Genetic Diversity and Selection Signatures in Sheep Breeds

Overview

Journal J Appl Genet

Publisher Springer

Date 2025 Jan 30

PMID 39883377

Authors

Julia Lisboa Rodrigues

Larissa Graciano Braga

Rafael Nakamura Watanabe

Flavio Schramm Schenkel

Donagh Pearse Berry

Marcos Eli Buzanskas

Danisio Prado Munari

Affiliations

Soon will be listed here.

Abstract

Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.

References

Abdoli R, Zamani P, Mirhoseini S, Ghavi Hossein-Zadeh N, Nadri S . A review on prolificacy genes in sheep. Reprod Domest Anim. 2016; 51(5):631-7. DOI: 10.1111/rda.12733. View

Alvarez I, Fernandez I, Traore A, Perez-Pardal L, Menendez-Arias N, Goyache F . Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Rep. 2020; 10(1):2824. PMC: 7028950. DOI: 10.1038/s41598-020-59839-x. View

Bao J, Xiong J, Huang J, Yang P, Shang M, Zhang L . Genetic Diversity, Selection Signatures, and Genome-Wide Association Study Identify Candidate Genes Related to Litter Size in Hu Sheep. Int J Mol Sci. 2024; 25(17). PMC: 11395453. DOI: 10.3390/ijms25179397. View

Brito L, Kijas J, Ventura R, Sargolzaei M, Porto-Neto L, Canovas A . Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics. 2017; 18(1):229. PMC: 5348779. DOI: 10.1186/s12864-017-3610-0. View

Brito L, McEwan J, Miller S, Pickering N, Bain W, Dodds K . Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip. BMC Genet. 2017; 18(1):25. PMC: 5348757. DOI: 10.1186/s12863-017-0492-8. View

Browning B, Zhou Y, Browning S . A One-Penny Imputed Genome from Next-Generation Reference Panels. Am J Hum Genet. 2018; 103(3):338-348. PMC: 6128308. DOI: 10.1016/j.ajhg.2018.07.015. View

Cadiz M, Lopez M, Diaz-Dominguez D, Caceres G, Yoshida G, Gomez-Uchida D . Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus). Sci Rep. 2020; 10(1):11514. PMC: 7359307. DOI: 10.1038/s41598-020-68064-5. View

Cao Y, Song X, Shan H, Jiang J, Xiong P, Wu J . Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms. Front Genet. 2020; 11:588. PMC: 7350885. DOI: 10.3389/fgene.2020.00588. View

Cao Y, Xu S, Shen M, Chen Z, Gao L, Lv F . Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol. 2020; 38(3):838-855. PMC: 7947771. DOI: 10.1093/molbev/msaa236. View

10.

Carlson C, Thomas D, Eberle M, Swanson J, Livingston R, Rieder M . Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 2005; 15(11):1553-65. PMC: 1310643. DOI: 10.1101/gr.4326505. View

11.

Estrada-Reyes Z, Rae O, Postley C, Jimenez Medrano M, Leal Gutierrez J, Mateescu R . Association study reveals Th17, Treg, and Th2 loci related to resistance to Haemonchus contortus in Florida Native sheep1. J Anim Sci. 2019; 97(11):4428-4444. PMC: 6827414. DOI: 10.1093/jas/skz299. View

12.

Estrada-Reyes Z, Tsukahara Y, Amadeu R, Goetsch A, Gipson T, Sahlu T . Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genomics. 2019; 20(1):735. PMC: 6792194. DOI: 10.1186/s12864-019-6150-y. View

13.

Eydivandi S, Roudbar M, Karimi M, Sahana G . Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep. 2021; 11(1):2834. PMC: 7854752. DOI: 10.1038/s41598-021-82625-2. View

14.

Fariello M, Servin B, Tosser-Klopp G, Rupp R, Moreno C, San Cristobal M . Selection signatures in worldwide sheep populations. PLoS One. 2014; 9(8):e103813. PMC: 4134316. DOI: 10.1371/journal.pone.0103813. View

15.

Fay J, Wu C . Hitchhiking under positive Darwinian selection. Genetics. 2000; 155(3):1405-13. PMC: 1461156. DOI: 10.1093/genetics/155.3.1405. View

16.

Garud N . Understanding soft sweeps: a signature of rapid adaptation. Nat Rev Genet. 2023; 24(7):420. PMC: 9936460. DOI: 10.1038/s41576-023-00585-x. View

17.

Gautier M, Vitalis R . rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics. 2012; 28(8):1176-7. DOI: 10.1093/bioinformatics/bts115. View

18.

Geibel J, Reimer C, Weigend S, Weigend A, Pook T, Simianer H . How array design creates SNP ascertainment bias. PLoS One. 2021; 16(3):e0245178. PMC: 8009414. DOI: 10.1371/journal.pone.0245178. View

19.

Hu Z, Park C, Reecy J . Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Res. 2018; 47(D1):D701-D710. PMC: 6323967. DOI: 10.1093/nar/gky1084. View

20.

Jeruzal-Swiatecka J, Fendler W, Pietruszewska W . Clinical Role of Extraoral Bitter Taste Receptors. Int J Mol Sci. 2020; 21(14). PMC: 7404188. DOI: 10.3390/ijms21145156. View