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Table 2 Genes, location, inferred or potential function, and origin of domestication signatures in alpaca and llama, revealed by FST outlier and extended haplotype homozygosity (XP-EHH) analysis

From: Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

Gene Chromosome Function Origin Domestic species FST, XP-EHH, or both
Anthrax toxin receptor 2 2 Anthrax resistance/susceptibility [15] Introgressed from llama Alpaca Both
Fibroblast growth factor 5 2 Longwool/shortwool fleece [16] Introgressed from llama Alpaca Both
C4orf22 2 ANTXR2, FGF5, C4orf22 region linked to high blood pressure susceptibility [17] Llama–Alpaca Alpaca Both
Luteinizing hormone receptor ChrUN Fecundity and development of male secondary sexual characters [38] Domestication Alpaca Both
Agouti signaling protein 19 Pigmentation [21, 22] Domestication Alpaca Both
Hypoxia upregulated 1 33 Cytoprotection under hypoxic conditions [39] Domestication Alpaca XP-EHH
Myomesin 1 24 Meat quality in cattle, sheep, and pigs [40,41,42] Domestication Alpaca FST
Melanocortin 5 receptor 23 Meat quality [43] Domestication Alpaca Both
Melanocortin 2 (adrenocorticotropic) receptor 24 Circadial rhythm [44] Domestication Alpaca FST
Melanocortin 1 receptor 24 Light fiber color [45] Domestication Alpaca FST
Olfactory receptor (OR5) family ChrUN Olfaction/dietary choice [14] Introgression from llama Alpaca FST
Olfactory receptor (OR2) family ChrUN Olfaction/dietary choice [14] Domestication Alpaca FST
G protein-coupled estrogen receptor 1 ChrUN Spatial memory and social behavior [46] Domestication Llama Both
Premelanosome protein ChrUN Skin and coat color in wild and domestic mammals [47] Domestication Llama FST
Anthrax toxin receptor 2 Anthrax resistance/susceptibility [15] Domestication Llama Both
Fibroblast growth factor 5 2 Longwool/shortwool fleece [16] Domestication Llama Both
Endothelin 3 19 Blue-eyed, white coat phenotype in Waardenburg syndrome of human [19] Introgression from alpaca Llama FST
Agouti signaling protein 19 Pigmentation [21, 22] Introgression from alpaca Llama XP-EHH
GNAS complex 19 Performance traits in cattle (imprinted) [24] Introgression from alpaca Llama FST
Agouti-related neuropeptide 9 Dietary restriction and appetite in cattle [37] Domestication Llama FST