1- Arak University, Arak, Iran.
Abstract: (50 Views)
Introduction and Objective:
Compared to other poultry, duck is more resistant to adverse environmental factors, so they are less likely to get sick. duck 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 depending on the purpose of breeding, they will answer the breeding costs and create the necessary productivity for the industry. 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 duck by humans left detectable signatures on the genome of modern duck. The identification of these signals can help us to improve the genetic characteristics of economically important traits in duck. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about 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 Peking ducks, holds a significant global market share, prized for their high meat yield and fat content. However, understanding of the molecular genetic mechanisms influencing carcass yield in ducks is limited. The aim of this study was to identify effective genes related to important economic traits and genomic region on positive signature of selection in pekin ducks using selection signature method. For this purpose, iHS analyses-based linkage disequilibrium were conducted using the genome-wide single nucleotide polymorphisms (SNPs)
Material and Methods: In this study, data from 643 pekin duck genotyped using the whole-genome re-sequencing data were generated on the Illumina Hiseq 4000 platform using 150- bp paired-end reads. were used to identify genomic regions under selection associated with important economic traits in pekin duck. Quality control measures were performed in Plink by setting animal call rate of 0.90, 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 duck were finally entered for further analysis. To identify the signatures of selection, 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 KOBAS software (https://bioinformaticshome.com/tools/rna-seq/descriptions/KOBAS.html#google_vignette) for the assignment of the genes to functional categories were used. 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 and Discussion Using iHS approach, we identified different genomic regions on chromosomes related to economic traits. In this research, we identified different sets of candidate genes related to production traits: CSMD1, THYN1, ACAD8, CALCR, FOXO1, TMEM161A and FRMPD3 in duck. According to pathway analysis, 14 pathways from gene ontology and biological pathways were associated with the egg production trait. Some of the genes were found are consistent with some previous studies and to be involved 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 duck is of great importance and is more important than the increase in the weight of breeding duck, and 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. By the way, various genes that were founded within these regions can be considered as candidates under selection based on function. Most of the genes under selection were found are consistent with some previous studies and to be involved in reproductive traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication 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 and considering, this study supported previous results from genome scan of production traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in duck for better body weight. Finally, this study identifies candidate genes influencing egg production and carcass traits in Peking ducks, offering genetic insights for optimizing breeding programs and economic potential.
Compared to other poultry, duck is more resistant to adverse environmental factors, so they are less likely to get sick. duck 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 depending on the purpose of breeding, they will answer the breeding costs and create the necessary productivity for the industry. 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 duck by humans left detectable signatures on the genome of modern duck. The identification of these signals can help us to improve the genetic characteristics of economically important traits in duck. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about 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 Peking ducks, holds a significant global market share, prized for their high meat yield and fat content. However, understanding of the molecular genetic mechanisms influencing carcass yield in ducks is limited. The aim of this study was to identify effective genes related to important economic traits and genomic region on positive signature of selection in pekin ducks using selection signature method. For this purpose, iHS analyses-based linkage disequilibrium were conducted using the genome-wide single nucleotide polymorphisms (SNPs)
Material and Methods: In this study, data from 643 pekin duck genotyped using the whole-genome re-sequencing data were generated on the Illumina Hiseq 4000 platform using 150- bp paired-end reads. were used to identify genomic regions under selection associated with important economic traits in pekin duck. Quality control measures were performed in Plink by setting animal call rate of 0.90, 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 duck were finally entered for further analysis. To identify the signatures of selection, 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 KOBAS software (https://bioinformaticshome.com/tools/rna-seq/descriptions/KOBAS.html#google_vignette) for the assignment of the genes to functional categories were used. 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 and Discussion Using iHS approach, we identified different genomic regions on chromosomes related to economic traits. In this research, we identified different sets of candidate genes related to production traits: CSMD1, THYN1, ACAD8, CALCR, FOXO1, TMEM161A and FRMPD3 in duck. According to pathway analysis, 14 pathways from gene ontology and biological pathways were associated with the egg production trait. Some of the genes were found are consistent with some previous studies and to be involved 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 duck is of great importance and is more important than the increase in the weight of breeding duck, and 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. By the way, various genes that were founded within these regions can be considered as candidates under selection based on function. Most of the genes under selection were found are consistent with some previous studies and to be involved in reproductive traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication 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 and considering, this study supported previous results from genome scan of production traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in duck for better body weight. Finally, this study identifies candidate genes influencing egg production and carcass traits in Peking ducks, offering genetic insights for optimizing breeding programs and economic potential.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد طیور
Received: 2024/12/7 | Accepted: 2026/05/4
Received: 2024/12/7 | Accepted: 2026/05/4
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