Detecting selection signatures in three Iranian sheep breeds

• Published in: Animal genetics Vol. 50; no. 3; pp. 298 - 302
• Main Authors: Manzari, Z., Mehrabani‐Yeganeh, H., Nejati‐Javaremi, A., Moradi, M. H., Gholizadeh, M.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.06.2019
• Subjects: Bioinformatics; Calcium channels (voltage-gated); candidate regions; Domestication; F ST; Gene mapping; Genetic diversity; Genomes; Genotypes; Haplotypes; Homozygosity; Identification methods; Linkage disequilibrium; Mapping; Nervous system; Ovis aries; Phenotypes; selective sweeps; Sheep; Signatures; Skeletal system; Sugar; XP‐EHH; candidate regions; F ST; selective sweeps; XP-EHH
• ISSN: 0268-9146; 1365-2052
• DOI: 10.1111/age.12772

Summary The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype–phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP‐EHH (cross‐population extend haplotype homozygosity) and FST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori‐Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.