Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats?
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. CNV Genotyping
2.3. Association Analysis
2.4. Cluster Analysis, LD Block, and Transcription Factor Binding Prediction
3. Results
3.1. Detection and Frequency Distribution Analysis
3.2. Association Analysis
3.3. Prediction of LD Block and Transcription Factor Binding
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Locus | CNV1 | CNV2 | CNV3 | CNV4 | CNV5 |
---|---|---|---|---|---|
Start | 30,065,201 | 30,086,001 | 30,116,801 | 30,121,201 | 30,180,401 |
End | 30,067,200 | 30,088,400 | 30,118,800 | 30,123,200 | 30,182,000 |
Length (bp) | 2000 | 2400 | 2000 | 2000 | 1600 |
Breed | Locus | Size | Frequency | ||
---|---|---|---|---|---|
Loss | Normal | Gain | |||
SBWC goat | CNV1 | n = 215 | 0.1163 (n = 25) | 0.1256 (n = 27) | 0.7581 (n = 163) |
CNV2 | n = 318 | 0.1384 (n = 44) | 0.1101 (n = 35) | 0.7515 (n = 239) | |
CNV3 | n = 318 | 0.1667 (n = 53) | 0.3019 (n = 96) | 0.5314 (n = 169) | |
CNV4 | n = 213 | 0.2113 (n = 45) | 0.3286 (n = 70) | 0.4601 (n = 98) | |
CNV5 | n = 302 | 0.0232 (n = 7) | 0.0232 (n = 7) | 0.9536 (n = 288) | |
GZHM goat | CNV1 | n = 203 | 0 (n = 0) | 0.0049 (n = 1) | 0.9951 (n = 202) |
CNV2 | n = 158 | 0.0696 (n = 11) | 0.0570 (n = 9) | 0.8734 (n = 138) | |
CNV3 | n = 150 | 0.1133 (n = 17) | 0.2800 (n = 42) | 0.6067 (n = 91) | |
CNV4 | n = 199 | 0.1206 (n = 24) | 0.2663 (n = 53) | 0.6131 (n = 122) | |
CNV5 | n = 158 | 0.0127 (n = 2) | 0 (n = 0) | 0.9873 (n = 156) | |
Nubian goat | CNV1 | n = 120 | 0 (n = 0) | 0.0083 (n = 1) | 0.9917 (n = 119) |
CNV2 | n = 120 | 0 (n = 0) | 0.0083 (n = 1) | 0.9917 (n = 119) | |
CNV3 | n = 116 | 0.1121 (n = 13) | 0.0603 (n = 7) | 0.8276 (n = 96) | |
CNV4 | n = 120 | 0.0417 (n = 5) | 0.0333 (n = 4) | 0.9250 (n = 111) | |
CNV5 | n = 120 | 0.0083 (n = 1) | 0 (n = 0) | 0.9917 (n = 119) |
Locus | Trait | Genotype (LSM ± SE) | p-Value | ||
---|---|---|---|---|---|
Loss | Normal | Gain | |||
CNV1 | Body Height (cm) | 58.98 ± 1.36 B (n = 25) | 60.92 ± 1.12 B (n = 27) | 65.49 ± 0.45 A (n = 163) | 6.1755 × 10−8 |
CNV2 | Height at Hip Cross (cm) | 60.36 ± 0.78 a (n = 44) | 59.02 ± 0.77 a (n = 35) | 57.87 ± 0.33 b (n = 239) | 0.013 |
CNV2 | Chest Width (cm) | 17.82 ± 0.41 B (n = 44) | 19.11 ± 0.59 A (n = 35) | 17.43 ± 0.18 B (n = 239) | 0.008 |
CNV3 | Cannon Bone Circumference (cm) | 7.81 ± 0.11 A (n = 53) | 8.01 ± 0.08 A (n = 96) | 7.37 ± 0.07 B (n = 169) | 2.5303 × 10−7 |
CNV3 | Chest Depth (cm) | 26.82 ± 0.36 a (n = 53) | 27.33 ± 0.26 a (n = 96) | 26.32 ± 0.23 b (n = 169) | 0.023 |
CNV4 | Body Length (cm) | 62.70 ± 1.14 b (n = 45) | 64.99 ± 0.67 a (n = 70) | 65.88 ± 0.46 a (n = 98) | 0.037 |
CNV5 | Chest Width (cm) | 20.40 ± 1.54 a (n = 7) | 18.80 ± 0.84 a (n = 7) | 17.41 ± 0.14 b (n = 288) | 0.011 |
CNV5 | Chest Depth (cm) | 28.40 ± 1.41 B (n = 7) | 30.10 ± 0.62 A (n = 7) | 26.68 ± 0.16 B (n = 288) | 0.010 |
Locus | Trait | Genotype (LSM ± SE) | p-Value | ||
---|---|---|---|---|---|
Loss | Normal | Gain | |||
CNV1 | Body Weight (kg) | - | 47.50 ± 0 (n = 1) | 32.74 ± 0.89 (n = 152) | - |
Body Height (cm) | - | 65.00 ± 0 (n = 1) | 63.46 ± 0.45 (n = 181) | - | |
Body Length (cm) | - | 70.00 ± 0 (n = 1) | 67.61 ± 0.50 (n = 181) | - | |
Chest Depth (cm) | - | 34.00 ± 0 (n = 1) | 32.29 ± 0.26 (n = 181) | - | |
Chest Width (cm) | - | 22.00 ± 0 (n = 1) | 22.27 ± 0.36 (n = 181) | - | |
Heart Girth (cm) | - | 84.00 ± 0 (n = 1) | 76.20 ± 0.54 (n = 181) | - | |
Cannon Bone Circumference (cm) | - | 8.00 ± 0 (n = 1) | 7.90 ± 0.03 (n = 181) | - | |
CNV2 | Body Weight (kg) | 32.5 ± 0.62 (n = 10) | 40.19 ± 0.14 (n = 9) | 32.22 ± 0.97 (n = 126) | 0.120 |
Body Height (cm) | 66.33 ± 1.40 (n = 9) | 64.11 ± 0.56 (n = 9) | 63.91 ± 0.53 (n = 123) | 0.495 | |
Body Length (cm) | 70.22 ± 1.23 (n = 9) | 70.22 ± 1.68 (n = 9) | 68.17 ± 0.66 (n = 123) | 0.523 | |
Chest Depth (cm) | 34.44 ± 0.50 (n = 9) | 33.66 ± 0.64 (n = 9) | 32.44 ± 0.33 (n = 123) | 0.186 | |
Chest Width (cm) | 22.67 ± 0.50 (n = 9) | 23.67 ± 0.74 (n = 9) | 22.02 ± 0.19 (n = 123) | 0.054 | |
Heart Girth (cm) | 81.00 ± 1.44 (n = 9) | 80.67 ± 0.69 (n = 9) | 76.66 ± 0.67 (n = 123) | 0.082 | |
Cannon Bone Circumference (cm) | 7.88 ± 0.16 (n = 9) | 8.00 ± 0.16 (n = 9) | 7.87 ± 0.04 (n = 123) | 0.564 | |
CNV3 | Body Weight (kg) | 31.41 ± 0.95 (n = 17) | 32.55 ± 1.66 (n = 35) | 32.83 ± 1.28 (n = 85) | 0.895 |
Body Height (cm) | 64.42 ± 0.76 (n = 14) | 64.30 ± 0.81 (n = 39) | 63.83 ± 0.75 (n = 80) | 0.926 | |
Body Length (cm) | 69.00 ± 0.85 (n = 14) | 67.85 ± 1.04 (n = 39) | 68.46 ± 0.87 (n = 80) | 0.775 | |
Chest Depth (cm) | 33.78 ± 0.54 (n = 14) | 32.28 ± 0.54 (n = 39) | 32.73 ± 0.44 (n = 80) | 0.166 | |
Chest Width (cm) | 22.71 ± 0.59 (n = 14) | 22.12 ± 0.33 (n = 39) | 22.13 ± 0.24 (n = 80) | 0.642 | |
Heart Girth (cm) | 78.57 ± 1.62 (n = 14) | 76.07 ± 1.07 (n = 39) | 77.53 ± 0.91 (n = 80) | 0.483 | |
Cannon Bone Circumference (cm) | 7.85 ± 0.14 (n = 14) | 7.87 ± 0.07 (n = 39) | 7.86 ± 0.05 (n = 80) | 0.994 | |
CNV4 | Body Weight (kg) | 33.06 ± 1.95 (n = 20) | 33.53 ± 1.88 (n = 34) | 32.71 ± 1.18 (n = 96) | 0.933 |
Body Height (cm) | 63.26 ± 1.01 (n = 23) | 63.86 ± 0.80 (n = 49) | 63.41 ± 0.62 (n = 107) | 0.894 | |
Body Length (cm) | 68.00 ± 1.06 (n = 23) | 67.80 ± 0.98 (n = 49) | 67.55 ± 0.68 (n = 107) | 0.950 | |
Chest Depth (cm) | 32.04 ± 0.64 (n = 23) | 32.59 ± 0.50 (n = 49) | 32.26 ± 0.35 (n = 107) | 0.797 | |
Chest Width (cm) | 22.04 ± 0.40 (n = 23) | 21.88 ± 0.26 (n = 49) | 22.51 ± 0.60 (n = 107) | 0.738 | |
Heart Girth (cm) | 76.26 ± 1.33 (n = 23) | 76.20 ± 1.12 (n = 49) | 76.27 ± 0.72 (n = 107) | 0.999 | |
Cannon Bone Circumference (cm) | 7.87 ± 0.09 (n = 23) | 7.84 ± 0.08 (n = 49) | 7.88 ± 0.04 (n = 107) | 0.764 | |
CNV5 | Body Weight (kg) | 29.30 ± 5.30 (n = 2) | - | 32.95 ± 0.93 (n = 143) | - |
Body Height (cm) | 54.00 ± 0 (n = 1) | - | 64.19 ± 0.49 (n = 140) | - | |
Body Length (cm) | 60.00 ± 0 (n = 1) | - | 68.49 ± 0.59 (n = 140) | - | |
Chest Depth (cm) | 27.00 ± 0 (n = 1) | - | 32.78 ± 0.30 (n = 140) | - | |
Chest Width (cm) | 20.00 ± 0 (n = 1) | - | 22.23 ± 0.18 (n = 140) | - | |
Heart Girth (cm) | 66.00 ± 0 (n = 1) | - | 77.32 ± 0.62 (n = 140) | - | |
Cannon Bone Circumference (cm) | 8.00 ± 0 (n = 1) | - | 7.87 ± 0.04 (n = 140) | - |
Locus | Trait | Genotype (LSM ± SE) | p-Value | ||
---|---|---|---|---|---|
Loss | Normal | Gain | |||
CNV1 | Body Weight (kg) | - | 47.55 ± 0.55 (n = 2) | 50.29 ± 0.98 (n = 118) | - |
Body Height (cm) | - | 75.15 ± 0.35 (n = 2) | 72.23 ± 0.50 (n = 118) | - | |
Body Length (cm) | - | 70.90 ± 1.30 (n = 2) | 65.05 ± 0.51 (n = 118) | - | |
Heart Girth (cm) | - | 89.50 ± 1.90 (n = 2) | 87.34 ± 0.78 (n = 118) | - | |
Chest Width (cm) | - | 21.15 ± 0.25 (n = 2) | 21.45 ± 0.39 (n = 118) | - | |
Chest Depth (cm) | - | 32.50 ± 2.00 (n = 2) | 34.91 ± 0.44 (n = 118) | - | |
Cannon Bone Circumference (cm) | - | 10.50 ± 0.80 (n = 2) | 10.41 ± 0.71 (n = 118) | - | |
CNV2 | Body Weight (kg) | 64.50 ± 0 (n = 1) | 44.52 ± 3.55 (n = 4) | 50.38 ± 1.00 (n = 112) | - |
Body Height (cm) | 73.00 ± 0 (n = 1) | 70.75 ± 1.02 (n = 4) | 72.18 ± 0.50 (n = 112) | - | |
Body Length (cm) | 68.50 ± 0 (n = 1) | 68.30 ± 1.86 (n = 4) | 64.95 ± 0.53 (n = 112) | - | |
Heart Girth (cm) | 97.30 ± 0 (n = 1) | 88.58 ± 1.16 (n = 4) | 87.11 ± 0.80 (n = 112) | - | |
Chest Width (cm) | 29.10 ± 0 (n = 1) | 21.60 ± 1.35 (n = 4) | 21.30 ± 0.41 (n = 112) | - | |
Chest Depth (cm) | 41.00 ± 0 (n = 1) | 32.80 ± 3.80 (n = 4) | 34.74 ± 0.43 (n = 112) | - | |
Cannon Bone Circumference (cm) | 10.50 ± 0 (n = 1) | 9.88 ± 0.55 (n = 4) | 10.42 ± 0.75 (n = 112) | - | |
CNV3 | Body Weight (kg) | 46.21 ± 1.46 (n = 13) | 52.53 ± 0.43 (n = 7) | 50.70 ± 1.02 (n = 96) | 0.309 |
Body Height (cm) | 69.77 ± 1.90 (n = 13) | 69.75 ± 2.55 (n = 7) | 72.56 ± 0.50 (n = 96) | 0.106 | |
Body Length (cm) | 63.95 ± 1.96 (n = 13) | 61.94 ± 0.78 (n = 7) | 65.45 ± 0.54 (n = 96) | 0.216 | |
Heart Girth (cm) | 32.33 ± 1.14 (n = 13) | 32.56 ± 1.58 (n = 7) | 35.13 ± 0.41 (n = 96) | 0.417 | |
Chest Width (cm) | 21.12 ± 1.24 (n = 13) | 18.75 ± 1.16 (n = 7) | 21.56 ± 0.44 (n = 96) | 0.251 | |
Chest Depth (cm) | 85.43 ± 1.50 (n = 13) | 83.96 ± 1.87 (n = 7) | 97.58 ± 0.84 (n = 96) | 0.060 | |
Cannon Bone Circumference (cm) | 9.51 ± 0.25 (n = 13) | 9.41 ± 0.20 (n = 7) | 10.60 ± 0.87 (n = 96) | 0.845 | |
CNV4 | Body Weight (kg) | 50.43 ± 3.16 (n = 6) | 47.77 ± 3.71 (n = 3) | 50.30 ± 1.01 (n = 111) | - |
Body Height (cm) | 69.77 ± 2.44 (n = 6) | 69.80 ± 1.61 (n = 3) | 72.48 ± 0.49 (n = 111) | - | |
Body Length (cm) | 65.88 ± 2.80 (n = 6) | 67.80 ± 2.66 (n = 3) | 65.04 ± 0.53 (n = 111) | - | |
Heart Girth (cm) | 88.18 ± 4.07 (n = 6) | 84.33 ± 5.58 (n = 3) | 87.38 ± 0.77 (n = 111) | - | |
Chest Width (cm) | 21.91 ± 2.01 (n = 6) | 18.37 ± 3.91 (n = 3) | 21.50 ± 0.40 (n = 111) | - | |
Chest Depth (cm) | 34.53 ± 2.78 (n = 6) | 32.07 ± 1.57 (n = 3) | 34.96 ± 0.44 (n = 111) | - | |
Cannon Bone Circumference | 9.67 ± 0.25 (n = 6) | 10.30 ± 1.15 (n = 3) | 10.46 ± 0.76 (n = 111) | - | |
CNV5 | Body Weight (kg) | 67.10 ± 0 (n = 1) | - | 50.01 ± 1.00 (n = 108) | - |
Body Height (cm) | 71.20 ± 0 (n = 1) | - | 72.05 ± 0.50 (n = 108) | - | |
Body Length (cm) | 67.50 ± 0 (n = 1) | - | 65.04 ± 0.53 (n = 108) | - | |
Heart Girth (cm) | 90.80 ± 0 (n = 1) | - | 87.04 ± 0.80 (n = 108) | - | |
Chest Width (cm) | 20.70 ± 0 (n = 1) | - | 21.27 ± 0.41 (n = 108) | - | |
Chest Depth (cm) | 34.30 ± 0 (n = 1) | - | 34.61 ± 0.42 (n = 108) | - | |
Cannon Bone Circumference (cm) | 9.00 ± 0 (n = 1) | - | 10.46 ± 0.78 (n = 108) | - |
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Bi, Y.; Wang, Z.; Wang, Q.; Liu, H.; Guo, Z.; Pan, C.; Chen, H.; Zhu, H.; Wu, L.; Lan, X. Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats? Animals 2022, 12, 1547. https://doi.org/10.3390/ani12121547
Bi Y, Wang Z, Wang Q, Liu H, Guo Z, Pan C, Chen H, Zhu H, Wu L, Lan X. Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats? Animals. 2022; 12(12):1547. https://doi.org/10.3390/ani12121547
Chicago/Turabian StyleBi, Yi, Zhiying Wang, Qian Wang, Hongfei Liu, Zhengang Guo, Chuanying Pan, Hong Chen, Haijing Zhu, Lian Wu, and Xianyong Lan. 2022. "Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats?" Animals 12, no. 12: 1547. https://doi.org/10.3390/ani12121547