Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran
Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to th...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Majid Bigham [verfasserIn] Mohammadreza Nassiry [verfasserIn] Mahyar Heydarpour [verfasserIn] Ali Javadmanesh [verfasserIn] |
|---|
| Format: |
E-Artikel |
|---|---|
| Sprache: |
Persisch |
| Erschienen: |
2023 |
|---|
| Schlagwörter: |
|---|
| Übergeordnetes Werk: |
In: پژوهشهای علوم دامی ایران ; 15(2023), 4, Seite 569-583 volume:15 ; year:2023 ; number:4 ; pages:569-583 |
|---|
| Links: |
Link aufrufen |
|---|
| DOI / URN: |
10.22067/ijasr.2023.79931.1112 |
|---|
| Katalog-ID: |
DOAJ097932434 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | DOAJ097932434 | ||
| 003 | DE-627 | ||
| 005 | 20240413201026.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 240413s2023 xx |||||o 00| ||per c | ||
| 024 | 7 | |a 10.22067/ijasr.2023.79931.1112 |2 doi | |
| 035 | |a (DE-627)DOAJ097932434 | ||
| 035 | |a (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a per | ||
| 050 | 0 | |a SF1-1100 | |
| 100 | 0 | |a Majid Bigham |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 520 | |a Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. | ||
| 650 | 4 | |a domestic sheep | |
| 650 | 4 | |a economic traits | |
| 650 | 4 | |a ontology | |
| 650 | 4 | |a selection signature | |
| 650 | 4 | |a wild sheep | |
| 653 | 0 | |a Animal culture | |
| 700 | 0 | |a Mohammadreza Nassiry |e verfasserin |4 aut | |
| 700 | 0 | |a Mahyar Heydarpour |e verfasserin |4 aut | |
| 700 | 0 | |a Ali Javadmanesh |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i In |t پژوهشهای علوم دامی ایران |g 15(2023), 4, Seite 569-583 |
| 773 | 1 | 8 | |g volume:15 |g year:2023 |g number:4 |g pages:569-583 |
| 856 | 4 | 0 | |u https://doi.org/10.22067/ijasr.2023.79931.1112 |z kostenfrei |
| 856 | 4 | 0 | |u https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c |z kostenfrei |
| 856 | 4 | 0 | |u https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf |z kostenfrei |
| 856 | 4 | 2 | |u https://doaj.org/toc/2008-3106 |y Journal toc |z kostenfrei |
| 856 | 4 | 2 | |u https://doaj.org/toc/2423-4001 |y Journal toc |z kostenfrei |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a SYSFLAG_A | ||
| 912 | |a GBV_DOAJ | ||
| 951 | |a AR | ||
| 952 | |d 15 |j 2023 |e 4 |h 569-583 | ||
| author_variant |
m b mb m n mn m h mh a j aj |
|---|---|
| matchkey_str |
majidbighammohammadrezanassirymahyarheyd:2023----:tdosgaueopstvslcinngnotlgismdmsia |
| hierarchy_sort_str |
2023 |
| callnumber-subject-code |
SF |
| publishDate |
2023 |
| allfields |
10.22067/ijasr.2023.79931.1112 doi (DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c DE-627 ger DE-627 rakwb per SF1-1100 Majid Bigham verfasserin aut Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. domestic sheep economic traits ontology selection signature wild sheep Animal culture Mohammadreza Nassiry verfasserin aut Mahyar Heydarpour verfasserin aut Ali Javadmanesh verfasserin aut In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 https://doi.org/10.22067/ijasr.2023.79931.1112 kostenfrei https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c kostenfrei https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf kostenfrei https://doaj.org/toc/2008-3106 Journal toc kostenfrei https://doaj.org/toc/2423-4001 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 15 2023 4 569-583 |
| spelling |
10.22067/ijasr.2023.79931.1112 doi (DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c DE-627 ger DE-627 rakwb per SF1-1100 Majid Bigham verfasserin aut Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. domestic sheep economic traits ontology selection signature wild sheep Animal culture Mohammadreza Nassiry verfasserin aut Mahyar Heydarpour verfasserin aut Ali Javadmanesh verfasserin aut In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 https://doi.org/10.22067/ijasr.2023.79931.1112 kostenfrei https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c kostenfrei https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf kostenfrei https://doaj.org/toc/2008-3106 Journal toc kostenfrei https://doaj.org/toc/2423-4001 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 15 2023 4 569-583 |
| allfields_unstemmed |
10.22067/ijasr.2023.79931.1112 doi (DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c DE-627 ger DE-627 rakwb per SF1-1100 Majid Bigham verfasserin aut Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. domestic sheep economic traits ontology selection signature wild sheep Animal culture Mohammadreza Nassiry verfasserin aut Mahyar Heydarpour verfasserin aut Ali Javadmanesh verfasserin aut In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 https://doi.org/10.22067/ijasr.2023.79931.1112 kostenfrei https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c kostenfrei https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf kostenfrei https://doaj.org/toc/2008-3106 Journal toc kostenfrei https://doaj.org/toc/2423-4001 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 15 2023 4 569-583 |
| allfieldsGer |
10.22067/ijasr.2023.79931.1112 doi (DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c DE-627 ger DE-627 rakwb per SF1-1100 Majid Bigham verfasserin aut Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. domestic sheep economic traits ontology selection signature wild sheep Animal culture Mohammadreza Nassiry verfasserin aut Mahyar Heydarpour verfasserin aut Ali Javadmanesh verfasserin aut In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 https://doi.org/10.22067/ijasr.2023.79931.1112 kostenfrei https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c kostenfrei https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf kostenfrei https://doaj.org/toc/2008-3106 Journal toc kostenfrei https://doaj.org/toc/2423-4001 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 15 2023 4 569-583 |
| allfieldsSound |
10.22067/ijasr.2023.79931.1112 doi (DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c DE-627 ger DE-627 rakwb per SF1-1100 Majid Bigham verfasserin aut Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. domestic sheep economic traits ontology selection signature wild sheep Animal culture Mohammadreza Nassiry verfasserin aut Mahyar Heydarpour verfasserin aut Ali Javadmanesh verfasserin aut In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 https://doi.org/10.22067/ijasr.2023.79931.1112 kostenfrei https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c kostenfrei https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf kostenfrei https://doaj.org/toc/2008-3106 Journal toc kostenfrei https://doaj.org/toc/2423-4001 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 15 2023 4 569-583 |
| language |
Persian |
| source |
In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 |
| sourceStr |
In پژوهشهای علوم دامی ایران 15(2023), 4, Seite 569-583 volume:15 year:2023 number:4 pages:569-583 |
| format_phy_str_mv |
Article |
| institution |
findex.gbv.de |
| topic_facet |
domestic sheep economic traits ontology selection signature wild sheep Animal culture |
| isfreeaccess_bool |
true |
| container_title |
پژوهشهای علوم دامی ایران |
| authorswithroles_txt_mv |
Majid Bigham @@aut@@ Mohammadreza Nassiry @@aut@@ Mahyar Heydarpour @@aut@@ Ali Javadmanesh @@aut@@ |
| publishDateDaySort_date |
2023-01-01T00:00:00Z |
| id |
DOAJ097932434 |
| language_de |
persisch |
| fullrecord |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000naa a22002652 4500</leader><controlfield tag="001">DOAJ097932434</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20240413201026.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">240413s2023 xx |||||o 00| ||per c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.22067/ijasr.2023.79931.1112</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)DOAJ097932434</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">per</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">SF1-1100</subfield></datafield><datafield tag="100" ind1="0" ind2=" "><subfield code="a">Majid Bigham</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">domestic sheep</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">economic traits</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">ontology</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">selection signature</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">wild sheep</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Animal culture</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Mohammadreza Nassiry</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Mahyar Heydarpour</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Ali Javadmanesh</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">In</subfield><subfield code="t">پژوهشهای علوم دامی ایران</subfield><subfield code="g">15(2023), 4, Seite 569-583</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:15</subfield><subfield code="g">year:2023</subfield><subfield code="g">number:4</subfield><subfield code="g">pages:569-583</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://doi.org/10.22067/ijasr.2023.79931.1112</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">https://doaj.org/toc/2008-3106</subfield><subfield code="y">Journal toc</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">https://doaj.org/toc/2423-4001</subfield><subfield code="y">Journal toc</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_DOAJ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">15</subfield><subfield code="j">2023</subfield><subfield code="e">4</subfield><subfield code="h">569-583</subfield></datafield></record></collection>
|
| callnumber-first |
S - Agriculture |
| author |
Majid Bigham |
| spellingShingle |
Majid Bigham misc SF1-1100 misc domestic sheep misc economic traits misc ontology misc selection signature misc wild sheep misc Animal culture Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| authorStr |
Majid Bigham |
| format |
electronic Article |
| delete_txt_mv |
keep |
| author_role |
aut aut aut aut |
| collection |
DOAJ |
| remote_str |
true |
| callnumber-label |
SF1-1100 |
| illustrated |
Not Illustrated |
| topic_title |
SF1-1100 Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran domestic sheep economic traits ontology selection signature wild sheep |
| topic |
misc SF1-1100 misc domestic sheep misc economic traits misc ontology misc selection signature misc wild sheep misc Animal culture |
| topic_unstemmed |
misc SF1-1100 misc domestic sheep misc economic traits misc ontology misc selection signature misc wild sheep misc Animal culture |
| topic_browse |
misc SF1-1100 misc domestic sheep misc economic traits misc ontology misc selection signature misc wild sheep misc Animal culture |
| format_facet |
Elektronische Aufsätze Aufsätze Elektronische Ressource |
| format_main_str_mv |
Text Zeitschrift/Artikel |
| carriertype_str_mv |
cr |
| hierarchy_parent_title |
پژوهشهای علوم دامی ایران |
| hierarchy_top_title |
پژوهشهای علوم دامی ایران |
| isfreeaccess_txt |
true |
| title |
Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| ctrlnum |
(DE-627)DOAJ097932434 (DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c |
| title_full |
Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| author_sort |
Majid Bigham |
| journal |
پژوهشهای علوم دامی ایران |
| journalStr |
پژوهشهای علوم دامی ایران |
| callnumber-first-code |
S |
| lang_code |
per |
| isOA_bool |
true |
| recordtype |
marc |
| publishDateSort |
2023 |
| contenttype_str_mv |
txt |
| container_start_page |
569 |
| author_browse |
Majid Bigham Mohammadreza Nassiry Mahyar Heydarpour Ali Javadmanesh |
| container_volume |
15 |
| class |
SF1-1100 |
| format_se |
Elektronische Aufsätze |
| author-letter |
Majid Bigham |
| doi_str_mv |
10.22067/ijasr.2023.79931.1112 |
| author2-role |
verfasserin |
| title_sort |
study of signatures of positive selection and gene ontology in some domestic and wild sheep breeds in iran |
| callnumber |
SF1-1100 |
| title_auth |
Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| abstract |
Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. |
| abstractGer |
Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. |
| abstract_unstemmed |
Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved. |
| collection_details |
GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ |
| container_issue |
4 |
| title_short |
Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran |
| url |
https://doi.org/10.22067/ijasr.2023.79931.1112 https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf https://doaj.org/toc/2008-3106 https://doaj.org/toc/2423-4001 |
| remote_bool |
true |
| author2 |
Mohammadreza Nassiry Mahyar Heydarpour Ali Javadmanesh |
| author2Str |
Mohammadreza Nassiry Mahyar Heydarpour Ali Javadmanesh |
| callnumber-subject |
SF - Animal Culture |
| mediatype_str_mv |
c |
| isOA_txt |
true |
| hochschulschrift_bool |
false |
| doi_str |
10.22067/ijasr.2023.79931.1112 |
| callnumber-a |
SF1-1100 |
| up_date |
2024-07-03T14:31:27.087Z |
| _version_ |
1803568637113532416 |
| fullrecord_marcxml |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000naa a22002652 4500</leader><controlfield tag="001">DOAJ097932434</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20240413201026.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">240413s2023 xx |||||o 00| ||per c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.22067/ijasr.2023.79931.1112</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)DOAJ097932434</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DOAJ5f0532c813a34bfab2c37182ed7e335c</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">per</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">SF1-1100</subfield></datafield><datafield tag="100" ind1="0" ind2=" "><subfield code="a">Majid Bigham</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Study of Signatures of Positive Selection and Gene Ontology in some Domestic and Wild Sheep Breeds in Iran</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. 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: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">domestic sheep</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">economic traits</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">ontology</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">selection signature</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">wild sheep</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Animal culture</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Mohammadreza Nassiry</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Mahyar Heydarpour</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Ali Javadmanesh</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">In</subfield><subfield code="t">پژوهشهای علوم دامی ایران</subfield><subfield code="g">15(2023), 4, Seite 569-583</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:15</subfield><subfield code="g">year:2023</subfield><subfield code="g">number:4</subfield><subfield code="g">pages:569-583</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://doi.org/10.22067/ijasr.2023.79931.1112</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://doaj.org/article/5f0532c813a34bfab2c37182ed7e335c</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://ijasr.um.ac.ir/article_43507_4c52a590762d286ff33508e2a705b8c0.pdf</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">https://doaj.org/toc/2008-3106</subfield><subfield code="y">Journal toc</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">https://doaj.org/toc/2423-4001</subfield><subfield code="y">Journal toc</subfield><subfield code="z">kostenfrei</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_DOAJ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">15</subfield><subfield code="j">2023</subfield><subfield code="e">4</subfield><subfield code="h">569-583</subfield></datafield></record></collection>
|
| score |
7.4030848 |