Conservation of animal genetic resources: Improvement of the relationship matrix

The main objective of breed conservation is the preservation of genetic diversity. Relationship coefficients are one possibility to measure the genetic variability. With a total size lower than 200 individuals, the Skyros small-horse may be called a small population. It is thus a good example of breed concerned by the management of genetic variability. Genetic variability within the Skyros breed was evaluated, at the genome level, using 16 microsatellites. The Factorial Correspondence Analysis of the molecular data showed that the population could be divided in three groups (Skyros, Thessaloniki and Corfu). A relatively high level of genetic variability within the breed was observed in terms of high values of mean effective number of alleles (3.2), observed heterozygosity (0.647), expected Levene’s heterozygosity (0.622), expected Nei’s heterozygosity (0.625), and polymorphism information content (0.598). This study demonstrated thus the existence of substantial genetic diversity in the Skyros small-horse population although two of the three sub-populations (Thessaloniki and Corfu) underwent a bottleneck. Finally, relationships were estimated using various estimators including a new one, which combines pedigree and markers information. Compared to the others, this combined estimator showed interesting results inter alia a higher correlation with genealogical relationship (0.889 or 0.883 according to the number and to the quality of the markers used). When the results are presented graphically, this estimator also allowed to do a better differentiation between the three sub-populations defined previously.