Patterns of homozygosity in insular and continental goat breeds

Abstract

Background: Genetic 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.

Results: Among 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 F_ROH 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.

Conclusions: These 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.

Fig. 1

a PCA plot of individuals from 25 insular or continental populations. Red and dark blue indicate insular and continental breeds, respectively, with a high level of homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with a low or moderate level of homozygosity. b Neighbor-joining tree based on allele-sharing distances representing the genetic relationships among insular and continental goat populations

Fig. 2

Number and total length of ROH in African, European and Mediterranean insular and continental goat populations. Red and dark blue indicate insular and continental breeds, respectively, with a high level of homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with a low or moderate level of homozygosity. The number of ROH found for each individual genome (y-axis) is plotted against total ROH size (i.e. number of Mb covered by ROH in each genome, x-axis). The following codes are used (insular populations in bold): AND, Androy (Madagascar); ARG, Argentata (Sicily); ARR, Arran (Ireland); ASP, Aspromontana; BLB, Bilberry (Ireland); CCG, Ciociara Grigia; CRS, Corse (Corsica); DIA, Diana (Madagascar); DKL, Danish Landrace; DUL, Dutch Landrace; FIN, Finnish Landrace; FSS, Fosses; GGT, Girgentana (Sicily); ICL, Icelandic goats (Iceland); MAL, Mallorquina (Mallorca); MEN, Menabe (Madagascar); MLS, Maltese Sarda (Sardinia); MOR, Moroccan goat; MTB, Matebele; MUL, Mulranny (Ireland); PAL, Palmera (La Palma); RAS, Blanca de Rasquera; SAR, Sarda (Sardinia); SOF, Sofia (Madagascar); SOU, SudOuest (Madagascar)

Fig. 3

Statistical analysis of the mean ROH numbers, ROH coverage and F_ROH. Red and dark blue indicate insular and continental breeds, respectively, with high homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with low or modest homozygosity. Different letters indicate statistically significant differences between groups (mean ± standard error, linear models with heteroscedastic within group-errors, P_adj-value < 0.05). The following codes are used (insular populations in bold): AND, Androy (Madagascar); ARG, Argentata (Sicily); ARR, Arran (Ireland); ASP, Aspromontana; BLB, Bilberry (Ireland); CCG, Ciociara Grigia; CRS, Corse (Corsica); DIA, Diana (Madagascar); DKL, Danish Landrace; DUL, Dutch Landrace; FIN, Finnish Landrace; FSS, Fosses; GGT, Girgentana (Sicily); ICL, Icelandic goats (Iceland); MAL, Mallorquina (Mallorca); MEN, Menabe (Madagascar); MLS, Maltese Sarda (Sardinia); MOR, Moroccan goat; MTB, Matebele; MUL, Mulranny (Ireland); PAL, Palmera (La Palma); RAS, Blanca de Rasquera; SAR, Sarda (Sardinia); SOF, Sofia (Madagascar); SOU, SudOuest (Madagascar)

Fig. 4

Plot of the fraction of the genome covered by ROH (F_ROH) in insular (red) and continental (blue) goat populations. The following codes are used (insular populations in bold): AND, Androy (Madagascar); ARG, Argentata (Sicily); ARR, Arran (Ireland); ASP, Aspromontana; BLB, Bilberry (Ireland); CCG, Ciociara Grigia; CRS, Corse (Corsica); DIA, Diana (Madagascar); DKL, Danish Landrace; DUL, Dutch Landrace; FIN, Finnish Landrace; FSS, Fosses; GGT, Girgentana (Sicily); ICL, Icelandic goats (Iceland); MAL, Mallorquina (Mallorca); MEN, Menabe (Madagascar); MLS, Maltese Sarda (Sardinia); MOR, Moroccan goat; MTB, Matebele; MUL, Mulranny (Ireland); PAL, Palmera (La Palma); RAS, Blanca de Rasquera; SAR, Sarda (Sardinia); SOF, Sofia (Madagascar); SOU, SudOuest (Madagascar)

Fig. 5

Distribution of ROH according to their size in African, European and Mediterranean insular and continental goat populations. The following codes are used (insular populations in bold): AND, Androy (Madagascar); ARG, Argentata; ARR, Arran (Ireland); ASP, Aspromontana; BLB, Bilberry (Ireland); CCG, Ciociara Grigia; CRS, Corse (Corsica); DIA, Diana (Madagascar); DKL, Danish Landrace; DUL, Dutch Landrace; FIN, Finnish Landrace; FSS, Fosses; GGT, Girgentana (Sicily); ICL, Icelandic goats (Iceland); MAL, Mallorquina (Mallorca); MEN, Menabe (Madagascar); MLS, Maltese Sarda (Sardinia); MOR, Moroccan goat; MTB, Matebele; MUL, Mulranny (Ireland); PAL, Palmera (La Palma); RAS, Blanca de Rasquera; SAR, Sarda (Sardinia); SOF, Sofia (Madagascar); SOU, SudOuest (Madagascar)