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RESEARCH PRODUCT

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

Filippo CendronGianluca SottileGiovanni NieroMartino CassandroFilippo BiscariniSalvatore MastrangeloBaldassare Portolano

subject

Candidate geneCandidate genegenome-wide analysesCandidate genes; Genome-wide analyses; Local chicken populations; Plumage color; SNPSNPSingle-nucleotide polymorphismGenome-wide association studyBiologyArticleFixation indexSettore AGR/17 - Zootecnica Generale E Miglioramento Genetico03 medical and health scienceslcsh:ZoologyGenetic variationlcsh:QL1-991GenotypingLocal chicken population030304 developmental biologyGeneticsGenome-wide analyse0303 health scienceslcsh:Veterinary medicineGeneral Veterinarylocal chicken populations0402 animal and dairy science04 agricultural and veterinary sciencesPhenotypic traitlocal chicken populations; genome-wide analyses; SNP; plumage color; candidate genes040201 dairy & animal sciencePlumage colorPlumagelcsh:SF600-1100Animal Science and Zoologycandidate genes

description

Simple Summary 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. 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.

yearjournalcountryeditionlanguage
2020-03-01Animals
https://doi.org/10.3390/ani10030493