Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep

Abstract

BackgroundGenomic technologies, such as high-throughput genotyping based on SNP arrays, have great potential to decipher the genetic architecture of complex traits and provide background information concerning genome structure in domestic animals, including the extent of linkage disequilibrium (LD) and haplotype blocks. The objective of this study was to estimate LD, the population evolution (past effective population size) and the level of inbreeding in Spanish Churra sheep.ResultsA total of 43,784 SNPs distributed in the ovine autosomal genome was analyzed in 1,681 Churra ewes. LD was assessed by measuring r2 between all pairs of loci. For SNPs up to 10 kb apart, the average r2 was 0.329; for SNPs separated by 200–500 kb the average r2 was 0.061. When SNPs are separated by more than 50 Mbp, the average r2 is the same as between non-syntenic SNP pairs (0.003). The effective population size has decreased through time, faster from 1,000 to 100 years ago and slower since the selection scheme started (15–25 generations ago). In the last generation, four years ago, the effective population size was estimated to be 128 animals. Inbreeding coefficients, although differed depending on the estimation approaches, were generally low and showed the same trend, which indicates that since 2003, inbreeding has been slightly increasing in the studied resource population.ConclusionsThe extent of LD in Churra sheep persists over much more limited distances than reported in dairy cattle and seems to be similar to other ovine populations. Churra sheep show a wide genetic base, with a long-term viable effective population size that has been slightly decreasing since selection scheme began in 1986. The genomic dataset analyzed provided useful information for identifying low-level inbreeding in the sample, whereas based on the parameters reported here, a higher marker density than that analyzed here will be needed to successfully conduct accurate mapping of genes underlying production traits and genomic selection prediction in this sheep breed. Although the Ovine Assembly development is still in a draft stage and future refinements will provide a more accurate physical map that will improve LD estimations, this work is a first step towards the understanding of the genetic architecture in sheep.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

“…However, it should be Runs of homozygosity in three local cattle breeds underlined that some parameters, as density and frequency of SNP pairs and distribution of MAF, affect the estimations of LD (Ober et al, 2013) and then of N e . Moreover, the methods used to convert physical distances between SNP pairs to genetic distance may result in different estimated N e values (García-Gámez et al, 2012). Estimate of N e obtained in this study for Italian Holstein was closed to those previously published for other Holstein population (Rodríguez-Ramilo et al, 2015).…”

Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips

“…Although the values were not consistent across the chromosomes, LD estimates were slightly greater for longer chromosomes compared to shorter chromosomes. Differences in LD among chromosomes have been reported in cattle (Khatkar et al 2008;Lu et al 2012) and sheep (García-Gámez et al 2012). These differences might be attributed to variation in autosomal recombination rates, genetic drift and selection influences (Arias et al 2009;Qanbari et al 2010).The variation in LD across autosomal chromosomes implies that LD estimates based on a limited number of chromosomes are likely to be inaccurate (Khatkar et al 2008).…”

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

“…Our findings can be compared directly with results from other studies conducted using a similar LD measure and SNP panel. For example, García-Gámez et al (2012), in Spanish Churra sheep, reported an average r 2 of 0.061 for SNPs separated by 200 to 500 kb. Mastrangelo et al (2014) reported an average r 2 for adjacent SNP pairs of 0.155, 0.156 and 0.128 in the Valle del Belice, Comisana and Pinzirita breeds, respectively.…”

“…The application of recently developed genomic technology has great potential to increase our understanding of the genetic architecture of complex traits, to improve selection efficiency in domestic animals through genomic selection, and to conduct association studies (García-Gámez et al, 2012). The success of these applications depends on the extent of linkage disequilibrium (LD) across the genome.…”