Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations
IntroductionIdentifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship be...
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Frontiers Media S.A.
2024-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1414717/full |
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| author | Sadegh Taheri Ali Javadmanesh Saeed Zerehdaran |
| author_facet | Sadegh Taheri Ali Javadmanesh Saeed Zerehdaran |
| author_sort | Sadegh Taheri |
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| description | IntroductionIdentifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs).MethodsGenomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection.ResultsThe results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN, and USP25, while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3, and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage.DiscussionThese results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep. |
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| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-993c878e59d540168e1f1e72d41bb7e32024-12-19T06:24:07ZengFrontiers Media S.A.Frontiers in Genetics1664-80212024-12-011510.3389/fgene.2024.14147171414717Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populationsSadegh TaheriAli JavadmaneshSaeed ZerehdaranIntroductionIdentifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs).MethodsGenomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection.ResultsThe results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN, and USP25, while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3, and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage.DiscussionThese results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep.https://www.frontiersin.org/articles/10.3389/fgene.2024.1414717/fulldomestic and wild sheepiHSRSBselective sweepQTLXP-EHH |
| spellingShingle | Sadegh Taheri Ali Javadmanesh Saeed Zerehdaran Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations Frontiers in Genetics domestic and wild sheep iHS RSB selective sweep QTL XP-EHH |
| title | Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations |
| title_full | Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations |
| title_fullStr | Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations |
| title_full_unstemmed | Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations |
| title_short | Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations |
| title_sort | identification of selective sweep and associated qtl traits in iranian ovis aries and ovis orientalis populations |
| topic | domestic and wild sheep iHS RSB selective sweep QTL XP-EHH |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1414717/full |
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