Patterns of homozygosity in insular and continental goat breeds

Abstract

BackgroundGenetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds.ResultsAmong the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and FROH values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity.ConclusionsThese results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0425-7) contains supplementary material, which is available to authorized users.

Genetic characterization of a small closed island population of Norwegian coastal goat

“…An alternative measure of inbreeding was based on the proportion of the genome covered by runs of homozygosity (ROH) (F ROH ) relative to the length of the autosome covered by SNP computed using the R package detec-tRUNS (Biscarini et al, 2018). ROH was detected using a sliding window size of 15 SNP, a threshold of overlapping windows of the same state (homozygous/heterozygous) to call an SNP in a run was 0.1, minimum number of SNP in a run of 15 and a maximum number of heterozygous SNP in a sliding window of 1, in agreement with parameters used in a previous study on continental and insular goat breeds (Cardoso et al, 2018).…”

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

“…For both POP A and B 284 it was possible to identify short and long segments in most of the animals analyzed, whereas 285 in the POP C a small number of animals (n = 7) presented ROH8-16 Mb and none ROH>16 Mb. 286 In recent years, some studies have investigated different genomic methods to estimate 287 inbreeding coefficients in cattle [12,25,26,45,47,48], pigs [27,28,49,50], goats [51][52][53] and 288 rainbow trout [32]. However, this is the first study aimed at characterizing the ROH patterns 289 and comparing different genomic-and pedigree-based methods to estimate inbreeding 290 coefficients in farmed coho salmon populations.…”

“…Thus, monitoring and managing the inbreeding levels is critical in the 50 operation of genetic improvement programs [8][9][10]. 51 Inbreeding is traditionally calculated using pedigree records, the estimates might not 52 reflect the true inbreeding level due to 1) the stochastic nature of recombination, 2) the 53 assumption that there are no changes in allele frequencies in time and 3) the persistence of 54 ancestral short segments through time [11]. In addition this approach fails to capture the 55 relatedness among founder animals from the base population [12].…”

Detection of copy number variants in African goats using whole genome sequence data

“…[68], Cardoso et al [69] and Colli et al [70], and some of them were also used for detection of CNV using 50 K SNP chip data, as reported by Liu et al [17]. A list of the breeds, populations and samples sizes used in the analysis is given in Table 4 while a full list of individual samples can be found in Supplementary Table 7 (Additional file 1).…”