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 | Domestication | Alpaca | Both | |
Hypoxia upregulated 1 | 33 | Cytoprotection under hypoxic conditions [39] | Domestication | Alpaca | XP-EHH |
Myomesin 1 | 24 | 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 | 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 |