Table 2.
Genes and variants associated with traits in AA lions and captive supplemental lions
| Trait/concern | Gene | Encoding | Chromosome | Position | Mutation | Genotype | Association or role |
|---|---|---|---|---|---|---|---|
| Mane color | MITF | Melanocyte Inducing Transcription Factor | CM018462.1 | 33847276 | c.G7T:p.A3S | T/T | Pigment deficiency and melanoma |
| TYR | Tyrosinase | CM018470.1 | 41554541 | c.C176T:p.T59M | 9(G/A),4(A/A) | Melanogenesis | |
| Body size | ODAD3 | Outer Dynein Arm Docking Complex Subunit 3 | CM018462.1 | 6449959 | c.G1156A:p.E386K | 4(C/T),11(T/T) | Loss of body fat and body size |
| Breeding and fertility | ACTL9 | Actin-like protein 9 | CM018462.1 | 3773231 | c.A344G:p.H115R | 3(A/G),12(G/G) | Infertility and sperm defects |
| CM018462.1 | 3773612 | c.C725A:p.P242Q | 3(C/A),12(A/A) | ||||
| CM018462.1 | 3773974 | c.C1087G:p.P363A | 3(C/G),12(G/G) | ||||
| ASTL | Astacin Like Metalloendopeptidase | CM018463.1 | 34800671 | c.G1224T:p.Q408H | 6(G/T),9(T/T) | ||
| CFAP54 | Cilia and Flagella Associated Protein 54 | CM018467.1 | 115165529 | c.A6055G:p.K2019E | 5(A/G),10(G/G) | ||
| Metabolism | CSF1R | Colony-stimulating factor 1 receptor | CM018460.1 | 42304012 | c.C419T:p.P140L | 6(G/A),9(A/A) | Diet, glucose metabolism, and lipid metabolic pathways |
| ACOT12 | Acyl-CoA thioesterase 12 | CM018460.1 | 93753098 | c.A365T:p.H122L | 5(A/T),10(T/T) | ||
| Cardiovascular | GATA5 | GATA transcription factor gene GNC | CM018463.1 | 135020743 | c.G783C:p.E261D | 4(C/G),11(G/G) | Heart development |
| NOTCH1 | NOTCH receptor 1 | CM018473.1 | 701639 | c.G6898A:p.A2300T | 4(C/T),11(T/T) | Cardiovascular morphogenesis | |
| Acoustic responsiveness | CDH23 | Cadherin 23 | CM018471.1 | 53296596 | c.A4684G:p.I1562V | C/C | Hair cell development and stereocilia formation |
| Neurological disorders | PEX6 | Peroxisome assembly factor 2 protein | CM018465.1 | 9323733 | c.A142G:p.T48A | C/C | Retinal degeneration and vision problems |
| Stress and social behavior | GAD1 | Glutamate decarboxylase-67 | CM018468.1 | 61614293 | c.G1086A:p.M362I | 5(C/T),10(T/T) | Anxiety disorders |
Genes and variants linked to specific traits in captive lions (AA and captive supplemental lions) are displayed. Genes exclusive to AA lions are highlighted in bold, and any genes with variants found in wild supplemental lions have been omitted.