Genetic diversity in the Belgian Draught Horse breed as revealed by pedigree analysis and molecular marker data (2010)

Source/description: The native Belgian draught horse (BTP) was bred as a large and well-muscled horse to serve in agriculture and transportation. The reduction in population size after 1950 and the unequal usage of stallions may have reduced the breed’s diversity. Genetic diversity was assessed using both pedigree data and molecular marker genotypes, making a comparison between inbreeding and multilocus heterozygosity feasible.1 Animals: Pedigree analysis was performed on horses born from 2003 to 2009, which corresponds to an approximate generation interval of one (computed in previous analysis). PEDIG and own software routines were used. Blood or hair root samples were collected at national shows in 2008 and 2009 (n = 127), mainly from stallions, and these were genotyped for 14 microsatellites, namely AHT4,2AHT5,2ASB2, ASB17, ASB23, CA425,3HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, VHL20. These include the nine core microsatellites of the ISAG Horse Panel and five additional markers that might be added to this panel in the future. Pedigree diversity: Inbreeding levels in the breed are low (Table S1), but in view of the limited pedigree depth and completeness (Table 1), these levels should be interpreted as a lower limit. Frequent import of animals that are not well integrated with the Belgian data (because of their foreign id numbers) has reduced pedigree depth and may also explain the minor loss of founder diversity (ratio of effective founders to effective ancestors). Although more founders were counted in mares than in stallions, effective diversity is equal between the sexes. Effective size, computed from individual inbreeding,4 varies from 83 to 102, which is in the range recommended for livestock.5 The fluctuations in effective size and in inbreeding may be related to the introduction of recent founders. However, a genetic concentration is expected in the coming generations, because six ancestors explain 31% and 34% of the remaining variability for stallions and mares, respectively. These ancestors were born from 1961 to 1995, which is only 4–6 generations from the sample studied here. Interestingly, the largest contribution to genetic variability is attributed to one mare (8%, born in 1976). Molecular data: Allele frequencies, polymorphism information content, heterozygosity and Hardy. Weinberg eguilibrium (HWE) were computed using Genepop46 (Table S2). On average, 6.07 alleles per locus were counted (standard deviation 1.73), which is on the upper side of the number of alleles reported in German heavy horse breeds (6).7 The least polymorphic locus in the BTP was HTG6 (three alleles) and the most variable was ASB17 (10 alleles), which is in line with overall allele counts.8 Heterozygosity values per locus ranged from 0.805 to 0.264. The overall expected and observed heterozygosities (0.657 ± 0.035 and 0.663 ± 0.012) are very similar to values reported previously in draught horses.7 HWE was not met at locus level for ASB17, HMS6 and HTG10, but a global test did not reject HWE. The average multilocus heterozygosity1 of 0.656 (±0.14) was significantly correlated with the level of inbreeding computed from the pedigree (Pearson correlation = −0.27, P-value 0.004). Our estimate is equal to the mean correlation computed from 12 animal populations.1 The low level of inbreeding in the Belgian draught horse and consequently the low variation in inbreeding levels might explain the poor correlation between (pedigree) inbreeding level and multilocus heterozygosity. Comments: Pedigree analysis and marker data indicate an ‘intermediate’ level of diversity in the Belgian draught, when compared to other horse breeds. Current effective size is in the recommended range and seems to be improving. However, marginal contributions from ancestors indicate a genetic concentration, which may compromise genetic diversity in the coming generations. The two approaches to assess diversity have led to the same general conclusions. Acknowledgements: We thank the breeding associations VFBT and KMBT for providing the pedigree file and for cooperation during sample collection. Funding was provided by FWO (Research Foundation – Flanders). The authors have declared no potential conflicts. Table S1 Diversity measures of Belgian draught horses based on pedigree information. Table S2 Descriptive statistics for 14 microsatellite loci typed on 127 Belgian draught horse individuals. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer-reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. 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