Molecular analysis of genetic diversity, population structure and inbreeding level of the Italian Lipizzan horse

摘要

In this study, we examine the population structure and inbreeding level of the Italian Lipizzan horse breed by means of AFLP fingerprinting and SSR genotyping. A total of 245 AFLP marker alleles were scored across all horses (n=140) living in the Italian Lipizzan stud in 2007, and microsatellite analysis was performed on all mares (n=42) and stallions (n=7) by genotyping at 30 SSR marker loci. A total of 53 (21.6%) AFLP marker alleles were scored as polymorphic among the animals, with a mean frequency of 0.722. Based on this subset of markers, 123 animals were assigned to three distinct subgroups of 44, 41 and 38 animals, respectively, each one showing a within-subgroup mean Dice's genetic similarity around 86% (standard error < 0.3%), whereas the remaining 17 animals that displayed an admixed ancestry (membership < 45%) were clustered apart, with a between-subgroup genetic similarity spanning from 80% to 83%. All animals could be discriminated from each other on the basis of multi-locus DNA fingerprints. However, only 6% of the genetic variation was found among subgroups, as supported by the low fixation index F-st=0.058. In the mares and stallions, a total number of 146 marker alleles were detected across the assayed SSR loci, with a mean marker allele frequency of 0.485 and an observed and effective number of alleles per locus of 4.710 and 2.921, respectively. The Nei's unbiased heterozygosity for the Italian Lipizzan horse breed was equal to H=63.5% and the Wright's inbreeding coefficient had an average value of F-is=-0.133, suggesting an excess of heterozygosity. Significant (P < 0.01) pair-wise linkage disequilibria between AFLP marker alleles as well as between SSR marker alleles were found in the whole Lipizzan population. It was found that mating plan optimization could reduce the average relatedness to 0.619, a lower value than that obtained by casual unions between stallions and mares (0.740). The findings described here will be useful for the indirect selection of animals based on markers linked to traits of interest and for the assessment of conservation priorities and strategies