Chickens are fascinating creatures, especially when you dive into their genetics. Among all the unique chicken breeds, Black Bone Chickens (BBCs) stand out. They aren’t just black-feathered; their skin, muscles, and even bones are black! This striking feature is due to a genetic phenomenon called fibromelanosis which has intrigued geneticists for over a century [1].  The primary genetic change responsible for this trait, the Fm locus, has been well-studied [2]. But as nature loves balance, another genetic factor—the Id locus—works to inhibit the pigmentation.  The Id locus, which inhibits dermal pigmentation, has remained a puzzle. We set out to uncover its genomic location, ancestral origins, and functional implications.

The Id locus: inhibitor of dermal melanin

Our study focused on the Id locus, hidden within the Z chromosome, a special sex-linked genetic structure. To locate and understand its role, we had to unravel some tricky genetic knots. Unraveling its structure is akin to solving a puzzle, where the high similarity of pieces complicates their placement. Thanks to the availability of large-scale genomic datasets, especially the recently generated long-read sequencing-based genomes [3, 4] , we discovered a fascinating chromosomal rearrangement, like flipping a section of DNA upside down. This rearrangement helps explain the unique features of Black Bone Chickens and sheds light on how such traits evolve.

Working on the Id locus presented formidable challenges. Its location in a highly repetitive region on chromosome Z and the presence of a chromosomal inversion complicated analysis. Traditional short-read sequencing methods are not well suited to resolve these complexities. To address this, we employed long-read sequencing datasets and innovative approaches for structural rearrangement identification. Annotating Z amplicon repeat units (ZARU) and validating the genome assemblies were crucial steps. Each breakthrough in these technical hurdles brought us closer to our goal.

Key findings

1. Precise Localization of the Id Locus: The Id locus was refined to a 1.6 Mb region (R1) at the distal end of chromosome Z. This region co-localizes with ZARU, revealing a BBC-specific inversion that suppresses recombination.
2. Identification of Candidate Genes: Within R1, we identified two strong candidates: the MTAP and CCDC112 genes. MTAP’s role in melanogenesis makes it a prime candidate for influencing pigmentation, while regulatory mutations in CCDC112 may contribute to dermal pigmentation variations.
3. Shared Ancestry Across BBC Breeds: Phylogenetic analyses and population structure studies revealed a shared ancestral origin for the Id locus among all BBC breeds, aligning with the patterns observed at the Fm locus [5,6].

What next?

The Id locus presents a wealth of questions for future research. How do specific mutations within the inversion influence the inhibition of pigmentation? Could the regulatory role of ZARU be linked to epigenetic changes? Answering these questions will require further functional studies and advanced genome editing techniques.

This journey wasn’t just about chickens. It’s a peek into how nature shapes living beings through twists and turns in their DNA (Saltation?). The journey to uncover the Id locus reminds us of the intricacies of nature’s designs and the power of perseverance in science. Each layer of complexity we unravel brings us closer to understanding the fascinating world of genomics.

We invite you to explore the detailed findings of this study in our published article in the Journal of Molecular Evolution. For those with an interest in collaborative research or further questions, we’d love to hear from you. Together, let’s push the boundaries of what’s possible in genetics.

References

1. Bateson BW, Punnett RC (1911) The inheritance of the peculiar pigmentation of the silky fowl. J Genet 13(1):185–203. https://doi.org/10.1007/BF02981551
2. Dorshorst B, Molin AM, Rubin CJ et al (2011) A complex genomic rearrangement involving the Endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. https://doi.org/10.1371/journal.pgen.1002412
3. Zhu F, Yin Z-T, Zhao Q-S et al (2023) A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 61(6):1–15. https://doi.org/10.1038/s42003-023-05619-y
4. Huang Z et al. 2023 Evolutionary analysis of a complete chicken genome. Proc. Natl Acad. Sci. USA 120, e2216641120. (doi:10.1073/PNAS.2216641120)
5. Shinde SS, Sharma A, Vijay N (2023) Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken. Front Genet 14:1180658. https://doi.org/10.3389/FGENE.2023.1180658/BIBTEX
6. Sharma A, Vijay N (2024) What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken? bioRxiv 2024.02.05.578760. https://doi.org/10.1101/2024.02.05.578760