Genomic mapping and comparative genomics of candidate loci regions
The candidate loci that we identified were located in intronic regions of the following genes. The loci 602-G/C is in one of the introns of the gene FAM135A (DUF676 domain-containing protein), a relatively unknown domain with GO-slim terms annotation related to cellular metabolic processes with putative lipase activity and QTLs associated with regulation of fat intramuscular deposition in chickens and cattle breeds (Poleti et al., 2018; Yuan et al., 2022). This section of our contig 602 is apparently orthologous to a similar region on theGallus gallus chromosome 3, and a region conserved across other bird taxa. The loci 3657-C/T was found within the gene formimidoyltransferase cyclodeaminase (FTCD ) and flanked by a feather β-keratin (BISK1) and collagen alpha-2(chain VI) (ColA62 ) (Fig. 2). The FTCD is a single copy gene coding for a key component of the folate metabolism (Wernimont et al., 2011). It also expresses a bifunctional enzyme involved in starvation-induce responses by downregulating the mTORC1 pathway towards the maintenance of homeostasis under low resource conditions (Zhang et al., 2021). While this region is also in synteny among other bird taxa (with theColA62 + FTCD clustering in the same orientation), theBISK1 is a relatively recently discovered copy of a β-keratin identified primarily in chicken but present also in blue and great tit genomes (Fig. 2). The novelty falls on BISK1 , a recently identified β-keratin found to be expressed only in cells defining pennaceous barbules in the contour feathers of chickens (Kowata et al., 2014).