | 5.80 ± 0.91 | 1.60 ± 0.24 | 2.45 ± 0.50 | 1.18 ± 0.23 | 0.94 ± 0.09 | 0.93 ± 0.16 | 2.68 ± 0.32 | ||||||||||
AG | 12 | 98.50 ± 51.91 | 4.72 ± 0.89 | 18.48 ± 3.92 | 15.18 ± 3.51 | 2.78 ± 0.69 | 6.09 ± 1.16 | 1.66 ± 0.26 | 2.60 ± 0.59 | 1.26 ± 0.25 | 0.96 ± 0.11 | 0.97 ± 0.21 | 2.63 ± 0.35 | |||||||||||
GG | 1 | 82.00 ± 0.00 | 4.60 ± 0.00 | 18.00 ± 0.00 | 14.50 ± 0.00 | 2.50 ± 0.00 | 6.00 ± 0.00 | 1.60 ± 0.00 | 2.30 ± 0.00 | 1.10 ± 0.00 | 0.90 ± 0.00 | 0.90 ± 0.00 | 2.69 ± 0.00 | |||||||||||
p-value | - | 0.828 | 0.979 | 0.802 | 0.829 | 0.875 | 0.557 | 0.741 | 0.570 | 0.502 | 0.790 | 0.783 | 0.870 | |||||||||||
AA/AG | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.863 | 1.000 | 0.931 | 0.798 | 1.000 | 1.000 | 1.000 | |||||||||||
AG/GG | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | |||||||||||
c.193G>A | GG/AA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | ||||||||||
GG | 101 | 93.62 ± 47.51 | 4.71 ± 0.79 | 18.05 ± 2.89 | 14.88 ± 2.53 | 2.78 ± 0.58 | 5.83 ± 0.98 | 1.61 ± 0.25 | 2.47 ± 0.52 | 1.20 ± 0.24 | 0.95 ± 0.10 | 0.95 ± 0.17 | 2.66 ± 0.33 | |||||||||||
GA | 80 | 89.40 ± 40.78 | 4.67 ± 0.68 | 17.85 ± 2.64 | 14.66 ± 2.26 | 2.71 ± 0.48 | 5.81 ± 0.91 | 1.60 ± 0.24 | 2.46 ± 0.50 | 1.18 ± 0.23 | 0.94 ± 0.08 | 0.93 ± 0.17 | 2.68 ± 0.31 | |||||||||||
AA | 19 | 88.42 ± 30.70 | 4.59 ± 0.59 | 18.05 ± 2.23 | 14.68 ± 1.97 | 2.74 ± 0.47 | 5.80 ± 0.75 | 1.59 ± 0.21 | 2.34 ± 0.44 | 1.17 ± 0.17 | 0.93 ± 0.07 | 0.92 ± 0.11 | 2.72 ± 0.27 | |||||||||||
p-value | - | 0.771 | 0.804 | 0.883 | 0.823 | 0.695 | 0.986 | 0.916 | 0.584 | 0.842 | 0.494 | 0.667 | 0.736 | |||||||||||
GG/GA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | |||||||||||
GA/AA | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | |||||||||||
AA/GG | - | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 0.906 | 1.000 | 0.815 | 1.000 | 1.000 | |||||||||||
c.360C>T | CC | 76 | 86.60 ± 37.50 | 4.61 ± 0.70 | 17.74 ± 2.76 | 14.54 ± 2.37 | 2.68 ± 0.48 | 5.78 ± 0.89 | 1.58 ± 0.22 | 2.41 ± 0.50 | 1.16 ± 0.21 | 0.94 ± 0.08 | 0.92 ± 0.16 | 2.68 ± 0.31 | ||||||||||
CT | 99 | 92.46 ± 46.06 | 4.70 ± 0.75 | 17.99 ± 2.64 | 14.81 ± 2.30 | 2.77 ± 0.57 | 5.80 ± 0.93 | 1.62 ± 0.26 | 2.46 ± 0.50 | 1.20 ± 0.25 | 0.95 ± 0.09 | 0.93 ± 0.16 | 2.67 ± 0.32 | |||||||||||
TT | 25 | 102.08 ± 48.72 | 4.82 ± 0.71 | 18.56 ± 2.94 | 15.34 ± 2.64 | 2.86 ± 0.52 | 6.01 ± 1.01 | 1.62 ± 0.26 | 2.58 ± 0.55 | 1.22 ± 0.20 | 0.96 ± 0.13 | 1.00 ± 0.17 | 2.68 ± 0.36 | |||||||||||
p-value | - | 0.288 | 0.410 | 0.428 | 0.340 | 0.312 | 0.537 | 0.552 | 0.326 | 0.428 | 0.522 | 0.119 | 0.944 | |||||||||||
CC/CT | - | 1.000 | 1.000 | 1.000 | 1.000 | 0.899 | 1.000 | 0.937 | 1.000 | 0.901 | 0.890 | 1.000 | 1.000 | |||||||||||
CT/TT | - | 0.969 | 1.000 | 1.000 | 0.966 | 1.000 | 0.938 | 1.000 | 0.795 | 1.000 | 0.785 | 0.261 | 1.000 | |||||||||||
TT/CC | - | 0.370 | 0.629 | 0.586 | 0.440 | 0.461 | 0.839 | 1.000 | 0.405 | 0.791 | 0.659 | 0.120 | 1.000 |
2.3. Discussion
3. Experimental Section
3.1. Materials and Phenotypic Data Collection
3.2. PCR Amplification and SNP Identification
3.3. SNP Identification and Genotyping
3.4. Statistical Analysis
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Huang, H.; Wei, Y.; Meng, Z.; Zhang, Y.; Liu, X.; Guo, L.; Luo, J.; Chen, G.; Lin, H. Polymorphisms of Leptin-b Gene Associated with Growth Traits in Orange-Spotted Grouper (Epinephelus coioides). Int. J. Mol. Sci. 2014, 15, 11996-12006. https://doi.org/10.3390/ijms150711996
Huang H, Wei Y, Meng Z, Zhang Y, Liu X, Guo L, Luo J, Chen G, Lin H. Polymorphisms of Leptin-b Gene Associated with Growth Traits in Orange-Spotted Grouper (Epinephelus coioides). International Journal of Molecular Sciences. 2014; 15(7):11996-12006. https://doi.org/10.3390/ijms150711996
Chicago/Turabian StyleHuang, Hai, Yun Wei, Zining Meng, Yong Zhang, Xiaochun Liu, Liang Guo, Jian Luo, Guohua Chen, and Haoran Lin. 2014. "Polymorphisms of Leptin-b Gene Associated with Growth Traits in Orange-Spotted Grouper (Epinephelus coioides)" International Journal of Molecular Sciences 15, no. 7: 11996-12006. https://doi.org/10.3390/ijms150711996