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

Risultato della ricerca: Other

Abstract

The Modicana (MOD) and Cinisara (CIN) are two Sicilian cattle breeds farmed in extensive systems and theireconomic importance lies on the traditional making of two typical ‘pasta filata’ cheeses. The aim of thisstudy was to explore the genetic structure and the extent of Linkage Disequilibrium (LD) of MOD and CINcattle breeds.A total of 144 animals were genotyped, using the Bovine SNP50K v2 BeadChip. The squared correlationcoefficient 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 therelationship 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 BTA2to 0.126±0.221 for BTA14 in MOD. Differences in LD among chromosomes can be attributed toheterozygosity, genetic drift and effect of selection. The highest average value of r2 was on chromosome 14in both breeds. Mutations in genes located on BTA14 have been found to have an effect on milk productiontraits. From this fact, it is possible to hypothesize that the highest value of r2 found for BTA 14 in bothbreeds, 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 mappingstudies and indicates the required marker density (Meuwissen et al., 2001). The PCA showed that animalsfrom the two breeds form non‐overlapping clusters. The MOD breed clustered alone, with some individualspositioned toward the CIN breed, whereas the CIN showed two clusters. The high F values (0.68 in CIN and0.69 in MOD) reveal a reduction of genetic variability within population. Considering a range of 1 to 6potential clusters (K), the highest average likelihood value LnPr(G|K) with the smallest variance betweenreplicates were obtained for K=3. The MOD is the most differentiated population with 76.8% of theindividuals assigned to cluster 3, whereas the CIN animals showed a lower value of assignment with aproportion of 54.3% of the individuals assigned to cluster 1. Therefore, although animals from the twobreeds clustered separately, model based clustering suggested that certain admixture has occurred andgenetic links exist between both breeds.The information generated from this study has important implications in order to maintain the geneticdiversity and for future milk breeding programs. Managing of inbreeding provides a general framework tocontrol the loss of variability avoiding or alleviating the reductions in viability and fertility; i.e., inbreedingdepression.
Lingua originaleEnglish
Pagine240-240
Numero di pagine1
Stato di pubblicazionePublished - 2013

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