Volume 16, Issue 1 (3-2025)
Res Anim Prod 2025, 16(1): 109-120 |
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Azizi P, Moradi Shahrbabak H, Moradi Shahrbabak M, Mokhber M. (2025). Identification of Genomic Regions Related to Litter Size With Divergent Selection between Iranian Indigenous Sheep Breeds and Iceland Sheep Breed using FST Unbiased Statistics. Res Anim Prod. 16(1), 109-120. doi:10.61186/rap.16.1.109
URL: http://rap.sanru.ac.ir/article-1-1449-en.html
URL: http://rap.sanru.ac.ir/article-1-1449-en.html
1- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
2- Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia, Iran
2- Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia, Iran
Abstract: (569 Views)
Extended Abstract
Background: Due to the increasing demand for animal products, reproductive efficiency considered as one of the main objectives of sheep breeding, even in cases where the main emphasis is on milk or wool production. In cases the meat production is the main breeding objective, increasing reproductive efficiency is the most important goal of breeding programs. Although increasing fertility in ewe is possible in different pathways, ovulation rate and liter size are the main goals in breeding programs to achieve high fertility. Then, this study was performed to detection selection signature between Iranian native (as a genetic group with low reproductive performance) and Icelandic (as a genetic group with high reproductive performance) sheep breeds, and identify genes related to fecundity and litter size in sheep.
Methods: In this regard, the genomic information of 154 samples including 11 Iranian sheep breeds (Kermani, Baluchi, Afshari, Karakul, Sanjabi, SiahKabud, LoriBakhtiari, Shal, Ghezel, Chios, GrayShiraz) and 54 Iceland sheep breeds, were used. The genomic data related to these genetic groups including Icelandic and Iranian sheep breeds were obtained from the iSheep database and the address https://disk.yandex.ru/d/3N2wEv0-9_NL0w, respectively. Quality control of genomic data and filtering was performed using the PLINK software. The individuals and SNP with more than 5% missing genotypes were excluded. Then, the data were screened based on Minor allele frequency (MAF) less than 1%, and Hardy-Weinberg equilibrium (HWE). From the total available data, including 552,847 SNP markers related to autosomal chromosomes with known locations from 204 animals, finally 527,292 SNP markers from 204 animals, with about 0.999376 genotyping rate, was remained for inter-population genetic differentiation and structure analyses. Then, data filtering was done for seprate genetic groups. In this edition of the data, 527,284 SNP markers related to 174 animals were endured to selection signature analysis. Genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. Ubiased FST (θ) estimator statistic were used to explore the signs of selection. In order to better identify the selection signals, numerical values of SNP markers were averaged using the creeping window method up to a maximum length of 100 kb for adjacent SNPs. Only 0.1% of the genome regions with the highest values, were identified and determined as selection signatures. The genes related to selected genomic regions was extracted using the BIOMART online database corresponding areas in the sheep genome assembly (Oar 3.1). The detected genes, related to the selected regions, were surveyed by DAVID 2021 (The Database for Annotation, Visualization and Integrated Discovery) and STRING (Version 12) to identifying biological pathways and probably gene interaction networks.
Results: According to the principal component analysis (PCA) results, the group with high reproductive performance (Icelandic sheep) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The complete differentiation between two groups with low and high reproductive performance can be related to the regional separation of these two groups. Kermani and Chios breeds (from the Chios breeding center in Kerman province of Iran) are seprated from other Iranian breeds with the second component. It was confirmed by further population structure analysis, with FST analysis and phylogeny tree extracted from the genetic distance determination information. The Icelandic breed had the greatest genetic distance with other studied breed. The GrayShiraz (SDK) and Kermani had the lowest and the highest genetically distance with Icelandic breed, respectively. In order to reduce the bias in selection signatures analysis, Kermani and Chios breeds was excluded from the further analysis. The results of principal component analysis (PCA), four distinc genetic groups was detected based on the information of the 1th component with one of the 2th to 6th components. According to the obtained results, the group with high reproductive performance or litter size (Icelandic) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The 2th to 6th components could demonstration differences among Iranian sheep breeds, and Kermani and Chios sheep breeds (raised in the Chios breeding center in Kerman province) were separated from the Iranian other sheep breeds. In the identified regions as selection signatures (N=55), including 0.1% of all studied markers, the number of 391 genes were identified. Of all detected genes, at least 13 genes including BMPR2, SLC26A4, WNT16, CREB3L4, PRLR, ACVR2B, PRKCSH, HOXA9, HOXA10, Dkks, KATNAL1, OSBP2 and W5PHY6_SHEEP genes were related to reproductive performance and probably litter size in sheep. Although no significant biological pathways (with high significance) related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep, could be effective in designing breeding programs to improve reproductive performance.
Conclusion: Survey on identified biological pathways related to genomic differences between Iranian native and Icelandic (which is considered one of the most significant multi-twin breeds in the world) sheep breeds, was shown that, the significant biological pathways involved in immunity, smell, and hemoglobin construction. Despite of the identification a large number of genes related to The reproductive performances, these genes did not involved in a significant biological pathways. However, although no significant biological pathways related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep breeds could be effective in designing breeding programs to improve reproductive performance.
Background: Due to the increasing demand for animal products, reproductive efficiency considered as one of the main objectives of sheep breeding, even in cases where the main emphasis is on milk or wool production. In cases the meat production is the main breeding objective, increasing reproductive efficiency is the most important goal of breeding programs. Although increasing fertility in ewe is possible in different pathways, ovulation rate and liter size are the main goals in breeding programs to achieve high fertility. Then, this study was performed to detection selection signature between Iranian native (as a genetic group with low reproductive performance) and Icelandic (as a genetic group with high reproductive performance) sheep breeds, and identify genes related to fecundity and litter size in sheep.
Methods: In this regard, the genomic information of 154 samples including 11 Iranian sheep breeds (Kermani, Baluchi, Afshari, Karakul, Sanjabi, SiahKabud, LoriBakhtiari, Shal, Ghezel, Chios, GrayShiraz) and 54 Iceland sheep breeds, were used. The genomic data related to these genetic groups including Icelandic and Iranian sheep breeds were obtained from the iSheep database and the address https://disk.yandex.ru/d/3N2wEv0-9_NL0w, respectively. Quality control of genomic data and filtering was performed using the PLINK software. The individuals and SNP with more than 5% missing genotypes were excluded. Then, the data were screened based on Minor allele frequency (MAF) less than 1%, and Hardy-Weinberg equilibrium (HWE). From the total available data, including 552,847 SNP markers related to autosomal chromosomes with known locations from 204 animals, finally 527,292 SNP markers from 204 animals, with about 0.999376 genotyping rate, was remained for inter-population genetic differentiation and structure analyses. Then, data filtering was done for seprate genetic groups. In this edition of the data, 527,284 SNP markers related to 174 animals were endured to selection signature analysis. Genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. Ubiased FST (θ) estimator statistic were used to explore the signs of selection. In order to better identify the selection signals, numerical values of SNP markers were averaged using the creeping window method up to a maximum length of 100 kb for adjacent SNPs. Only 0.1% of the genome regions with the highest values, were identified and determined as selection signatures. The genes related to selected genomic regions was extracted using the BIOMART online database corresponding areas in the sheep genome assembly (Oar 3.1). The detected genes, related to the selected regions, were surveyed by DAVID 2021 (The Database for Annotation, Visualization and Integrated Discovery) and STRING (Version 12) to identifying biological pathways and probably gene interaction networks.
Results: According to the principal component analysis (PCA) results, the group with high reproductive performance (Icelandic sheep) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The complete differentiation between two groups with low and high reproductive performance can be related to the regional separation of these two groups. Kermani and Chios breeds (from the Chios breeding center in Kerman province of Iran) are seprated from other Iranian breeds with the second component. It was confirmed by further population structure analysis, with FST analysis and phylogeny tree extracted from the genetic distance determination information. The Icelandic breed had the greatest genetic distance with other studied breed. The GrayShiraz (SDK) and Kermani had the lowest and the highest genetically distance with Icelandic breed, respectively. In order to reduce the bias in selection signatures analysis, Kermani and Chios breeds was excluded from the further analysis. The results of principal component analysis (PCA), four distinc genetic groups was detected based on the information of the 1th component with one of the 2th to 6th components. According to the obtained results, the group with high reproductive performance or litter size (Icelandic) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The 2th to 6th components could demonstration differences among Iranian sheep breeds, and Kermani and Chios sheep breeds (raised in the Chios breeding center in Kerman province) were separated from the Iranian other sheep breeds. In the identified regions as selection signatures (N=55), including 0.1% of all studied markers, the number of 391 genes were identified. Of all detected genes, at least 13 genes including BMPR2, SLC26A4, WNT16, CREB3L4, PRLR, ACVR2B, PRKCSH, HOXA9, HOXA10, Dkks, KATNAL1, OSBP2 and W5PHY6_SHEEP genes were related to reproductive performance and probably litter size in sheep. Although no significant biological pathways (with high significance) related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep, could be effective in designing breeding programs to improve reproductive performance.
Conclusion: Survey on identified biological pathways related to genomic differences between Iranian native and Icelandic (which is considered one of the most significant multi-twin breeds in the world) sheep breeds, was shown that, the significant biological pathways involved in immunity, smell, and hemoglobin construction. Despite of the identification a large number of genes related to The reproductive performances, these genes did not involved in a significant biological pathways. However, although no significant biological pathways related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep breeds could be effective in designing breeding programs to improve reproductive performance.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2024/04/28 | Accepted: 2024/08/28
Received: 2024/04/28 | Accepted: 2024/08/28
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