Table 2 Signatures of selection identified between resistant (Kiko or Spanish) and susceptible (Boer) goat breeds. Breeds compared (comparison), gene name, gene region, SNP name (chromosome and position), SNP, mutation type (synonymous or missense), and Fst value for the SNPs under selection
From: Signatures of selection for resistance to Haemonchus contortus in sheep and goats
Comparison | Gene | Region | SNP name | SNP | MAF across breeds | Mutation | Fst (Bayesian) | Fst (Frequentist) | alpha |
|---|---|---|---|---|---|---|---|---|---|
Kiko and Spanish vs Boer (Resistant and Resistant vs Susceptible) | IL12A | 5’UTR | CHR1: 106973801 | A/G | Boer: 0, Kiko: 0.3, Spanish:0 |  | 0.23 | 0.4 | 0.55 |
TLR4 | Exon 3 | CHR8:106725462 | T/C | Boer: 0.05, Kiko: 0.36, Spanish: 0 | Synonymous (Ser → Ser) | 0.30 | 0.36 | 0.91 | |
TLR4 | Exon 3 | CHR8:106725265 | A/G | Boer: 0.05, Kiko: 0.3, Spanish: 0 | Synonymous (Leu → Leu) | 0.28 | 0.35 | 1 | |
ITGA9 | 3’UTR | CHR22:11106216 | A/T | Boer: 0.48, Kiko: 0.42, Spanish: 0 |  | 0.28 | 0.36 | 0.75 | |
Kiko vs Boer (Resistant vs Susceptible) | CD86 | Intron 1 | CHR1:66217253 | C/T | Boer: 0, Kiko: 0.15 | Â | 0.21 | 0.54 | 0.46 |
Spanish vs Boer (Resistant vs Susceptible) | CD1D | Exon 2 | CHR3:107890049 | T/G | Boer: 0.20, Spanish: 0.28 | Synonymous (Ser → Ser) | 0.27 | 0.61 | 0.57 |
TGFB2 | 3’UTR | CHR16:20438403 | T/G | Boer: 0, Spanish: 0.38 |  | 0.35 | 0.22 | 0.98 | |
ITGA9 | 3’UTR | CHR22:11106216 | A/T | Boer: 0.48, Spanish: 0 |  | 0.21 | 0.37 | 0.3 | |
IL13RA1 | 3’UTR | CHRX:25115674 | G/T | Boer: 0, Spanish: 0.27 |  | 0.22 | 0.21 | 0.3 | |
Spanish vs Kiko (Resistant vs Resistant) | TLR4 | Exon 3 | CHR8:106725462 | T/C | Kiko: 0.36, Spanish: 0 | Synonymous (Ser → Ser) | 0.3 | 0.45 | 1 |
TLR4 | Exon 3 | CHR8:106725265 | A/G | Kiko: 0.3, Spanish: 0 | Synonymous (Leu → Leu) | 0.29 | 0.45 | 1 | |
TLR4 | Exon 4 | CHR8:106725156 | G/A | Kiko: 0.32, Spanish:0 | Synonymous (His → His) | 0.29 | 0.44 | 0.99 | |
TLR4 | Exon 4 | CHR8:106725045 | C/T | Kiko: 0.34, Spanish:0 | Synonymous (Leu → Leu) | 0.29 | 0.43 | 0.99 | |
ITGA9 | 3’UTR | CHR22:11106216 | A/T | Kiko: 0.42, Spanish: 0 |  | 0.32 | 0.35 | 1 |