Identification of polymorphisms associated with production traits on chicken (Gallus gallus) chromosome 4

Pértille, Fábio; Zanella, Ricardo; Felício, Andrezza Maria; Ledur, Mônica Corrêa; Peixoto, J. O.; Coutinho, Luiz Lehmann

doi:10.4238/2015.september.9.11

Cited by 17 publications

(23 citation statements)

References 34 publications

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“…The descriptive statistics for the eight performance traits analyzed can be observed in Table 1 . Detailed description of these animals and traits were provided elsewhere 7 16 . The large variability is expected since the animals are from a broiler x layer F 2 population.…”

Section: Resultsmentioning

confidence: 99%

“…For better understanding of complex traits control in a segregating F 2 population, our research group have focused the attention on genetic association and linkage analyses using different approaches, as: candidate genes 14 15 16 17 and QTL mapping 3 4 5 6 7 , respectively, and more recently, NGS approaches 27 28 . We have presented here the first study using a higher density of SNPs in this F 2 population with GWAS purpose.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have been conducted in chickens using markers randomly distributed in the genome (microsatellites), which have allowed the identification of several QTLs for production traits 3 4 5 6 7 8 9 10 11 12 13 . Following these, some of the studies have focused their attention on the identification of SNPs in functional and positional candidate genes and to test their association on target QTL regions 14 15 16 17 18 19 . With the advent of next-generation sequencing (NGS), it was possible to identify a global SNP profile and to perform genome-wide association studies (GWAS) to find novel QTL regions 20 21 22 23 24 25 26 and also to refine the previously published regions 27 28 29 30 31 .…”

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confidence: 99%

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Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Pértille

Moreira

Zanella

et al. 2017

Sci Rep

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Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F2 chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Pértille

Moreira

Zanella

et al. 2017

Sci Rep

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“…For example, genotyping-by-sequencing (GBS) on livestock has been a sufficient solution that is required for population genetic and genomic studies [15]. This method has been successfully used to identify selection signatures of important economic traits in cattle [16], pigs [17,18], chicken [19], and camels [20]. The goal of this investigation was to perform a pair-wise marker differentiation comparison in a genome-wide scan between Noire de Thibar and Queue fine de l'ouest Tunisian sheep breeds, using genotyping-by-sequencing data to reveal putative regions under strong and recent selection.…”

Section: Introductionmentioning

confidence: 99%

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

Baazaoui

McEwan

Anderson

et al. 2019

Animals

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Simple Summary: Maintaining the flexibility of the genetic resources of native animals to face local environment constraints is still a major challenge. In Tunisia, the Noire de Thibar breed is a local sheep, typically with black coloration, known for its ability to tolerate "hypericum perforatum", which causes skin photosensitization in white colored sheep. The goal of this study was to perform a genome scan, by considering genotyping-by-sequencing (GBS) markers that were genotyped in divergent coat colored sheep (black vs. white) to identify strong, and recent, artificial selection that is involved in skin-photosensitization. Interestingly, the genomic differentiation analysis identified F ST markers within genomic regions containing key pigmentation and photosensitivity related-genes. These findings help in understanding the background of coat color genetics and its potential role in adaptation to local environment constraints.Abstract: The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker F ST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.

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“…(FORNARI et al, 2014). Chickens of the parental broiler parental line TT underwent selection since 1992 over many generations for several traits such as body weight, feed conversion, carcass and cuts yield, viability, fertility, hatchability and to reduce abdominal fat (NONES et al, 2012;PÉRTILLE et al, 2015). In this population, QTLs were mapped for abdominal fat weight and percentage on GGA2 (FORNARI et al, 2014).…”

Section: Baéza and Le Bihan-duval 2013)mentioning

confidence: 99%

Genome-wide association studies reveal genomic regions and positional candidate genes for fat deposition in chickens

Moreira¹

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Genome-wide association studies reveal genomic regions and positional candidate genes for fat deposition in chickens Excess of fat deposition is a negative factor for poultry production, which affects feed efficiency and consequently the costs of meat production. The incorporation of genomic tools in poultry breeding programs may help to accelerate the selection for increased production efficiency. In this context, we genotyped approximately 2,000 42 days-old chickens from two different populations (Brazilian F2 Chicken Resource population and TT broiler Reference Population) using a high-density SNP array (600K, Affymetrix) to estimate genomic heritability of fatness-related traits, to identify genomic regions and positional candidate genes (PCGs) associated with these traits. We performed genome-wide association (GWAS) analysis using GenSel software (Bayesian approach) to identify 1 Mb genomic windows associated with abdominal fat, skin and carcass fat content traits. The search for PCGs were made within each genomic windows associated considering their Gene Ontology (GO) terms and also the literature information. We also integrated into this study NGS-SNPs data from both populations and selection signature regions identified in Brazilian F2 Chicken Resource population to refine the list of PCGs. The genomic heritability values for fatness-related traits were from moderate to high (greater than 0.30). We identified quantitative trait loci (QTL) for abdominal fat, skin and carcass fat content traits harboring several PCGs involved in biological processes of fat deposition. We identified several NGS-SNPs annotated in potential functional regions in our PCGs and some of those were predicted as deleterious and high impact mutations. Besides that, some genes overlapped with selection signature regions in Brazilian F2 Chicken Resource population. Important candidate genes for fat deposition were identified, providing new insights to achieve a better understanding of the genetic control of fat deposition in chickens.

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Identification of polymorphisms associated with production traits on chicken (Gallus gallus) chromosome 4

Cited by 17 publications

References 34 publications

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

Genome-wide association studies reveal genomic regions and positional candidate genes for fat deposition in chickens

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