Expression of the SIRT2 Gene and Its Relationship with Body Size Traits in Qinchuan Cattle (Bos taurus)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Molecular Cloning and Sequence of the Bovine SIRT2 Gene
Species | GenBank Accession | Similarity |
---|---|---|
Sus scrofa | NP_001107743.1 | 93.30% |
Homo sapiens | NP_036369.2 | 88.92% |
Mus musculus | NP_001116237.1 | 85.27% |
Rattus norvegicus | NP_001008369.1 | 88.00% |
Gallus gallus | NP_001088636.1 | 68.63% |
Drosophila melanogaster | NP_001287422.1 | 49.86% |
Danio rerio | NP_955890.1 | 61.93% |
2.2. Ontogenic Expression of SIRT2 in Qinchuan Cattle
2.3. Genetic Polymorphism of Qinchuan Cattle SIRT2 and χ2 Test
Locus | Genotypic Frequencies (N) | Total | Allelic Frequencies | χ2 (HWE) | PIC | He | Ne | |||
---|---|---|---|---|---|---|---|---|---|---|
CC | CT | TT | C | T | ||||||
g.19501 C > T | 0.7991 | 0.2009 | 0 | 468 | 0.8996 | 0.1004 | 5.8328 | 0.1644 | 0.1807 | 1.2205 |
g.19518 C > T | 0.4103 | 0.4316 | 0.1581 | 468 | 0.6261 | 0.3739 | 2.8581 | 0.3586 | 0.4682 | 1.8805 |
2.4. Effects of Single Marker on Body Size Traits
Locus | Genotypes | BL (cm) | WH (cm) | RL (cm) | HW (cm) | CD (cm) | CC (cm) | PBW (cm) | BF (cm) | ULA (cm2) |
---|---|---|---|---|---|---|---|---|---|---|
g.19501 C > T | CC (374) | 132.608 ± 0.478 a | 119.222 ± 0.481 | 41.664 ± 0.201 | 38.286 ± 0.258 | 58.345 ± 0.315 | 161.993 ± 0.734 | 18.409 ± 0.142 | 0.873 ± 0.014 | 45.188 ± 0.673 |
CT (94) | 129.210 ± 0.721 b | 117.329 ± 0.770 | 41.287 ± 0.351 | 36.968 ± 0.324 | 57.159 ± 0.447 | 158.596 ± 0.959 | 17.776 ± 0283 | 0.860 ± 0.023 | 42.343 ± 0.962 | |
P-value | 0.0022 | 0.0593 | 0.3071 | 0.0204 | 0.1051 | 0.0193 | 0.0387 | 0.3685 | 0.0367 | |
g.19518 C > T | CC (192) | 130.844 ± 0.672 | 118.612 ± 0.671 | 41.099 ± 0.278 b | 37.177 ± 0.359 | 57.419 ± 0.440 | 159.276 ± 1.023 | 17.849 ± 0.197 | 0.850 ± 0.019 | 44.600 ± 2.162 |
CT (202) | 132.810 ± 0.655 | 118.381 ± 0.654 | 41.683 ± 0.271 | 38.649 ± 0.350 | 58.369 ± 0.429 | 162.552 ± 0.998 | 18.629 ± 0.193 | 0.883 ± 0.021 | 45.017 ± 2.246 | |
TT (74) | 133.682 ± 1.082 | 120.696 ± 0.882 | 42.608 ± 0.447 a | 38.500 ± 0.578 | 59.176 ± 0.522 | 163.203 ± 1.648 | 18.459 ± 0.318 | 0.890 ± 0.031 | 43.566 ± 1.554 | |
P-value | 0.0175 | 0.1004 | 0.0025 | 0.0031 | 0.0267 | 0.0127 | 0.0380 | 0.2007 | 0.2068 |
2.5. Linkage Disequilibrium (LD) and Haplotype Analysis
Haplotype | g.19501 C > T | g.19518 C > T | Frequency |
---|---|---|---|
Hap1 | C | C | 0.621 |
Hap2 | C | T | 0.279 |
Hap3 | T | T | 0.095 |
Hap4 | T | C | 0.005 |
2.6. Effects of Haplotype Combinations on Body Size Traits
Combined Genotypes | Body Measurement | Meat Quality Trait | |||||||
---|---|---|---|---|---|---|---|---|---|
BL (cm) | WH (cm) | RL (cm) | HW (cm) | CD (cm) | CC (cm) | PBW (cm) | BF (cm) | ULA (cm2) | |
Hap1/1 (188) | 131.016 ± 0.658 b | 118.332 ± 0.674 | 41.309 ± 0.281 | 37.319 ± 0.357 | 57.582 ± 0.440 | 159.297 ± 1.016 | 17.899 ± 0.197 b | 0.851 ± 0.020 | 44.054 ± 1.152 |
Hap1/2 (168) | 133.717 ± 0.696 a,b | 119.884 ± 0.713 a | 41.851 ± 0.297 | 39.089 ± 0.377 a | 58.919 ± 0.465 | 164.354 ± 1.075 a | 18.863 ± 0.209 | 0.891 ± 0.021 | 46.341 ± 1.073 |
Hap1/3 (34) | 125.359 ± 1.520 c | 113.779 ± 1.584 b | 40.294 ± 0.660 | 35.735 ± 0.839 b | 55.588 ± 0.881 b | 153.970 ± 2.389 b | 17.088 ± 0.464 b | 0.811 ± 0.046 | 40.579 ± 1.741 |
Hap2/2 (18) | 138.868 ± 1.776 a | 122.333 ± 1.399 a | 43.667 ± 0.907 | 40.726 ± 0.559 a | 60.944 ± 0.824 a | 168.121 ± 2.283 a | 19.500 ± 0.638 a | 0.927 ± 0.063 | 46.266 ± 1.271 |
Hap2/3 (56) | 132.009 ± 1.204 a,b | 119.438 ± 1.234 | 41.857 ± 0.514 | 37.788 ± 0.653 | 58.161 ± 0.806 | 161.464 ± 1.861 | 18.161 ± 0.362 | 0.898 ± 0.036 | 43.347 ± 2.271 |
P-value | 0.0004 | 0.0005 | 0.0028 | 0.0024 | 0.0023 | 0.0084 | 0.0019 | 0.1142 | 0.0192 |
3. Experimental Section
3.1. Bioinformatic Study
3.2. Collection of RNA Samples
3.3. RNA Purification and cDNA Synthesis
3.4. SYBR Green RT-PCR Analysis of Expression Patterns
Name | Function | Primer Sequence (5' to 3') | Tm (°C) | Product Length | Amplified Region |
---|---|---|---|---|---|
SIRT2 | RT-PCR | CAACCTGGAGAAATACCGTCTT | 61.0 | 166 bp | 400–565 |
CAGTCCTTTTTCCTTCAGCAG | |||||
β-actin | Reference | CACCAACTGGGACGACAT | 61.0 | 202 bp | 320–521 |
ATACAGGGACAGCACAGC | |||||
RPS9 | Reference | CCTCGACCAAGAGCTGAAG | 61.0 | 64 bp | 128–191 |
CCTCCAGACCTCACGTTTGTTC | |||||
GAPDH | Reference | CCAACGTGTCTGTTGTGGAT | 61.0 | 80 bp | 778–857 |
CTGCTTCACCACCTTCTTGA | |||||
Primer A | 3'UTR region amplification | ACCCCTGACCTCACCAAAT | 56.5 | 549 bp | 19411–19959 |
GCACCTTTCAGCACTCTTC | |||||
Primer B | 3'UTR region amplification | ACCCCTGACCTCACCAAAT | 62.3 | 138 bp | 19411–19548 |
CCTGTGGCCCCCTGAGCAGTTAGAGTCTAG |
3.5. Animal Source, Data Collection and Genomic DNA Isolation
3.6. PCR Amplification and Sequencing
3.7. DNA Pooling, PCR-RFLP and DNA Sequencing
3.8. Statistical Analysis
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Gui, L.-S.; Zhang, Y.-R.; Liu, G.-Y.; Zan, L.-S. Expression of the SIRT2 Gene and Its Relationship with Body Size Traits in Qinchuan Cattle (Bos taurus). Int. J. Mol. Sci. 2015, 16, 2458-2471. https://doi.org/10.3390/ijms16022458
Gui L-S, Zhang Y-R, Liu G-Y, Zan L-S. Expression of the SIRT2 Gene and Its Relationship with Body Size Traits in Qinchuan Cattle (Bos taurus). International Journal of Molecular Sciences. 2015; 16(2):2458-2471. https://doi.org/10.3390/ijms16022458
Chicago/Turabian StyleGui, Lin-Sheng, Ya-Ran Zhang, Gui-Yao Liu, and Lin-Sen Zan. 2015. "Expression of the SIRT2 Gene and Its Relationship with Body Size Traits in Qinchuan Cattle (Bos taurus)" International Journal of Molecular Sciences 16, no. 2: 2458-2471. https://doi.org/10.3390/ijms16022458
APA StyleGui, L.-S., Zhang, Y.-R., Liu, G.-Y., & Zan, L.-S. (2015). Expression of the SIRT2 Gene and Its Relationship with Body Size Traits in Qinchuan Cattle (Bos taurus). International Journal of Molecular Sciences, 16(2), 2458-2471. https://doi.org/10.3390/ijms16022458