LINKAGE DISEQUILIBRIUM AND GENETIC DIVERSITY IN TWO SICILIAN CATTLE BREEDS ASSESSED BY BOVINE SNP CHIP

Abstract

The Modicana (MOD) and Cinisara (CIN) are two Sicilian cattle breeds farmed in extensive systems and their economic importance lies on the traditional making of two typical ‘pasta filata’ cheeses. The aim of this study was to explore the genetic structure and the extent of Linkage Disequilibrium (LD) of MOD and CIN cattle breeds. A total of 144 animals were genotyped, using the Bovine SNP50K v2 BeadChip. The squared correlation coefficient between two loci (r2) was used as a measure of LD. Principal components analysis (PCA), molecular inbreeding (F) and Bayesian clustering algorithm (Pritchard et al., 2000) were used to explore the relationship between individuals and populations. The r2 ranged from 0.018±0.026 for BTA5 to 0.106±0.199 for BTA14 in CIN, and from 0.019±0.027 for BTA2 to 0.126±0.221 for BTA14 in MOD. Differences in LD among chromosomes can be attributed to heterozygosity, genetic drift and effect of selection. The highest average value of r2 was on chromosome 14 in both breeds. Mutations in genes located on BTA14 have been found to have an effect on milk production traits. From this fact, it is possible to hypothesize that the highest value of r2 found for BTA 14 in both breeds, may be due to a selection to increase milk production traits make by farmers in an empirical way. Moreover, the value of LD in a genome determines the power of QTL detection in association mapping studies and indicates the required marker density (Meuwissen et al., 2001). The PCA showed that animals from the two breeds form non‐overlapping clusters. The MOD breed clustered alone, with some individuals positioned toward the CIN breed, whereas the CIN showed two clusters. The high F values (0.68 in CIN and 0.69 in MOD) reveal a reduction of genetic variability within population. Considering a range of 1 to 6 potential clusters (K), the highest average likelihood value LnPr(G|K) with the smallest variance between replicates were obtained for K=3. The MOD is the most differentiated population with 76.8% of the individuals assigned to cluster 3, whereas the CIN animals showed a lower value of assignment with a proportion of 54.3% of the individuals assigned to cluster 1. Therefore, although animals from the two breeds clustered separately, model based clustering suggested that certain admixture has occurred and genetic links exist between both breeds. The information generated from this study has important implications in order to maintain the genetic diversity and for future milk breeding programs. Managing of inbreeding provides a general framework to control the loss of variability avoiding or alleviating the reductions in viability and fertility; i.e., inbreeding depression.