Academic Journal
Genome-wide scan for runs of homozygosity in South American Camelids
| العنوان: | Genome-wide scan for runs of homozygosity in South American Camelids |
|---|---|
| المؤلفون: | Pallotti S., Picciolini M., Antonini M., Renieri C., Napolioni V. |
| المساهمون: | Pallotti, S., Picciolini, M., Antonini, M., Renieri, C., Napolioni, V. |
| سنة النشر: | 2023 |
| المجموعة: | ENEA Open Archive (Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo economico sostenibile) |
| مصطلحات موضوعية: | Alpaca, Domestication, Guanaco, Llama, Runs of homozygosity, Signatures of selection, South American camelids, Vicugna |
| الوصف: | Background: Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results: A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500kb) and genomic inbreeding values. Longer ROHs (> 500kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions: The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | volume:24; numberofpages:11; journal:BMC GENOMICS; https://hdl.handle.net/20.500.12079/73970; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85168446843; https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09547-3 |
| DOI: | 10.1186/s12864-023-09547-3 |
| الاتاحة: | https://hdl.handle.net/20.500.12079/73970 https://doi.org/10.1186/s12864-023-09547-3 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09547-3 |
| Rights: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.B59515FE |
| قاعدة البيانات: | BASE |
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