GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Origin of Animals and Challenge to P. salmonis
2.2. Genotyping of Challenged Animals
2.3. Whole-Genome Sequence Data
2.4. Imputation to Whole Genome Sequence Level
2.5. Genome-Wide Association Study (GWAS)
2.6. Identification of Candidate Genes
3. Results
3.1. Summary Statistics
3.2. Quality Control of Genotypes and Imputation
3.3. Genome-Wide Association Studies
3.4. Gene Identification
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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Number of samples | 2130 | 102 | 2130 |
Initial SNPs | 46,482 | 22,649,022 | 579,960 |
Call-rate | 38,744 | 3,787,940 | 579,960 |
Minor allele frequency | 37,672 | 2,599,032 | 537,784 |
Hardy–Weinberg equilibrium | 31,215 | 2,382,000 | 488,979 |
Trait/Parameter | |||
---|---|---|---|
TD a | 13.59 | 36.18 | 0.27 (0.02) |
BS b | 0.045 | 0.134 | 0.25 (0.02) |
CHR a | START b | STOP c | p d | Name e | Trait f | Function g |
---|---|---|---|---|---|---|
3 | 15,087,418 | 15,094,391 | Cation-dependent mannose-6-phosphate receptor | TD | Lysosomal | |
3 | 15,408,170 | 15,722,916 | Pleckstrin homology domain containing, family G (with RhoGef domain) member 6 | TD | Apoptosis | |
3 | 66,685,266 | 66,751,795 | TSC22 domain family protein 1 | BS | Inflammation/Apoptosis | |
13 | 40,702,364 | 40,707,470 | Erythropoietin receptor | TD | Inflammation | |
17 | 48,001,343 | 48,015,360 | Striatin-interacting protein 1 homolog | BS | Organization of the cytoskeleton | |
26 | 12,843,404 | 12,851,300 | N-acetylgalactosamine-6-sulfatase-like | TD | Phagocytosis | |
26 | 12,858,495 | 12,910,113 | protein CBFA2T3 | TD | Immune response | |
26 | 26,219,318 | 26,284,525 | TOX high mobility group box family member 3 | TD | Immune response | |
26 | 18,051,513 | 18,080,240 | Myotubularin related protein 10 | TD/BS | Lipid metabolism | |
26 | 21,925,171 | 21,942,499 | AP-2 complex subunit alpha-2 | BS | Immune response | |
27 | 9,997,966 | 10,017,806 | Smoothelin protein 2 | TD | Immune response | |
27 | 10,055,887 | 10,086,375 | Leucine-rich repeat-containing protein 75A | TD | Immune response | |
27 | 10,112,119 | 10,185,117 | Unconventional myosin-Ic | TD | Immune response | |
27 | 10,192,105 | 10,217,956 | Large neutral amino acids transporter small subunit 4 | TD | Organization of the cytoskeleton | |
27 | 10,221,995 | 10,236,446 | Phosphatidylinositol transfer protein alpha | TD | Organization of the cytoskeleton | |
27 | 10,238,047 | 10,250,315 | Inositol polyphosphate 5-phosphatase K | TD | Organization of the cytoskeleton | |
27 | 10,252,627 | 10,257,723 | Tektin-1 | TD | Organization of the cytoskeleton | |
27 | 10,257,875 | 10,260,754 | F-box only protein 39-like | TD | immune response | |
27 | 10,260,862 | 10,263,488 | XIAP-associated factor 1 | TD | Apoptosis | |
27 | 10,384,815 | 10,405,300 | Bleomycin Hydrolase | TD | Immune response | |
27 | 10,409,313 | 10,439,943 | Sodium-dependent serotonin transporter | TD | Posttraumatic stress | |
27 | 10,606,714 | 10,608,776 | Mediator of RNA polymerase II transcription subunit 19a | TD | Inflammation | |
27 | 10,300,075 | 10,379,486 | RAP1 GTPase activating protein 2a | TD/BS | immune response | |
27 | 10,493,554 | 10,513,502 | Protein phosphatase Slingshot homolog 2 | TD/BS | Inflammation |
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Sánchez-Roncancio, C.; García, B.; Gallardo-Hidalgo, J.; Yáñez, J.M. GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss). Genes 2023, 14, 114. https://doi.org/10.3390/genes14010114
Sánchez-Roncancio C, García B, Gallardo-Hidalgo J, Yáñez JM. GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss). Genes. 2023; 14(1):114. https://doi.org/10.3390/genes14010114
Chicago/Turabian StyleSánchez-Roncancio, Charles, Baltasar García, Jousepth Gallardo-Hidalgo, and José M. Yáñez. 2023. "GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)" Genes 14, no. 1: 114. https://doi.org/10.3390/genes14010114
APA StyleSánchez-Roncancio, C., García, B., Gallardo-Hidalgo, J., & Yáñez, J. M. (2023). GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss). Genes, 14(1), 114. https://doi.org/10.3390/genes14010114