Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

Open Access

Abstract

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. ; This research was partially funded by a grant (RZ2011-00015-C03-01) from the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (Spain). We acknowledge the support of the Spanish Ministerio de Economía y Competitividad for the Centro de Excelencia Severo Ochoa 2016–2019 award SEV-2015-0533. We are indebted to all the veterinarians that, in the course of sanitation campaigns and paternity controls, provided us sheep blood samples. We would also like to thank María Inés Fariello for helpful advice when performing the HapFLK analyses. Many thanks also to the International Sheep Genomics Consortium (and specially to Drs. Hans Lenstra and Elena Ciani) for kindly providing ovine 50 K data from 5 Spanish breeds. Taina F Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education (MEC) of the Federal Government of Brazil. ; Peer reviewed