Low genome‐wide homozygosity in 11 Spanish ovine breeds

Abstract

The population of Spanish sheep has decreased from 24 to 15 million heads in the last 75 years due to multiple social and economic factors. Such a demographic reduction might have caused an increase in homozygosity and inbreeding, thus limiting the viability of local breeds with excellent adaptations to harsh ecosystems. The main goal of our study was to investigate the homozygosity patterns of 11 Spanish ovine breeds and to elucidate the relationship of these Spanish breeds with reference populations from Europe, Africa and the Near East. By using Ovine SNP50 BeadChip data retrieved from previous publications, we have found that the majority of studied Spanish ovine breeds have close genetic relatedness with other European populations; the one exception is the Canaria de Pelo breed, which is similar to North African breeds. Our analysis has also demonstrated that, with few exceptions, the genomes of Spanish sheep harbor fewer than 50 runs of homozygosity (ROH) with a total length of less than 350 Mb. Moreover, the frequencies of very long ROH (>30 Mb) are very low, and the inbreeding coefficients (F ROH ) are generally small (F ROH < 0.10), ranging from 0.008 (Rasa Aragonesa) to 0.086 (Canaria de Pelo). The low levels of homozygosity observed in the 11 Spanish sheep under analysis might be due to their extensive management and the high number of small to medium farms.

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

“…The ROH hotspot with highest SNP occurrence was located on OAR6 , which consisted of the NCAPG/LCORL gene. Similar findings were also reported in Italian sheep breeds [22], Spanish sheep breeds [21], Swiss sheep breeds, and Merino [18,31]. Moreover, the selective signatures in NCAPG/LCORL region were found in many sheep breeds [18,32,33], including Merino [34].…”

“…In Chinese Merino, the mean values of F ROH were all less than 0.03, suggesting the low levels of inbreeding in this breed (Table 1). Similar F ROH values were found in Italian sheep breeds and Spanish sheep breeds [21,22]. The main reason is that Chinese Merino sheep do not undergo intense selection and have a large effective population size [28].…”

“…The maximum frequency of SNPs in ROH in Chinese Merino was around 6.15%-9.46%, Similar SNP frequency in ROH was found in Italian sheep breeds and Spanish sheep breeds [21,22]. On the contrary, the incidence of SNPs in commercial meat sheep breeds is higher than 20% [19].…”

“…Taken altogether, these results suggest that the ROH hotspots detected on OAR6 (35.07-38.67 Mb) and OAR11 (28.02-28.52 Mb) in Chinese Merino are caused by the artificial selection for body size trait performed on candidate genes. The ROH on OAR10 found in this study overlapped a common ROH island in Swiss sheep breeds [18] and Spanish sheep breeds [21]. More importantly, relaxin-like receptor 2 (RXFP2) gene was harbored in this genomic region.…”

“…The obtained data were plotted against the chromosomal positions of SNPs. The genomic regions with top 1% SNPs were considered as a potential ROH ROH hotspot in the genome [21,22].…”