Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples and Data Collection
2.2. Primer Design and Variation Genotyping
2.3. Dual-Luciferase Reporter Assay
2.4. Statistical Analysis
3. Results
3.1. Thirteen Variations Were Identified in Bovine PSAP
3.2. Population Parameters of 13 Variations in Four Cattle Breeds
3.3. Association between 13 Variations and Morphological Traits
3.4. Association of Four Haplotypes of PSAP 3’ UTR and Morphological Traits in NY Cattle
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Breed | Sampling Location | Population |
---|---|---|
QC (Qinchuan cattle) | Yangling, Shaanxi | 123 |
NY (Nanyang cattle) | Nanyang, Henan | 137 |
JX (Jiaxian red cattle) | Nanyang, Henan | 137 |
LX (Luxi cattle) | Jining, Shandong | 104 |
Primers | Sequence | Notes |
---|---|---|
PSAP-HAP1-F1 | TCGAGgtggaactagaggcacgctccatcctggagaagctgcagcgtcttttcctgGC | Vector construction |
PSAP-HAP1-R1 | GGCCGCcaggaaaagacgctgcagcttctccaggatggagcgtgcctctagttccacC | |
PSAP-HAP2-F2 | TCGAGgtggaactaggggcacgctccgtcctggagaagctgcagcgtcttttcctgGC | Vector construction |
PSAP-HAP2-R2 | GGCCGCcaggaaaagacgctgcagcttctccaggacggagcgtgcccctagttccacC | |
PSAP-HAP3-F3 | TCGAGgtggaactaggggcacgttccaccctggagaagctgcagcatcttttcctgGC | Vector construction |
PSAP-HAP3-R3 | GGCCGCcaggaaaagatgctgcagcttctccagggtggaacgtgcccctagttccacC | |
PSAP-HAP4-F4 | TCGAGgtggaactaggggcacgttccaccctggagaagctgcagcgtcttttcctgGC | Vector construction |
PSAP-HAP4-R4 | GGCCGCcaggaaaagacgctgcagcttctccagggtggaacgtgcccctagttccacC | |
PSAP-F | GGTGTCGGGTCCTCTTTCTG | Variations screening |
PSAP-R | GCGTGTCGGCATCTGTCTAG |
Locus | Breed | Size | Genotype Frequency | Allele Frequency | HWE | Population Parameters | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
N | GG | GA | AA | G | A | pValue | Ho | He | Ne | PIC | ||
P1 | LX | 104 | 11 | 6 | 87 | 0.135 | 0.865 | p < 0.05 | 0.767 | 0.233 | 1.304 | 0.206 |
QC | 123 | 6 | 21 | 96 | 0.134 | 0.866 | p < 0.05 | 0.768 | 0.232 | 1.303 | 0.205 | |
NY | 137 | 8 | 12 | 117 | 0.102 | 0.898 | p < 0.05 | 0.817 | 0.183 | 1.225 | 0.167 | |
JX | 137 | 12 | 40 | 85 | 0.234 | 0.766 | p < 0.05 | 0.642 | 0.358 | 1.558 | 0.294 | |
N | CC | TC | TT | C | T | pValue | Ho | He | Ne | PIC | ||
P2 | LX | 104 | 65 | 19 | 20 | 0.716 | 0.284 | p < 0.05 | 0.594 | 0.406 | 1.685 | 0.324 |
QC | 123 | 93 | 24 | 6 | 0.854 | 0.146 | p < 0.05 | 0.750 | 0.250 | 1.333 | 0.219 | |
NY | 137 | 99 | 17 | 21 | 0.785 | 0.215 | p < 0.05 | 0.662 | 0.338 | 1.510 | 0.281 | |
JX | 137 | 113 | 21 | 3 | 0.901 | 0.099 | p < 0.05 | 0.822 | 0.178 | 1.216 | 0.162 | |
N | CC | TC | TT | C | T | pValue | Ho | He | Ne | PIC | ||
P3 | LX | 104 | 88 | 7 | 9 | 0.880 | 0.120 | p < 0.05 | 0.789 | 0.211 | 1.268 | 0.189 |
QC | 123 | 14 | 6 | 103 | 0.138 | 0.862 | p < 0.05 | 0.762 | 0.238 | 1.313 | 0.210 | |
NY | 137 | 111 | 13 | 13 | 0.858 | 0.142 | p < 0.05 | 0.756 | 0.244 | 1.323 | 0.214 | |
JX | 137 | 122 | 12 | 3 | 0.934 | 0.066 | p < 0.05 | 0.877 | 0.123 | 1.140 | 0.115 | |
N | GG | GA | AA | G | A | pValue | Ho | He | Ne | PIC | ||
P4 | LX | 104 | 91 | 5 | 8 | 0.899 | 0.101 | p < 0.05 | 0.818 | 0.182 | 1.222 | 0.165 |
QC | 123 | 107 | 15 | 1 | 0.930 | 0.070 | p < 0.05 | 0.871 | 0.129 | 1.148 | 0.120 | |
NY | 137 | 113 | 13 | 11 | 0.872 | 0.128 | p < 0.05 | 0.777 | 0.223 | 1.287 | 0.198 | |
JX | 137 | 122 | 12 | 3 | 0.934 | 0.066 | p < 0.05 | 0.877 | 0.123 | 1.140 | 0.115 | |
N | CC | TC | TT | C | T | pValue | Ho | He | Ne | PIC | ||
P5 | LX | 104 | 33 | 21 | 50 | 0.418 | 0.582 | p < 0.05 | 0.513 | 0.487 | 1.948 | 0.368 |
QC | 123 | 9 | 27 | 87 | 0.183 | 0.817 | p < 0.05 | 0.701 | 0.299 | 1.426 | 0.254 | |
NY | 137 | 30 | 18 | 89 | 0.285 | 0.715 | p < 0.05 | 0.593 | 0.407 | 1.687 | 0.324 | |
JX | 137 | 8 | 47 | 82 | 0.230 | 0.770 | p < 0.05 | 0.646 | 0.354 | 1.548 | 0.291 | |
N | GG | GC | CC | G | C | pValue | Ho | He | Ne | PIC | ||
P12 | LX | 104 | 48 | 28 | 28 | 0.596 | 0.404 | p < 0.05 | 0.518 | 0.482 | 1.929 | 0.366 |
QC | 123 | 24 | 42 | 57 | 0.366 | 0.634 | p < 0.05 | 0.536 | 0.464 | 1.866 | 0.356 | |
NY | 137 | 54 | 30 | 53 | 0.504 | 0.496 | p < 0.05 | 0.500 | 0.500 | 2.000 | 0.375 | |
JX | 137 | 21 | 59 | 57 | 0.369 | 0.631 | p > 0.05 | 0.535 | 0.465 | 1.871 | 0.357 | |
N | CC | C- | -- | C | - | pValue | Ho | He | Ne | PIC | ||
P13 | LX | 104 | 32 | 14 | 58 | 0.375 | 0.625 | p < 0.05 | 0.531 | 0.496 | 1.882 | 0.359 |
QC | 123 | 26 | 67 | 30 | 0.484 | 0.516 | p > 0.05 | 0.501 | 0.499 | 1.998 | 0.375 | |
NY | 137 | 36 | 31 | 70 | 0.376 | 0.624 | p < 0.05 | 0.531 | 0.469 | 1.884 | 0.359 | |
JX | 137 | 34 | 44 | 59 | 0.409 | 0.591 | p < 0.05 | 0.517 | 0.483 | 1.936 | 0.367 |
Locus | Breed | Size | Genotype Frequency | Allele Frequency | HWE | Population Parameters | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
N | GG | GA | AA | G | A | pValue | Ho | He | Ne | PIC | ||
P6 (N1) | LX | 104 | 91 | 8 | 5 | 0.913 | 0.087 | p < 0.05 | 0.842 | 0.158 | 1.188 | 0.146 |
QC | 123 | 109 | 13 | 1 | 0.939 | 0.061 | p > 0.05 | 0.885 | 0.115 | 1.129 | 0.108 | |
NY | 137 | 115 | 10 | 12 | 0.876 | 0.124 | p < 0.05 | 0.783 | 0.217 | 1.278 | 0.194 | |
JX | 137 | 122 | 12 | 3 | 0.908 | 0.092 | p < 0.05 | 0.877 | 0.123 | 1.140 | 0.115 | |
N | CC | TC | TT | C | T | pValue | Ho | He | Ne | PIC | ||
P7 (N6) | LX | 104 | 101 | 1 | 2 | 0.976 | 0.024 | p < 0.05 | 0.953 | 0.046 | 1.049 | 0.046 |
QC | 123 | 113 | 9 | 1 | 0.955 | 0.045 | p > 0.05 | 0.914 | 0.085 | 1.093 | 0.082 | |
NY | 137 | 127 | 7 | 3 | 0.953 | 0.047 | p < 0.05 | 0.910 | 0.090 | 1.100 | 0.086 | |
JX | 137 | 132 | 3 | 2 | 0.947 | 0.053 | p < 0.05 | 0.950 | 0.050 | 1.052 | 0.049 | |
N | TT | TC | CC | T | C | pValue | Ho | He | Ne | PIC | ||
P8 (N8) | LX | 104 | 15 | 18 | 71 | 0.231 | 0.769 | p < 0.05 | 0.645 | 0.355 | 1.550 | 0.292 |
QC | 123 | 13 | 26 | 84 | 0.211 | 0.789 | p < 0.05 | 0.667 | 0.333 | 1.500 | 0.279 | |
NY | 137 | 91 | 25 | 21 | 0.755 | 0.245 | p < 0.05 | 0.630 | 0.369 | 1.586 | 0.301 | |
JX | 137 | 13 | 49 | 75 | 0.266 | 0.734 | p > 0.05 | 0.602 | 0.398 | 1.660 | 0.319 | |
N | AA | GA | GG | A | G | pValue | Ho | He | Ne | PIC | ||
P9 (N12) | LX | 104 | 85 | 7 | 12 | 0.851 | 0.149 | p < 0.05 | 0.746 | 0.254 | 1.340 | 0.221 |
QC | 123 | 99 | 16 | 8 | 0.870 | 0.130 | p < 0.05 | 0.774 | 0.226 | 1.293 | 0.201 | |
NY | 137 | 113 | 17 | 7 | 0.887 | 0.113 | p < 0.05 | 0.799 | 0.201 | 1.251 | 0.181 | |
JX | 137 | 92 | 33 | 12 | 0.770 | 0.230 | p < 0.05 | 0.670 | 0.330 | 1.491 | 0.275 | |
N | CC | TC | TT | C | T | pValue | Ho | He | Ne | PIC | ||
P10 (N13) | LX | 104 | 72 | 17 | 15 | 0.774 | 0.226 | P < 0.05 | 0.650 | 0.350 | 1.538 | 0.289 |
QC | 123 | 85 | 27 | 11 | 0.801 | 0.199 | p < 0.05 | 0.681 | 0.319 | 1.468 | 0.268 | |
NY | 137 | 92 | 29 | 16 | 0.777 | 0.223 | p < 0.05 | 0.654 | 0.346 | 1.529 | 0.286 | |
JX | 137 | 82 | 39 | 16 | 0.720 | 0.280 | p < 0.05 | 0.616 | 0.384 | 1.623 | 0.310 | |
N | AA | GA | GG | A | G | pValue | Ho | He | Ne | PIC | ||
P11 (N31) | LX | 104 | 11 | 7 | 86 | 0.139 | 0.861 | p < 0.05 | 0.760 | 0.240 | 1.316 | 0.211 |
QC | 123 | 11 | 19 | 93 | 0.167 | 0.833 | p < 0.05 | 0.722 | 0.278 | 1.385 | 0.239 | |
NY | 137 | 13 | 9 | 115 | 0.128 | 0.872 | p < 0.05 | 0.777 | 0.223 | 1.287 | 0.198 | |
JX | 137 | 4 | 27 | 106 | 0.124 | 0.876 | p > 0.05 | 0.777 | 0.223 | 1.287 | 0.198 |
Locus | Breed | Morphological Trait | Observed Genotypes (Mean a ± SE) | |||
---|---|---|---|---|---|---|
GG | GA | AA | p Value | |||
P1 | JX | Waist width (cm) | 41.38 b ± 2.60 (n = 8) | 42.13 ab ± 1.43 (n = 24) | 45.58 a ± 0.61 (n = 69) | 0.015 |
P1 | JX | Hucklebone width (cm) | 24.17 b ± 2.08 (n = 12) | 23.74 b ± 1.04 (n = 39) | 27.91 a ± 0.50 (n = 85) | 0.000 |
P1 | NY | Body length (cm) | 146.38 a ± 5.63 (n = 8) | 145.08 a ± 5.41 (n = 12) | 138.13 b ± 1.00 (n =115) | 0.038 |
TT | TC | CC | pValue | |||
P3 | LX | Abdominal circumference (cm) | 183.78 c ± 5.89 (n = 9) | 214.71 a ± 12.81 (n = 7) | 198.06 b ± 1.69 (n = 88) | 0.003 |
GG | GA | AA | pValue | |||
P4 | NY | Waist width (cm) | 44.59 b ± 0.84 (n = 45) | 49.83 ab ± 0.17 (n = 3) | 51.83 a ± 5.09 (n = 3) | 0.045 |
P4 | LX | Abdominal circumference (cm) | 197.79 b ± 1.68 (n = 89) | 216.14 a ± 12.43 (n = 7) | 183.75 c ± 6.62 (n = 8) | 0.002 |
GG | GA | AA | pValue | |||
N1 | NY | Abdominal circumference (cm) | 174.11 a ± 1.09 (n = 114) | 160.90 b ± 6.72 (n = 10) | 177.77 a ± 6.95 (n = 11) | 0.009 |
GG | GA | AA | pValue | |||
N12 | JX | Hucklebone width (cm) | 24.08 b ± 6.36 (n = 12) | 24.72 ab ± 6.61 (n = 32) | 27.27 a ± 5.18 (n = 92) | 0.033 |
GG | GA | AA | pValue | |||
N31 | NY | Abdominal circumference (cm) | 219.65 a ± 3.80 (n = 42) | 175.67 b ± 12.39 (n = 3) | 211.17 a ± 6.16 (n = 6) | 0.011 |
N31 | JX | Body length (cm) | 145.83 a ± 0.89 (n = 106) | 139.27 b ± 1.76 (n = 26) | 142.00 ab ± 5.40 (n = 4) | 0.005 |
N31 | JX | Waist width (cm) | 45.45 a ± 0.50 (n = 83) | 38.00 b ± 2.29 (n = 15) | 48.33 a ± 2.33 (n = 3) | 0.000 |
N31 | JX | Hucklebone width (cm) | 27.28 a ± 0.49 (n = 106) | 22.65 b ± 1.38 (n = 26) | 27.00 ab ± 2.65 (n = 4) | 0.001 |
CC | GC | GG | pValue | |||
P12 | NY | Abdominal circumference (cm) | 228.03 a ± 3.51 (n = 18) | 217.00 ab ± 8.18 (n = 13) | 204.70 b ± 5.89 (n = 20) | 0.016 |
P12 | LX | Waist width (cm) | 48.11 a ± 0.80 (n = 28) | 45.50 ab ± 1.14 (n = 28) | 44.23 b ± 0.78 (n = 48) | 0.011 |
P12 | LX | Body weight (kg) | 426.57 a ± 12.39 (n = 28) | 409.04 ab ± 20.17 (n = 28) | 367.69 b ± 10.27 (n = 48) | 0.029 |
Morphological Trait | Observed Genotypes (LSMa ± SE) | ||||
---|---|---|---|---|---|
AA-CC-AA-TT-GG | GG-CC-GG-TT-GG | GG-TT-AA-CC-AA | GG-TT-AA-CC-GG | p Value | |
Body height (cm) | 134.28 ± 1.34 a (n = 7) | 137.00 ± 1.96 a (n = 4) | 129.58 ± 1.40 b (n = 12) | 128.02 ± 0.59 b (n = 66) | 0.001 |
Body length (cm) | 146.00 ± 2.85 a (n = 7) | 152.00 ± 3.14 a (n = 4) | 140.42 ± 1.52 b (n = 12) | 139.11 ± 1.07 b (n = 66) | 0.007 |
Chest circumference (cm) | 184.57 ± 2.72 a (n = 7) | 189.50 ± 2.60 a (n = 4) | 176.17 ± 2.62 b (n = 12) | 174.16 ± 1.07 b (n = 66) | 0.001 |
Body weight (kg) | 440.86 ± 11.53 a (n = 7) | 440.25 ± 5.56 a (n = 4) | 398.42 ± 11.41 b (n = 12) | 395.06 ± 6.30 b (n = 66) | 0.040 |
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Zhao, H.; Wu, M.; Yi, X.; Tang, X.; Chen, P.; Wang, S.; Sun, X. Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits. Animals 2021, 11, 49. https://doi.org/10.3390/ani11010049
Zhao H, Wu M, Yi X, Tang X, Chen P, Wang S, Sun X. Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits. Animals. 2021; 11(1):49. https://doi.org/10.3390/ani11010049
Chicago/Turabian StyleZhao, Haidong, Mingli Wu, Xiaohua Yi, Xiaoqin Tang, Pingbo Chen, Shuhui Wang, and Xiuzhu Sun. 2021. "Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits" Animals 11, no. 1: 49. https://doi.org/10.3390/ani11010049
APA StyleZhao, H., Wu, M., Yi, X., Tang, X., Chen, P., Wang, S., & Sun, X. (2021). Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits. Animals, 11(1), 49. https://doi.org/10.3390/ani11010049