Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. DNA Samples and Data Collection
2.2. DNA Isolation and Genomic DNA Pools Construction
2.3. Primer Design and PCR Amplification
2.4. Statistical Analyses
3. Results
3.1. InDel Identification and Distribution
3.2. Population Genetic Analysis of Six Mutation Sites in Seven Varieties
3.3. InDel Association Analyses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Breed | Abbreviation | Sampling Location | n | Sample Form |
---|---|---|---|---|
Small tail han | STHS | Lanzhou city (Gansu province) | 184 | Musculature of ear margin |
Tong | TS | Baishui county (Shanxi province) | 268 | Venous blood |
Lanzhou fat-tail | LFTS | Lanzhou city (Gansu province) | 67 | Musculature of ear margin |
Hu | HS | Huzhou city (Zhejiang province) | 166 | Venous blood |
Duolang | DLS | Shihezi city (Xinjiang autonomous region) | 92 | Venous blood |
Bashbay | BBS | Shihezi city (Xinjiang autonomous region) | 96 | Venous blood |
Altay | ATS | Altay city (Xinjiang autonomous region) | 96 | Venous blood |
Total | 969 |
Gene(Gene ID) | Name | Primer Sequences (5′-3′) | Product Size (bp) | Notes |
---|---|---|---|---|
GHR (443333) | GHR-21 | F: CGGTCCAATTCACCAGAT | 202 − 23 | Upstream |
R: AGAATCCCACGGACAAAG | ||||
GHR-43 | F: CTGTGAAGTCTCACCAGTGC | 77 + 23 | Upstream | |
R: GGATAGGCAGAATGCTAAAG | ||||
GHR-44 | F: GAAATACCCTTGTGGACAGA | 245 − 31 | Upstream | |
R: CTGGATTTATTGTTATTGTCTATTG | ||||
GHR-53 | F: ATGTTAGGCAGCCAAAAGG | 200 + 23 | 1st intron | |
R: GCCCAACCCAATGTTAATAGA | ||||
GHRH (100101237) | GHRH | F: ACGACTGAAGCGATTTAGCAC | 159 + 6 | Promoter region |
R: TCCATCTGTAAAATGGGCATG | ||||
GHRHR (443511) | GHRHR-2 | F: AACCCCTGTCTCAGTTTCTCC | 129 + 21 | 12th intron |
R: GATCTCAGTCCTCACCTCCAA |
Locus | Breed | Size | Genotypic Frequency | Allelic Frequency | Population Parameters | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
n | II | ID | DD | I | D | Ho | He | Ne | PIC | ||
GHR-21 | HS | 184 | 161 | 18 | 5 | 0.924 | 0.076 | 0.859 | 0.141 | 1.164 | 0.131 |
STHS | 268 | 203 | 57 | 8 | 0.864 | 0.136 | 0.765 | 0.235 | 1.308 | 0.208 | |
LFTS | 67 | 52 | 13 | 2 | 0.873 | 0.127 | 0.778 | 0.222 | 1.285 | 0.197 | |
TS | 166 | 146 | 20 | 0 | 0.940 | 0.060 | 0.887 | 0.113 | 1.128 | 0.107 | |
ATS | 92 | 53 | 36 | 3 | 0.772 | 0.228 | 0.648 | 0.352 | 1.544 | 0.290 | |
BBS | 96 | 78 | 15 | 3 | 0.891 | 0.109 | 0.805 | 0.195 | 1.242 | 0.176 | |
DLS | 96 | 63 | 31 | 2 | 0.818 | 0.182 | 0.702 | 0.298 | 1.425 | 0.254 | |
GHR-43 | HS | 184 | 132 | 47 | 5 | 0.845 | 0.155 | 0.738 | 0.262 | 1.355 | 0.228 |
STHS | 268 | 133 | 111 | 24 | 0.703 | 0.297 | 0.583 | 0.417 | 1.716 | 0.330 | |
LFTS | 67 | 37 | 16 | 4 | 0.672 | 0.328 | 0.621 | 0.389 | 1.610 | 0.307 | |
TS | 165 | 114 | 49 | 2 | 0.839 | 0.161 | 0.730 | 0.270 | 1.369 | 0.233 | |
ATS | 92 | 76 | 16 | 0 | 0.913 | 0.087 | 0.841 | 0.159 | 1.189 | 0.146 | |
BBS | 96 | 41 | 47 | 8 | 0.672 | 0.328 | 0.559 | 0.441 | 1.789 | 0.344 | |
DLS | 96 | 66 | 28 | 2 | 0.833 | 0.167 | 0.722 | 0.278 | 1.385 | 0.239 | |
GHR-44 | HS | 184 | 142 | 38 | 4 | 0.875 | 0.125 | 0.781 | 0.219 | 1.280 | 0.377 |
STHS | 268 | 184 | 76 | 8 | 0.828 | 0.172 | 0.716 | 0.284 | 1.397 | 0.244 | |
LFTS | 67 | 45 | 19 | 3 | 0.813 | 0.187 | 0.696 | 0.304 | 1.436 | 0.257 | |
TS | 166 | 62 | 83 | 21 | 0.623 | 0.377 | 0.531 | 0.469 | 1.885 | 0.359 | |
ATS | 92 | 54 | 26 | 12 | 0.728 | 0.272 | 0.604 | 0.396 | 1.655 | 0.317 | |
BBS | 96 | 53 | 39 | 4 | 0.755 | 0.245 | 0.630 | 0.370 | 1.587 | 0.301 | |
DLS | 96 | 82 | 11 | 3 | 0.911 | 0.089 | 0.839 | 0.161 | 1.192 | 0.148 | |
GHR-53 | HS | 184 | 49 | 97 | 38 | 0.530 | 0.470 | 0.502 | 0.498 | 1.993 | 0.374 |
STHS | 268 | 70 | 114 | 84 | 0.474 | 0.526 | 0.501 | 0.499 | 1.994 | 0.374 | |
LFTS | 67 | 17 | 29 | 21 | 0.470 | 0.530 | 0.502 | 0.498 | 1.993 | 0.374 | |
TS | 166 | 16 | 98 | 52 | 0.392 | 0.608 | 0.524 | 0.476 | 1.910 | 0.363 | |
ATS | 92 | 25 | 46 | 21 | 0.522 | 0.478 | 0.501 | 0.499 | 1.996 | 0.375 | |
BBS | 96 | 19 | 44 | 33 | 0.427 | 0.573 | 0.511 | 0.489 | 1.958 | 0.301 | |
DLS | 96 | 21 | 57 | 18 | 0.516 | 0.484 | 0.500 | 0.500 | 1.998 | 0.374 | |
GHRH | HS | 184 | 6 | 73 | 105 | 0.231 | 0.769 | 0.645 | 0.355 | 1.550 | 0.292 |
STHS | 268 | 24 | 68 | 176 | 0.216 | 0.784 | 0.661 | 0.339 | 1.513 | 0.282 | |
LFTS | 67 | 4 | 11 | 52 | 0.142 | 0.858 | 0.757 | 0.243 | 1.322 | 0.408 | |
TS | 166 | 23 | 53 | 90 | 0.298 | 0.702 | 0.581 | 0.419 | 1.720 | 0.331 | |
ATS | 92 | 3 | 24 | 65 | 0.163 | 0.837 | 0.727 | 0.273 | 1.375 | 0.236 | |
BBS | 96 | 6 | 34 | 56 | 0.240 | 0.760 | 0.636 | 0.364 | 1.573 | 0.298 | |
DLS | 96 | 1 | 13 | 82 | 0.078 | 0.922 | 0.856 | 0.144 | 1.168 | 0.134 | |
GHRHR-2 | HS | 184 | 167 | 15 | 2 | 0.948 | 0.052 | 0.902 | 0.097 | 1.109 | 0.093 |
STHS | 268 | 173 | 80 | 15 | 0.795 | 0.205 | 0.673 | 0.326 | 1.484 | 0.273 | |
LFTS | 67 | 42 | 17 | 8 | 0.754 | 0.246 | 0.502 | 0.498 | 1.993 | 0.374 | |
TS | 166 | 82 | 76 | 8 | 0.723 | 0.277 | 0.629 | 0.371 | 1.590 | 0.302 | |
ATS | 92 | 66 | 24 | 2 | 0.848 | 0.152 | 0.742 | 0.258 | 1.348 | 0.225 | |
BBS | 96 | 61 | 31 | 4 | 0.797 | 0.203 | 0.676 | 0.324 | 1.489 | 0.271 | |
DLS | 96 | 86 | 9 | 1 | 0.943 | 0.057 | 0.892 | 0.108 | 1.121 | 0.102 |
Loci | Breeds | Growth Traits | Observed Genotypes (LSM a ± SE) | p Values | ||
---|---|---|---|---|---|---|
II | ID | DD | ||||
GHR-21 | LFHS | Hip height (cm) | 77.92 a ± 1.27 (n = 25) | 71.50 b ± 2.07 (n = 7) | 84.50 a ± 3.50 (n = 2) | 0.019 |
GHR-43 | STHS | Body height (cm) | 62.60 b ± 0.45 (n = 90) | 64.26 a ± 0.46 (n = 80) | 62.37 a,b ± 0.85 (n = 20) | 0.023 |
STHS | Chest depth (cm) | 27.17 b ± 0.29 (n = 90) | 27.89 a,b ± 0.27 (n = 80) | 28.66 a ± 0.61 (n = 20) | 0.036 | |
TS | Hip width (cm) | 13.88 b ± 0.27 (n = 48) | 15.10 a,b ± 0.30 (n = 27) | 16.50 a ± 0.50 (n = 2) | 0.005 | |
GHR-44 | HS | Body weight (kg) | 32.73 a ± 0.36 (n = 141) | 31.03 b ± 0.83 (n = 38) | 27.18 b ± 1.94 (n = 4) | 0.009 |
STHS | Body height (cm) | 62.82 b ± 0.36 (n = 129) | 64.00 a,b ± 0.62 (n = 54) | 66.14 a ± 1.30 (n = 7) | 0.044 | |
TS | Head depth (cm) | 14.53 b ± 1.32 (n = 26) | 14.94 a ± 0.11 (n = 42) | 14.20 b ± 0.32 (n = 10) | 0.007 | |
GHR-53 | HS | Cannon girth (cm) | 6.96 b ± 0.09 (n = 49) | 7.12 a,b ± 0.05 (n = 97) | 7.25 a ± 0.10 (n = 38) | 0.049 |
STHS | Chest circumference (cm) | 72.20 a,b ± 0.78 (n = 52) | 71.00 b ± 0.61 (n = 83) | 73.60 a ± 0.91 (n = 55) | 0.043 | |
TS | Forehead width (cm) | 12.00 b ± 0.27 (n = 5) | 12.86 a ± 0.11 (n = 47) | 12.90 a ± 0.15 (n = 25) | 0.049 | |
GHRHR-2 | LFHS | Body weight (kg) | 47.27 b ± 2.96 (n = 23) | 58.95 a,b ± 4.88 (n = 8) | 62.87 a ± 3.68 (n = 3) | 0.050 |
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Wu, M.; Zhao, H.; Tang, X.; Li, Q.; Yi, X.; Liu, S.; Sun, X. Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds. Animals 2020, 10, 1883. https://doi.org/10.3390/ani10101883
Wu M, Zhao H, Tang X, Li Q, Yi X, Liu S, Sun X. Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds. Animals. 2020; 10(10):1883. https://doi.org/10.3390/ani10101883
Chicago/Turabian StyleWu, Mingli, Haidong Zhao, Xiaoqin Tang, Qi Li, Xiaohua Yi, Shirong Liu, and Xiuzhu Sun. 2020. "Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds" Animals 10, no. 10: 1883. https://doi.org/10.3390/ani10101883