Table 2.
List of Protein-Coding Genes Overlapping SNPS Identified in the Top 0.00001 Proportion of PBS and Baypass Results (Raw Values, Mean of 9-SNP Sliding Windows, and Median of 9-SNP Sliding Windows)
| Test | Measure | Region | Gene(s) | Raw | Mean | Median |
|---|---|---|---|---|---|---|
| PBS | 1: 3613547 | COL6A3 | X | |||
| 6: 65810002 | GABRB1 | X | ||||
| 10: 83019595 | TNFSF13B | X | ||||
| 12: 1252208–1254663 | sox13 | X | X | |||
| 13: 23128001 | ARMC3 | X | ||||
| 13: 60735094–60737256 | TTLL9 | X | X | |||
| 19: 44257952 | ARHGEF3 | X | ||||
| 24: 1069638 | CLCN7, GNPTG | X | ||||
| Baypass | Altitude | 1: 3611207–3614677 | COL6A3 | X | X | |
| 1: 85041405 | slc25a24* | X | ||||
| 1: 137114512–137114990 | CHODL | X | ||||
| 1: 176389163–176390001 | CFAP44 | X | X | |||
| 6: 16572800 | COL25A1 | X | ||||
| 6: 45116627–45116714 | SEL1L3 | X | ||||
| 10: 49326426–49329922 | KLF12 | X | X | X | ||
| 11: 47750060 | ERN1 | X | ||||
| 12: 24880669 | SUSD4 | X | ||||
| 12: 50210421–50251954 | FHAD1 | X | ||||
| 12: 62775717 | ARPC5 | X | ||||
| 19: 12980756 | MYRIP | X | ||||
| 20: 18875378 | RUNX2 | X | ||||
| 23: 3614782–3625866 | ZNF407 | X | X | |||
| 24: 40438889 | GNA12 | X | ||||
| BIO2 | 2: 164700044 | GTDC1 | X | X | ||
| 3: 7650048 | wdr34 | X | ||||
| 5: 85161518 | TMEM161B | X | ||||
| 11: 14022260–14023453 | ?? | X | X | |||
| 12: 50249074 | FHAD1 | X | ||||
| 16: 1644696 | DOCK2 | X | ||||
| 18: 54417311 | WDR76 | X | ||||
| 18: 54472266 | FRMD5 | X | ||||
| 19: 17298138 | SRGAP3 | X | ||||
| 22: 14992803 | PLCE1 | X | ||||
| BIO5 | 3: 155499198–155500086 | SRGAP1 | X | X | ||
| 5: 17981229 | DOHH | X | ||||
| 6: 45116627–45116714 | SEL1L3 | X | ||||
| 9: 59109369 | EXT1 | X | ||||
| 10: 29455988 | eef1a1, RXFP2 | X | ||||
| 10: 49326426–49329922 | KLF12 | X | X | X | ||
| 12: 24880669–24882063 | SUSD4 | X | ||||
| 12: 50233808 | FHAD1 | X | ||||
| 14: 36257047 | WWP2 | X | ||||
| 17: 4544219 | fhdc1 | X | ||||
| 18: 5985784 | MEF2A | X | ||||
| 23: 3624493 | ZNF407 | X | ||||
| 24: 40438889 | GNA12 | X | ||||
| BIO12 | 1: 84016733 | NTNG1 | X | |||
| 1: 128633412 | APP | X | ||||
| 2: 146151992 | KCNH7 | X | ||||
| 2: 243930374–243935443 | USP48 | X | ||||
| 8: 66843820 | ADGRG6 | X | ||||
| 8: 75177143 | CCDC170 | X | ||||
| 8: 84032474 | PRKN | X | ||||
| 11: 11682275 | BCAS3 | X | ||||
| 24: 39452609–39488863 | sdk1 | X | X | X | ||
| BIO16 | 1: 243634916 | SLC9A9 | X | |||
| 3: 212789216 | CACNA1C | X | ||||
| 11: 11862030–11862364 | BCAS3 | X | X | |||
| 11: 46933828 | TANC2 | X | ||||
| 13: 20669196 | PLXDC2 | X | ||||
| 18: 21134743 | CRTC3 | X | ||||
| 19: 4490590 | RBMS3 | X | ||||
| 23: 34985947 | GREB1L | X |
Genes in small letters indicate that they are not named within the Ovis aries v3.1 annotation (for most genes, orthologs were identified in goat or cattle reference genomes, otherwise, indicated by *, orthologs were identified in another reference genome; ?? indicates no gene was identified for any ortholog). Regions indicate the range of SNP positions that overlapped with the named gene. The results cover the PBS analysis and Baypass analyses for altitude, BIO2 (Mean Diurnal Range), BIO5 (Max Temp of Warmest Month), BIO12 (Annual Precipitation), and BIO16 (Precipitation of Wettest Quarter).