Genome-Wide Association Study of Fiber Diameter in Alpacas
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. DNA Samples and Genotyping
2.3. Data Quality Control
2.4. Genome-Wide Association Study
2.4.1. Method 1. Linear Model
2.4.2. Method 2. Haplotype and Marker Analysis
2.4.3. Method 3. Selection Signatures
2.5. Candidate Regions
3. Results
3.1. Data Quality Control
3.2. Genome-Wide Association Study
3.2.1. Method 1. Linear Model
3.2.2. Method 2. Haplotype and Marker Analysis
3.2.3. Method 3. Selection Signatures
3.3. Candidate Regions
4. Discussion
4.1. Sample
4.2. Genome-Wide Association Study
4.3. Discussion by Method
4.3.1. Method 1. Linear Model
4.3.2. Method 2. Haplotype and Marker Analysis
4.3.3. Method 3. Selection Signatures
4.4. Gene Annotation
4.5. Candidate Regions
4.6. Genome Annotation
4.7. Future Studies
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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VPA | Scaffolds | Start | End | Methods | SNPs |
---|---|---|---|---|---|
6 | ABRR03077257.1 | 41319229 | 41714500 | Linear model—All the alpacas and selection signatures | AX-468770712 AX-417339934 AX-468704215 (*) AX-468766588 AX-417339050 AX-468763899 AX-468788057 AX-468767891 AX-417339948 AX-417339057 AX-468770136 AX-417339951 AX-468709166 |
9 | ABRR03004037.1 | 19580657 | 19719247 | Linear model—Extreme alpacas and selection signatures | AX-417305708 AX-468712525 |
29 | ABRR03000003.1 | 4613849 | 4659732 | Linear model—Extreme alpacas and selection signatures | AX-468751446 AX-417267477 AX-417266118 (*) |
na | ABRR03000033.1 | 13561792 | 14451734 | Linear model—All the alpacas and extreme alpacas | AX-417286284 AX-432730912 AX-417286293 AX-417284656 AX-417280615 AX-417286315 AX-417284681 |
VPA | Gene Name | Alpaca Scaffold | SNP | Distance (bp) Gene Marker | Method |
---|---|---|---|---|---|
2 | TACC3 | ABRR03000026.1 | AX-417277871 | 289,181 | Linear model—Extreme alpacas |
7 | PSMA2 | ABRR03008474.1 | AX-468769383 | 279,078 | Linear model—Extreme alpacas |
7 | POLD2 | ABRR03008474.1 | AX-468769383 | 446,076 | Linear model—Extreme alpacas |
27 | NTRK3 | ABRR03000011.1 | AX-468719480 | 127,219 | Linear model—Extreme alpacas |
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More, M.; Veli, E.; Cruz, A.; Gutiérrez, J.P.; Gutiérrez, G.; Ponce de León, F.A. Genome-Wide Association Study of Fiber Diameter in Alpacas. Animals 2023, 13, 3316. https://doi.org/10.3390/ani13213316
More M, Veli E, Cruz A, Gutiérrez JP, Gutiérrez G, Ponce de León FA. Genome-Wide Association Study of Fiber Diameter in Alpacas. Animals. 2023; 13(21):3316. https://doi.org/10.3390/ani13213316
Chicago/Turabian StyleMore, Manuel, Eudosio Veli, Alan Cruz, Juan Pablo Gutiérrez, Gustavo Gutiérrez, and F. Abel Ponce de León. 2023. "Genome-Wide Association Study of Fiber Diameter in Alpacas" Animals 13, no. 21: 3316. https://doi.org/10.3390/ani13213316