Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data
2.2. Population Stratification
2.3. Selection Signature Detection
2.4. Marker-of-Interest Selection
2.5. Gene and Quantitative Trait Loci Research
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Group | Breed | Code | Animals |
---|---|---|---|
Meat | Angus | ANG | 62 |
Meat | Charolais | CHA | 46 |
Meat | Hereford | HFD | 31 |
Meat | Limousin | LMS | 44 |
Meat | Piedmontese | PMT | 24 |
Milk | Brown Swiss | BSW | 42 |
Milk | Holstein | HOL | 63 |
Milk | Jersey | JER | 49 |
Milk | Montbéliarde | MON | 30 |
Chromosome | Average FST Value | SNP FST | Average CDA Value | SNP CDA | Common SNPs |
---|---|---|---|---|---|
1 | 0.079 ± 0.008 | 38 | −1.67 ± 8.21 | 12 | – |
2 | 0.076 ± 0.003 | 24 | 0.72 ± 3.72 | 6 | – |
3 | 0.086 ± 0.006 | 19 | −1.76 ± 3.78 | 10 | – |
4 | 0.084 ± 0.009 | 29 | −0.13 ± 9.39 | 16 | – |
5 | 0.109 ± 0.011 | 31 | 0.91 ± 8.36 | 7 | – |
6 | 0.078 ± 0.005 | 30 | 1.40 ± 7.73 | 18 | – |
7 | 0.086 ± 0.008 | 24 | −1.58 ± 6.92 | 14 | 1 |
8 | 0.073 ± 0.001 | 9 | 1.26 ± 7.63 | 12 | – |
9 | 0.076 ± 0.005 | 14 | −0.38 ± 1.7 | 9 | – |
10 | 0.095 ± 0.018 | 26 | 0.76 ± 6.17 | 10 | 2 |
11 | 0.095 ± 0.014 | 23 | 2.09 ± 3.19 | 8 | – |
12 | 0.070 ± 0.002 | 6 | −1.44 ± 5.36 | 8 | – |
13 | 0.114 ± 0.020 | 16 | 1.49 ± 8.99 | 17 | – |
14 | 0.120 ± 0.019 | 28 | 2.41 ± 5.98 | 9 | 1 |
15 | 0.077 ± 0.007 | 11 | −0.31 ± 2.72 | 11 | – |
16 | 0.088 ± 0.008 | 17 | 3.19 ± 10.58 | 15 | 2 |
17 | 0.079 ± 0.006 | 10 | 2.04 ± 5.74 | 10 | 1 |
18 | 0.087 ± 0.006 | 19 | 4.47 ± 4.09 | 7 | 2 |
19 | 0.093 ± 0.020 | 11 | 1.60 ± 3.86 | 9 | – |
20 | 0.089 ± 0.023 | 14 | −1.27 ± 7.41 | 12 | – |
21 | 0.138 ± 0.053 | 11 | −0.04 ± 5.22 | 8 | 1 |
22 | 0.071 ± 0.003 | 6 | 0.72 ± 5.79 | 11 | – |
23 | 0.095 ± 0.037 | 6 | −1.21 ± 4.04 | 15 | – |
24 | 0.084 ± 0.014 | 15 | 1.79 ± 5.50 | 8 | 1 |
25 | 0.060 ± 0.003 | 12 | 3.98 ± 4.97 | 7 | – |
26 | 0.087 ± 0.007 | 19 | −1.52 ± 6.00 | 6 | 1 |
27 | 0.088 ± 0.011 | 9 | 1.48 ± 6.13 | 8 | – |
28 | 0.086 ± 0.016 | 15 | 5.68 ± 9.83 | 6 | – |
29 | 0.079 ± 0.009 | 10 | −2.78 ± 6.93 | 6 | – |
Total | 502 | 295 | 12 |
BTA | SNP Name | Position | CDA Score | FST Smoothed Value |
---|---|---|---|---|
7 | Hapmap53962-rs29017056 | 107,797,993 | 6.7711 | 0.0788 |
10 | ARS-BFGL-NGS-112081 | 36,489,310 | −1.1832 | 0.0750 |
10 | ARS-BFGL-NGS-34863 | 40,333,013 | −9.9492 | 0.0983 |
14 | ARS-BFGL-NGS-110022 | 38,481,264 | 7.8295 | 0.1158 |
16 | BTB-00639530 | 38,137,107 | 5.6524 | 0.0853 |
16 | ARS-BFGL-NGS-114895 | 38,205,760 | 33.8328 | 0.0940 |
17 | Hapmap44543-BTA-40914 | 39,220,916 | 14.5565 | 0.0821 |
18 | Hapmap47624-BTA-44484 | 12,578,668 | 0.9083 | 0.0931 |
18 | ARS-BFGL-NGS-100080 | 57,529,674 | 8.6108 | 0.0939 |
24 | BTB-00886858 | 34,750,786 | 7.6451 | 0.0959 |
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Congiu, M.; Cesarani, A.; Falchi, L.; Macciotta, N.P.P.; Dimauro, C. Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle. Genes 2024, 15, 1516. https://doi.org/10.3390/genes15121516
Congiu M, Cesarani A, Falchi L, Macciotta NPP, Dimauro C. Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle. Genes. 2024; 15(12):1516. https://doi.org/10.3390/genes15121516
Chicago/Turabian StyleCongiu, Michele, Alberto Cesarani, Laura Falchi, Nicolò Pietro Paolo Macciotta, and Corrado Dimauro. 2024. "Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle" Genes 15, no. 12: 1516. https://doi.org/10.3390/genes15121516
APA StyleCongiu, M., Cesarani, A., Falchi, L., Macciotta, N. P. P., & Dimauro, C. (2024). Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle. Genes, 15(12), 1516. https://doi.org/10.3390/genes15121516