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. 2020 Mar 15;10(3):493.
doi: 10.3390/ani10030493.

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

Salvatore Mastrangelo  1 , Filippo Cendron  2 , Gianluca Sottile  3 , Giovanni Niero  2 , Baldassare Portolano  1 , Filippo Biscarini  4 , Martino Cassandro  2
Affiliations

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

Salvatore Mastrangelo et al. Animals (Basel). .

Abstract

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.

Keywords: SNP; candidate genes; genome-wide analyses; local chicken populations; plumage color.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Specimens of Polverara White (PW) and Polverara Black (PB) chickens.
Figure 2
Figure 2
(a) Manhattan plot of the p-values in the genome-wide association study (GWAS). The horizontal lines represent the Bonferroni-corrected genome-wide significance (red; p < 0.0001); (b) Manhattan plot of the genome-wide fixation index (FST). The horizontal line represents the genome-wide significance single nucleotide polymorphisms (SNP) above the 99.98th percentile distribution) (FST = 0.74). Significant SNPs are highlighted in green.
Figure 3
Figure 3
Linkage Disequilibrium decay (measured as r2) as a function of inter-marker distance (Kbp) in the Polverara breed.
See this image and copyright information in PMC

References

    1. Leroy G., Besbes B., Boettcher P., Hoffmann I., Capitan A., Baumung R. Rare phenotypes in domestic animals: Unique resources for multiple applications. Anim. Genet. 2016;47:141–153. doi: 10.1111/age.12393. - DOI - PubMed
    1. Kijas J.W., Serrano M., McCulloch R., Li Y., Salces Ortiz J., Calvo J.H., Pérez-Guzmán M.D. The International Sheep Genomics Consortium. Genome wide association for a dominant pigmentation gene in sheep. J. Anim. Breed. Genet. 2013;130:468–475. doi: 10.1111/jbg.12048. - DOI - PubMed
    1. Schiavo G., Bertolini F., Utzeri V.J., Ribani A., Geraci C., Santoro L., Ovilo C., Fernandez A.I., Gallo M., Fontanesi L. Taking advantage from phenotype variability in a local animal genetic resource: Identification of genomic regions associated with the hairless phenotype in Casertana pigs. Anim. Genet. 2018;49:321–325. doi: 10.1111/age.12665. - DOI - PubMed
    1. Mastrangelo S., Sottile G., Sutera A.M., Di Gerlando R., Tolone M., Moscarelli A., Sardina M.T., Portolano B. Genome-wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed. Anim. Genet. 2018;49:636–640. doi: 10.1111/age.12719. - DOI - PubMed
    1. Zanetti E., De Marchi M., Dalvit C., Cassandro M. Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poult. Sci. 2010;89:420–427. doi: 10.3382/ps.2009-00324. - DOI - PubMed

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