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Open AccessArticle

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

1
Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
2
Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
3
Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, 90128 Palermo, Italy
4
CNR-IBBA, 20133 Milano, Italy
*
Author to whom correspondence should be addressed.
Animals 2020, 10(3), 493; https://doi.org/10.3390/ani10030493
Received: 5 February 2020 / Revised: 2 March 2020 / Accepted: 14 March 2020 / Published: 15 March 2020
In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait.
Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken. View Full-Text
Keywords: local chicken populations; genome-wide analyses; SNP; plumage color; candidate genes local chicken populations; genome-wide analyses; SNP; plumage color; candidate genes
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MDPI and ACS Style

Mastrangelo, S.; Cendron, F.; Sottile, G.; Niero, G.; Portolano, B.; Biscarini, F.; Cassandro, M. Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color. Animals 2020, 10, 493.

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