Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed

• Published in: Genes & genomics Vol. 42; no. 2; pp. 203 - 215
• Main Authors: Moradian, Hasan, Esmailizadeh Koshkoiyeh, Ali, Mohammadabadi, Mohammadreza, Asadi Fozi, Masood
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01.02.2020; Springer Nature B.V; 한국유전학회
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Cattle; Genomes; Haplotypes; Human Genetics; KCNQ3 protein; Life Sciences; Microbial Genetics and Genomics; Phenotypes; Plant Genetics and Genomics; Positive selection; Potassium channels (voltage-gated); Quantitative trait loci; Research Article; Single-nucleotide polymorphism; 생물학; Iranian breed; Selection signatures; Sarabi cattle; Single nucleotide polymorphisms; iHS; Bos taurus
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/s13258-019-00888-6

Background The identification of genomic regions under selection can potentially permit a better understanding of the biology of the specific phenotypes which are useful for the development of tools designed to increase selection efficiency. Objective The aim of this study was to detect any traces of recent selection signatures as well as to identify corresponding genes and QTLs underlying these selection signatures in Sarabi cattle. Methods Samples from 20 animals were genotyped for 777,962 SNPs across the genome using the Illumina BovineHD BeadChip. Selection signatures analysis was performed using the integrated haplotype score (iHS) methodology. Results A total of eight significant regions ( P  < 0.0001) of possible recent selection signatures were detected on BTA14 and BTA17. In addition, nine genes were identified in regions harboring selection signatures, such as KCNQ3, HHLA1, OC90, EFR3A, ADCY8, ASAP1, TMEM132B , and TMEM132C . Study of the reported QTLs in these regions of the bovine genome has showed that they are associated with important traits such as milk, reproduction and production traits. Conclusion The results revealed multiple genomic regions as well as multiple new genes under positive selection on BTA14 and BTA17. Moreover, candidate selected regions that overlap with QTL reported in the cattle QTL database provided additional evidence for the significance of the detected regions under selection. This study provides a foundation for detailed analysis of the identified putative selection signatures in the cattle genome particularly of the indigenous and locally-developed cattle breeds and provides an avenue for a well-structured breed improvement.