Application of genomic data to assist a community-based breeding program: A preliminary study of coat color genetics in Morada Nova sheep

Muniz, Maria Malane Magalhães; Caetano, Alexandre Rodrigues; McManus, Concepta; Cavalcanti, Lillian Cristina Gomes; Façanha, Débora Andréa Evangelista; Leite, Jacinara Hody Gurgel Morais; Facó, Olivardo; Paiva, Samuel Rezende

doi:10.1016/j.livsci.2016.06.006

Cited by 21 publications

(17 citation statements)

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“…Despite the lack of individual phenotypes and the small sample size, our GWAS case–control study was effective for identifying variants potentially associated with phenotypic differentiation in Sardinian sheep. Therefore, as well as reported by Muniz et al (), our findings confirmed the reliability of this method, in particular when the animal tested are easily phenotyped (e.g., coat colour or body size), as in our case.…”

Section: Discussionsupporting

confidence: 92%

“…This aspect tends to minimize the confounding effects due to genetic divergence and allowed us to adopt a GWAS with a case–control model, generally applied to identify genes affecting phenotypic variations within the same breed, especially for qualitative traits or when few genes control the trait of interest. In sheep, GWAS case–control studies have been carried out to map candidate genomic regions for coat colour in two different ecotypes from the same breed (e.g., Kijas et al, ; Mastrangelo et al, ; Muniz et al, ). Typically, all these studies reported few associated markers.…”

Section: Discussionmentioning

confidence: 99%

“…Another candidate marker for phenotypic differentiation is rs405180718 on OAR14 (at position 14,415,727 bp), located 230.2 kb away from MC1R , a well‐known gene that plays a central role in regulation of animal coat colour (Våge, Klungland, Lu, & Cone, ). A previous case–control GWAS performed in the Morada Nova sheep breed using animals with different coat colours, identified seven significant SNPs located in or near MC1R (Muniz et al, ). The same results were reported by Kijas et al () in the Manchega sheep (with black and white animals), where the most significant SNP in the GWAS was also the closest to MC1R gene.…”

Section: Discussionmentioning

confidence: 99%

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Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Mastrangelo

Jemaa

Sottile

et al. 2019

J Animal Breeding Genetics

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Selective breeding has led to modifications in the genome of many livestock breeds.In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (F ST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and F ST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and F ST analyses. Moreover, one candidate marker identified by GWAS and F ST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations. K E Y W O R D Sgenome-wide methods, genomic regions, Ovine BeadChip50K, Sardinian sheep breeds

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Mastrangelo

Jemaa

Sottile

et al. 2019

J Animal Breeding Genetics

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“…As visual characteristics of animals, pigmentation traits are often used for breed identification, and represent an important phenotype of interest for breeding and research [16]. Several genome-wide studies for coat color have been conducted in livestock species including cattle [16][17][18], sheep [2,19], goat [20,21]. In this work, genome-wide analyses have been performed in the Polverara chicken breed, PW and PB subpopulations.…”

Section: Discussionmentioning

confidence: 99%

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

Mastrangelo

Cendron

Sottile

et al. 2020

Animals

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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 (F ST ) 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 F ST 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.

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“…In general, the presence of the MC1R wildtype allele is required for the observation of ASIP gene products (Vage et al, 1999;Fontanesi et al, 2011;Hepp et al, 2012). Few studies have been performed to evaluate these genes in locally adapted sheep breeds in Brazil (Hepp et al, 2012(Hepp et al, , 2016Muniz et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus

Cavalcanti

Moraes

Faria

et al. 2017

Pesq. agropec. bras.

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-The objective of this work was to identify single nucleotide polymorphisms (SNPs) in resequencing data from MC1R, ASIP, and TYRP1 genes derived from Crioula sheep (Ovis aris) with different coat colors. Polymorphisms in the ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor), and TRYP1 (tyrosinase-related protein 1) genes were analyzed in 115 sheep from Embrapa's conservation nucleus of crioula sheep, in Brazil. A total of 7,914 bp were sequenced per animal, and 14 SNPs were identified. Two additional assays were performed to detect duplications and deletions in the ASIP gene. Ninety-five percent of the coat color variation was explained by epistatic interactions observed between specific alleles in the MC1R and ASIP genes. Evidence suggests an important role of TYRP1 variants for wool color, despite their low frequencies. The marker panel was efficient enough in predicting coat color in the studied animals and, therefore, can be used to implement a marker-assisted selection program in the conservation nucleus of sheep of the crioula breed.Index terms: Ovis aris, ASIP, genetic resources conservation, marker-assisted selection, MC1R, TYRP1. Caracterização genética de genes para cor da pelagem do núcleo de conservação da ovelha Crioula no BrasilResumo -O objetivo deste trabalho foi identificar polimorfismo de nucleotídeo único (SNPs) em dados de ressequenciamento dos genes MC1R, ASIP e TYRP1, obtidos de ovelhas Crioulas (Ovis aries) com cores de pelagem distintas. Polimorfismos nos genes ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor) e TYRP1 (tyrosinase-related protein 1) foram analisados em 115 ovinos, provenientes do núcleo de conservação da ovelha Crioula, da Embrapa. No total, 7.914 pb foram sequenciados por animal, e 14 SNPs foram identificados. Dois ensaios adicionais foram realizados para detectar duplicações e deleções no gene ASIP. Noventa e cinco por cento da variação de cor da pelagem foi explicada pelas interações epistáticas entre alelos específicos dos genes MC1R e ASIP. Evidências sugerem um importante papel das variantes TYRP1 para cor da lã, apesar das suas baixas frequências. O painel de marcadores usado foi eficiente em detectar alelos associados à coloração da pelagem nos animais estudados e, portanto, pode ser usado na implementação de um programa de seleção assistida por marcadores, no núcleo de conservação de ovinos da raça Crioula.Termos para indexação: Ovis aris, ASIP, conservação de recursos genéticos, seleção assistida por marcadores, MC1R, TYRP1.

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Application of genomic data to assist a community-based breeding program: A preliminary study of coat color genetics in Morada Nova sheep

Cited by 21 publications

References 18 publications

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

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

Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus

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