Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Phenotypic Data Collection and DNA Extraction
2.2. Single Nucleotide Polymorphism Detection and Genotyping
2.3. Population Parameter Calculation and Quality Control
2.4. Single Nucleotide Polymorphism Association Analysis
2.5. The Haplotype Analysis
3. Results
3.1. Genotyping and Quality Control
3.2. Population Genetic Parameters
3.3. Single Nucleotide Polymorphisms Associated with Litter Size
3.4. The Haplotype Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sheep Breed | Litter Size | Total Samples | ||||
---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | ||
Hu sheep (sample size) | 3 | 2 | 2 | 2 | 1 | 10 |
Small-tailed Han sheep (sample size) | 3 | 3 | 2 | 2 | 0 | 10 |
SNP ID | Breed | MA | MAF | He | Ho | PIC | χ2 | p Value |
---|---|---|---|---|---|---|---|---|
KIT: g.70199073A>G | HUS | G | 0.19 | 0.30 | 0.31 | 0.26 | 0.21 | 0.6442 |
STH | G | 0.28 | 0.40 | 0.44 | 0.32 | 4.10 | 0.0430 | |
KITLG: g.124520653G>C | HUS | C | 0.10 | 0.19 | 0.19 | 0.17 | 0.01 | 0.9410 |
STH | C | 0.12 | 0.22 | 0.23 | 0.19 | 1.31 | 0.2530 | |
ADAMTS1: g.127751615C>T | HUS | - | - | - | - | - | - | - |
STH | T | 0.11 | 0.20 | 0.19 | 0.18 | 0.18 | 0.6729 | |
ADAMTS1: g.127753565T>C | HUS | C | 0.37 | 0.47 | 0.50 | 0.36 | 2.05 | 0.1519 |
STH | C | 0.46 | 0.50 | 0.53 | 0.37 | 1.93 | 0.1652 | |
ADAMTS1: g.127753643C>T | HUS | - | - | - | - | - | - | - |
STH | T | 0.20 | 0.32 | 0.31 | 0.27 | 0.45 | 0.5023 | |
ADAMTS1: g.127754640T>G | HUS | T | 0.48 | 0.50 | 0.54 | 0.37 | 3.19 | 0.0740 |
STH | G | 0.45 | 0.50 | 0.49 | 0.37 | 0.01 | 0.9216 | |
NCOA1: g.31928165C>T | HUS | T | 0.40 | 0.48 | 0.51 | 0.36 | 2.89 | 0.0891 |
STH | T | 0.33 | 0.44 | 0.45 | 0.35 | 0.10 | 0.7507 | |
NCOA1: g.31928230C>T | HUS | T | 0.15 | 0.26 | 0.27 | 0.23 | 0.83 | 0.3630 |
STH | T | 0.25 | 0.38 | 0.35 | 0.31 | 1.71 | 0.1916 | |
NCOA1: g.32072394C>T | HUS | T | 0.19 | 0.31 | 0.30 | 0.26 | 0.92 | 0.3371 |
STH | T | 0.22 | 0.34 | 0.36 | 0.28 | 1.54 | 0.2142 | |
NCOA1: g.32116034A>G | HUS | G | 0.22 | 0.34 | 0.32 | 0.28 | 1.60 | 0.2064 |
STH | G | 0.20 | 0.32 | 0.33 | 0.27 | 0.75 | 0.3867 | |
NCOA1: g.32140565G>A | HUS | A | 0.11 | 0.20 | 0.22 | 0.18 | 2.84 | 0.0922 |
STH | A | 0.20 | 0.32 | 0.32 | 0.27 | 0.03 | 0.8540 | |
NCOA1: g.32140837T>C | HUS | C | 0.24 | 0.36 | 0.34 | 0.30 | 2.13 | 0.1448 |
STH | C | 0.24 | 0.36 | 0.38 | 0.29 | 1.28 | 0.2589 | |
NPM1: g.3245714T>C | HUS | C | 0.43 | 0.49 | 0.49 | 0.37 | 0.04 | 0.8432 |
STH | T | 0.45 | 0.50 | 0.46 | 0.37 | 2.68 | 0.1019 | |
NPM1: g.3245741C>T | HUS | T | 0.43 | 0.49 | 0.50 | 0.37 | 0.07 | 0.7901 |
STH | C | 0.46 | 0.50 | 0.47 | 0.37 | 0.91 | 0.3407 | |
NPM1: g.3245965C>T | HUS | T | 0.43 | 0.49 | 0.49 | 0.37 | 0.01 | 0.9257 |
STH | C | 0.45 | 0.49 | 0.45 | 0.37 | 3.05 | 0.0808 | |
NPM1: g.3246266T>G | HUS | G | 0.24 | 0.36 | 0.34 | 0.30 | 3.12 | 0.0774 |
STH | G | 0.20 | 0.32 | 0.28 | 0.27 | 6.62 | 0.0101 | |
NPM1: g.3247499A>T | HUS | T | 0.29 | 0.41 | 0.44 | 0.33 | 2.04 | 0.1534 |
STH | T | 0.31 | 0.43 | 0.41 | 0.34 | 0.65 | 0.4218 | |
NPM1: g.3251189A>T | HUS | T | 0.42 | 0.49 | 0.49 | 0.37 | 0.00 | 0.9940 |
STH | T | 0.46 | 0.50 | 0.48 | 0.37 | 0.77 | 0.3811 | |
LIF: g.68801067C>T | HUS | - | - | - | - | - | - | - |
STH | T | 0.12 | 0.21 | 0.20 | 0.19 | 1.63 | 0.2019 | |
LIF: g.68816215C>T | HUS | T | 0.06 | 0.12 | 0.12 | 0.11 | 0.59 | 0.4418 |
STH | T | 0.11 | 0.19 | 0.19 | 0.17 | 0.00 | 0.9715 | |
LIFR: g.35813711C>T | HUS | T | 0.43 | 0.49 | 0.50 | 0.37 | 0.33 | 0.5646 |
STH | T | 0.32 | 0.43 | 0.44 | 0.34 | 0.03 | 0.8658 | |
LIFR: g.35814094C>T | HUS | T | 0.43 | 0.49 | 0.51 | 0.37 | 0.59 | 0.4418 |
STH | T | 0.32 | 0.44 | 0.44 | 0.34 | 0.10 | 0.7568 | |
LIFR: g.35813931G>A | HUS | T | 0.19 | 0.31 | 0.28 | 0.26 | 3.33 | 0.0680 |
STH | T | 0.29 | 0.41 | 0.37 | 0.33 | 3.88 | 0.0489 | |
LIFR: g.35813935A>G | HUS | G | 0.45 | 0.50 | 0.47 | 0.37 | 1.22 | 0.2690 |
STH | G | 0.35 | 0.46 | 0.41 | 0.35 | 4.52 | 0.0334 | |
LIFR: g.35817147A>G | HUS | G | 0.17 | 0.28 | 0.27 | 0.24 | 0.97 | 0.3250 |
STH | G | 0.27 | 0.40 | 0.40 | 0.32 | 0.00 | 0.9578 | |
LIFR: g.35817247G>A | HUS | A | 0.17 | 0.28 | 0.27 | 0.24 | 0.97 | 0.3250 |
STH | A | 0.27 | 0.40 | 0.40 | 0.32 | 0.00 | 0.9888 | |
LIFR: g.35835329G>A | HUS | A | 0.39 | 0.48 | 0.46 | 0.36 | 0.40 | 0.5280 |
STH | A | 0.43 | 0.49 | 0.53 | 0.37 | 2.54 | 0.1113 | |
LIFR: g.35835474G>T | HUS | T | 0.07 | 0.13 | 0.13 | 0.12 | 0.14 | 0.7117 |
STH | T | 0.23 | 0.35 | 0.37 | 0.29 | 0.66 | 0.4154 | |
LIFR: g.35841608T>C | HUS | C | 0.09 | 0.16 | 0.16 | 0.14 | 0.27 | 0.6044 |
STH | C | 0.23 | 0.35 | 0.37 | 0.29 | 1.07 | 0.3022 | |
LIFR: g.35845633T>C | HUS | T | 0.24 | 0.36 | 0.35 | 0.30 | 0.79 | 0.3743 |
STH | C | 0.15 | 0.25 | 0.27 | 0.22 | 1.64 | 0.2009 | |
LIFR: g.35847837A>G | HUS | G | 0.09 | 0.17 | 0.18 | 0.15 | 0.72 | 0.3954 |
STH | G | 0.25 | 0.37 | 0.38 | 0.30 | 0.43 | 0.5103 | |
LIFR: g.35847864A>T | HUS | T | 0.41 | 0.48 | 0.50 | 0.37 | 0.89 | 0.3463 |
STH | T | 0.42 | 0.49 | 0.54 | 0.37 | 5.34 | 0.0209 | |
LIFR: g.35848079G>A | HUS | A | 0.38 | 0.47 | 0.48 | 0.36 | 0.13 | 0.7151 |
STH | A | 0.42 | 0.49 | 0.52 | 0.37 | 2.27 | 0.1318 | |
LIFR: g.35848108A>G | HUS | G | 0.41 | 0.48 | 0.51 | 0.37 | 1.28 | 0.2571 |
STH | G | 0.45 | 0.49 | 0.56 | 0.37 | 8.43 | 0.0037 | |
LIFR: g.35847912C>T | HUS | T | 0.41 | 0.48 | 0.49 | 0.37 | 0.03 | 0.8553 |
STH | T | 0.43 | 0.49 | 0.53 | 0.37 | 2.63 | 0.1047 | |
LIFR: g.35851829T>C | HUS | C | 0.22 | 0.34 | 0.34 | 0.28 | 0.00 | 0.9701 |
STH | C | 0.18 | 0.30 | 0.30 | 0.25 | 0.33 | 0.5640 | |
LIFR: g.35853589T>C | HUS | C | 0.35 | 0.45 | 0.46 | 0.35 | 0.04 | 0.8470 |
STH | C | 0.42 | 0.49 | 0.51 | 0.37 | 0.70 | 0.4014 | |
LIFR: g.35853637T>G | HUS | G | 0.30 | 0.42 | 0.41 | 0.33 | 0.17 | 0.6765 |
STH | G | 0.37 | 0.46 | 0.50 | 0.36 | 2.46 | 0.1167 | |
LIFR: g.35853852T>C | HUS | C | 0.22 | 0.34 | 0.32 | 0.28 | 0.98 | 0.3211 |
STH | C | 0.13 | 0.23 | 0.23 | 0.20 | 0.01 | 0.9251 | |
LIFR: g.35862868C>T | HUS | T | 0.44 | 0.49 | 0.49 | 0.37 | 0.06 | 0.8061 |
STH | T | 0.48 | 0.50 | 0.55 | 0.37 | 4.63 | 0.0314 | |
LIFR: g.35862947G>T | HUS | T | 0.45 | 0.49 | 0.49 | 0.37 | 0.09 | 0.7616 |
STH | G | 0.49 | 0.50 | 0.55 | 0.37 | 5.07 | 0.0244 | |
LIFR: g.35867028T>C | HUS | C | 0.42 | 0.49 | 0.48 | 0.37 | 0.08 | 0.7815 |
STH | - | - | - | - | - | - | - | |
NGF: g.91795933T>C | HUS | C | 0.47 | 0.50 | 0.52 | 0.37 | 0.79 | 0.3734 |
STH | C | 0.40 | 0.48 | 0.46 | 0.37 | 0.72 | 0.3961 | |
NTRK1: g.105276945C>T | HUS | T | 0.34 | 0.45 | 0.42 | 0.35 | 3.18 | 0.0745 |
STH | T | 0.17 | 0.28 | 0.31 | 0.24 | 3.05 | 0.0807 | |
NTRK1: g.105288550C>G | HUS | C | 0.47 | 0.50 | 0.44 | 0.37 | 6.71 | 0.0096 |
STH | C | 0.46 | 0.50 | 0.44 | 0.37 | 5.47 | 0.0193 |
SNP ID | Gene Symbol | Genotype | Hu Sheep | Small-Tailed Han Sheep | ||
---|---|---|---|---|---|---|
N | Mean ± S.D. | N | Mean ± S.D. | |||
KIT: g.70199073A>G | KIT (intron 2) | AA | 354 | 2.25 ± 1.05 | 211 | 1.88 ± 0.78b |
GA | 166 | 2.13 ± 1.02 | 185 | 1.94 ± 0.85ab | ||
GG | 17 | 2.12 ± 1.32 | 24 | 2.42 ± 0.83a | ||
p-value | 0.42 | 0.00945 ** | ||||
KITLG: g.124520653G>C | KITLG (intron 9) | CC | 6 | 3.17 ± 0.75a | 4 | 1.50 ± 0.58 |
GC | 100 | 2.10 ± 1.11b | 97 | 1.93 ± 0.79 | ||
GG | 431 | 2.22 ± 1.03ab | 319 | 1.94 ± 0.84 | ||
p-value | 0.0461 * | 0.568 | ||||
ADAMTS1: g.127753565T>C | ADAMTS1 (exon 5) Ser→Ser | CC | 66 | 2.24 ± 1.02ab | 114 | 2 ± 0.79 |
CT | 266 | 2.09 ± 1.02b | 223 | 1.93 ± 0.85 | ||
TT | 205 | 2.35 ± 1.07a | 83 | 1.84 ± 0.80 | ||
p-value | 0.0262 * | 0.42 | ||||
ADAMTS1: g.127754640G>T | ADAMTS1 (intron 7) | GG | 137 | 2.39 ± 1.07a | 86 | 1.88 ± 0.79 |
GT | 288 | 2.10 ± 1.01b | 207 | 1.94 ± 0.83 | ||
TT | 111 | 2.25 ± 1.11ab | 127 | 1.95 ± 0.84 | ||
p-value | 0.0297* | 0.817 | ||||
NCOA1: g.31928165C>T | NCOA1 (intron 1) | CC | 184 | 2.28 ± 1.09 | 185 | 1.98 ± 0.86a |
CT | 276 | 2.13 ± 1.01 | 189 | 1.97 ± 0.79a | ||
TT | 76 | 2.3 ± 1.08 | 45 | 1.60 ± 0.75b | ||
p-value | 0.217 | 0.0158* | ||||
NCOA1: g.32140565G>A | NCOA1 (intron 21) | AA | 3 | 3.00 ± 1.70 | 16 | 1.38 ± 0.50b |
GA | 116 | 2.25 ± 1.02 | 135 | 2.02 ± 0.84a | ||
GG | 418 | 2.19 ± 1.05 | 269 | 1.92 ± 0.82a | ||
p-value | 0.368 | 0.0109* | ||||
LIFR: g.35862868C>T | LIFR (intron 19) | CC | 169 | 2.19 ± 1.03 | 104 | 1.71 ± 0.81b |
CT | 262 | 2.21 ± 1.08 | 231 | 2.00 ± 0.83 a | ||
TT | 106 | 2.25 ± 1.01 | 84 | 2.04 ± 0.78a | ||
p-value | 0.91 | 0.0054** | ||||
LIFR: g.35862947G>T | LIFR (intron 19) | GG | 166 | 2.18 ± 1.03 | 90 | 1.74 ± 0.84b |
GT | 262 | 2.21 ± 1.08 | 233 | 1.96 ± 0.81ab | ||
TT | 109 | 2.23 ± 1.01 | 97 | 2.05 ± 0.82a | ||
p-value | 0.915 | 0.0309* | ||||
NGF: g.91795933T>C | NGF (intron 2) | CC | 115 | 2.32 ± 1.06 | 73 | 1.73 ± 0.79b |
CT | 278 | 2.13 ± 1.05 | 194 | 1.94 ± 0.85ab | ||
TT | 144 | 2.28 ±1.02 | 153 | 2.02 ± 0.79a | ||
p-value | 0.157 | 0.0418* |
SNP ID | QTL ID | QTL Region (Chr:Mb) | Distance (Mb) | Reference |
---|---|---|---|---|
KIT: g.70199073A>G | 13975 | Chr6:68.3-68.4 | 1.80 | [35] |
130449 | Chr6: 42.6-42.6 | 27.60 | [36] | |
154661 | Chr6: 29.4-29.4 | 40.80 | [21] | |
154662 | Chr6:29.4-29.4 | 40.80 | [21] | |
KITLG: g.124520653G>C | 14242 | Chr3:75.2-75.3 | 49.22 | [37] |
ADAMTS1: g.127753565T>C | - | - | - | - |
ADAMTS1: g.127754640G>T | - | - | - | - |
NCOA1: g.31928165C>T | 14242 | Chr3:75.2-75.3 | 43.27 | [37] |
NCOA1: g.32140565G>A | 14242 | Chr3:75.2-75.3 | 43.27 | [37] |
LIFR: g.35862868C>T | 154682 | Chr16:31.8-31.8 | 4.06 | [21] |
154683 | Chr16:31.8-31.8 | 4.06 | [21] | |
154684 | Chr16:31.9-31.9 | 3.96 | [21] | |
LIFR: g.35862947G>T | 154682 | Chr16:31.8-31.8 | 4.06 | [21] |
154683 | Chr16:31.8-31.8 | 4.06 | [21] | |
154684 | Chr16:31.9-31.9 | 3.96 | [21] | |
NGF: g.91795933T>C | - | - | - | - |
Haplotype Combination (n) | Litter Size (Mean ± S.D.) | p Value |
---|---|---|
H1H1 (87) | 1.70 ± 0.82b | 0.0284* |
H1H2 (214) | 1.97 ± 0.81a | |
H1H3 (17) | 1.76 ± 0.75ab | |
H2H2 (83) | 2.02 ± 0.78a | |
H2H3 (14) | 2.21 ± 1.05a |
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Yuan, Z.; Zhang, J.; Li, W.; Wang, W.; Li, F.; Yue, X. Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds. Animals 2019, 9, 958. https://doi.org/10.3390/ani9110958
Yuan Z, Zhang J, Li W, Wang W, Li F, Yue X. Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds. Animals. 2019; 9(11):958. https://doi.org/10.3390/ani9110958
Chicago/Turabian StyleYuan, Zehu, Junxia Zhang, Wanhong Li, Weimin Wang, Fadi Li, and Xiangpeng Yue. 2019. "Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds" Animals 9, no. 11: 958. https://doi.org/10.3390/ani9110958
APA StyleYuan, Z., Zhang, J., Li, W., Wang, W., Li, F., & Yue, X. (2019). Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds. Animals, 9(11), 958. https://doi.org/10.3390/ani9110958