1- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
2- Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
2- Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
Abstract: (780 Views)
Extended Abstract
Background: Compared to other poultry, ducks are more resistant to adverse environmental factors, thus they are less likely to become ill. Ducks are fast-growing poultry, and they are easy to raise. According to the need in industrial duck breeding, meat, egg, and even dual-purpose strains should be created so that they will cover the breeding costs and create the necessary productivity for the industry, depending on the purpose of breeding. Identification of selection-targeted genomic regions is one of the main aims of biological research. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic poultry. The selection of ducks by humans left detectable signatures on the genome of modern ducks. The identification of these signals can help us to improve the genetic characteristics of economically important traits in ducks. Interest in the detection of genes or genomic regions that are targeted by selection has been growing over the last decade. Identifying the signatures of selection can provide valuable insights into the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. Poultry meat, particularly Pekin ducks, holds a significant global market share, prized for their high meat yield and fat content. However, the understanding of molecular genetic mechanisms influencing carcass yield in ducks is limited. This study aimed to identify effective genes related to important economic traits and genomic regions on positive signatures of selection in Pekin ducks using the selection signature method. For this purpose, iHS analyses-based linkage disequilibrium was conducted using genome-wide single-nucleotide polymorphisms (SNPs).
Methods: In this study, data from 643 Pekin ducks genotyped using the whole-genome re-sequencing data were generated on the Illumina HiSeq 4000 platform using 150- bp paired-end reads. They were used to identify genomic regions under selection associated with important economic traits in Pekin ducks. Quality control measures were performed in Plink by setting an animal call rate of 0.90, a SNP call rate of 0.90, and SNPs with minor allele frequencies (MAF) lower than 0.01 or that do not conform to the indep-pairwise 25 5 0.2 parameter and unknown position. After quality control of the initial data using Plink software (v1.90; http://pngu.mgh.harvard.edu/purcell/plink), 67,856 SNP markers in 643 ducks were finally entered for further analysis. To identify the signatures of selection, the statistical method of iHS was used under Selscan v.2.0 software. Candidate genes were identified by SNPs located at 1% upper range of iHS using Plink v1.9 software. Additionally, a gene enrichment analysis was performed with the DAVID software for the assignment of the genes to functional categories. Finally, GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Results: Using the iHS approach, different genomic regions were identified on chromosomes related to economic traits. In this research, different sets of candidate genes related to production traits: CSMD1, THYN1, ACAD8, CALCR, FOXO1, TMEM161A, and FRMPD3, were identified in ducks. According to pathway analysis, 14 pathways from gene ontology and biological pathways were associated with the egg production trait. Some of the found genes are consistent with some previous studies and are involved in biological pathways related to skeletal muscle growth and development, positive regulation of skeletal muscle fiber development, negative regulation of negative chemotaxis, release of sequestered calcium ion into cytosol, and cellular response to hormone stimulus. Considering that the economic coefficient of egg production in ducks is of great importance and is more important than the increase in the weight of breeding ducks, the economic activities of the station are more in line with increasing the number of chicks produced per breeding duck.
Conclusion: As global demand for duck meat rises, it drives researchers to concentrate on duck carcass traits to enhance meat yields, reflecting the industry's growth potential. Additionally, various genes that were found within these regions can be regarded as candidates under selection based on function. Most of the genes found under selection are consistent with some previous studies and are involved in reproductive traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implications of these genes. Using these findings can accelerate the genetic progress in the breeding programs and can be used to understand the genetic mechanism controlling this trait. The results of our research can be used to understand the genetic mechanism controlling growth and egg production traits. Since this study supported previous results from a genome scan of production traits and revealed additional regions, using these findings could potentially be useful for genetic selection in ducks for better body weight. Finally, this study identifies candidate genes influencing egg production and carcass traits in Pekin ducks, offering genetic insights into optimizing breeding programs and economic potential.
Background: Compared to other poultry, ducks are more resistant to adverse environmental factors, thus they are less likely to become ill. Ducks are fast-growing poultry, and they are easy to raise. According to the need in industrial duck breeding, meat, egg, and even dual-purpose strains should be created so that they will cover the breeding costs and create the necessary productivity for the industry, depending on the purpose of breeding. Identification of selection-targeted genomic regions is one of the main aims of biological research. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic poultry. The selection of ducks by humans left detectable signatures on the genome of modern ducks. The identification of these signals can help us to improve the genetic characteristics of economically important traits in ducks. Interest in the detection of genes or genomic regions that are targeted by selection has been growing over the last decade. Identifying the signatures of selection can provide valuable insights into the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. Poultry meat, particularly Pekin ducks, holds a significant global market share, prized for their high meat yield and fat content. However, the understanding of molecular genetic mechanisms influencing carcass yield in ducks is limited. This study aimed to identify effective genes related to important economic traits and genomic regions on positive signatures of selection in Pekin ducks using the selection signature method. For this purpose, iHS analyses-based linkage disequilibrium was conducted using genome-wide single-nucleotide polymorphisms (SNPs).
Methods: In this study, data from 643 Pekin ducks genotyped using the whole-genome re-sequencing data were generated on the Illumina HiSeq 4000 platform using 150- bp paired-end reads. They were used to identify genomic regions under selection associated with important economic traits in Pekin ducks. Quality control measures were performed in Plink by setting an animal call rate of 0.90, a SNP call rate of 0.90, and SNPs with minor allele frequencies (MAF) lower than 0.01 or that do not conform to the indep-pairwise 25 5 0.2 parameter and unknown position. After quality control of the initial data using Plink software (v1.90; http://pngu.mgh.harvard.edu/purcell/plink), 67,856 SNP markers in 643 ducks were finally entered for further analysis. To identify the signatures of selection, the statistical method of iHS was used under Selscan v.2.0 software. Candidate genes were identified by SNPs located at 1% upper range of iHS using Plink v1.9 software. Additionally, a gene enrichment analysis was performed with the DAVID software for the assignment of the genes to functional categories. Finally, GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Results: Using the iHS approach, different genomic regions were identified on chromosomes related to economic traits. In this research, different sets of candidate genes related to production traits: CSMD1, THYN1, ACAD8, CALCR, FOXO1, TMEM161A, and FRMPD3, were identified in ducks. According to pathway analysis, 14 pathways from gene ontology and biological pathways were associated with the egg production trait. Some of the found genes are consistent with some previous studies and are involved in biological pathways related to skeletal muscle growth and development, positive regulation of skeletal muscle fiber development, negative regulation of negative chemotaxis, release of sequestered calcium ion into cytosol, and cellular response to hormone stimulus. Considering that the economic coefficient of egg production in ducks is of great importance and is more important than the increase in the weight of breeding ducks, the economic activities of the station are more in line with increasing the number of chicks produced per breeding duck.
Conclusion: As global demand for duck meat rises, it drives researchers to concentrate on duck carcass traits to enhance meat yields, reflecting the industry's growth potential. Additionally, various genes that were found within these regions can be regarded as candidates under selection based on function. Most of the genes found under selection are consistent with some previous studies and are involved in reproductive traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implications of these genes. Using these findings can accelerate the genetic progress in the breeding programs and can be used to understand the genetic mechanism controlling this trait. The results of our research can be used to understand the genetic mechanism controlling growth and egg production traits. Since this study supported previous results from a genome scan of production traits and revealed additional regions, using these findings could potentially be useful for genetic selection in ducks for better body weight. Finally, this study identifies candidate genes influencing egg production and carcass traits in Pekin ducks, offering genetic insights into optimizing breeding programs and economic potential.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد طیور
Received: 2025/09/2 | Accepted: 2025/12/29
Received: 2025/09/2 | Accepted: 2025/12/29
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