Mitochondrial Genome Variation in Breast Muscle of Tibetan Fragrant Chickens Across an Altitudinal Gradient and Its Association with Meat Quality

This study aimed to characterize the mitochondrial (MT) genome of Tibetan fragrant chickens along an altitudinal gradient and to relate it to meat quality. Eighteen 150-day-old male chickens were selected from three groups (LX, 1500 m; MX, 2800 m; HX, 3500 m; n = 6 each; six birds were randomly chosen from 30 reared per group) and subjected to whole-genome resequencing (reference: Gallus gallus GCA_000002315.5). Ninety MT variants (85 polymorphic; transition/transversion 83:7) were identified, comprising 58 coding (42 synonymous, 16 non-synonymous), 20 D-loop/non-coding, 10 rRNA and 2 tRNA sites; no MT insertions/deletions or structural variants were found. The 18 birds clustered into three maternal lineages (A, B, C) that were only partially structured by altitude (A more frequent at low altitude; B at mid and high altitude). A neighbour-joining tree with 12 Gallus mitogenomes placed the population close to Gallus gallus gallus and Chinese local breeds. Fifteen heteroplasmic sites were detected, with 16S rRNA nt3946 (G/C/A) heteroplasmic in all birds. Relative mtDNA copy number did not differ among groups (p = 0.52). Meat quality varied with altitude (highest protein and lowest fat at 2800 m; highest inosine monophosphate at 3500 m) but not with maternal lineage, suggesting that the observed phenotypic differences are associated mainly with altitude of rearing rather than with maternal mitochondrial lineage, and that the MT genome contributes standing genetic variation rather than a direct functional basis for these differences.