Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Abstract

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data

“…In general, GEN inbreeding coefficients (F ROH, ) were higher than those estimated from the GEL data, but showed a correlation of 0.68. This value is higher than that reported for the Noriker and Austrian Haflinger horse breeds (0.19 and 0.38, respectively) (Druml et al, 2017) and similar to Italian Heavy Draught horses (0.65) (Mancin et al, 2020). Those differences were even more remarkable in PRE_C horses, but showed a lower correlation.…”

“…Although N e estimated with GEN data was larger than that measured with the GEL information in PRE_CI and PRE_ NC, those differences were not detected in PRE_C, where they were very similar (Tables 1 and 3). To our knowledge, our N e estimation for PRE_C is possibly the lowest population size reported to date, compared with other breeds such as Berdigiano (39) (Ablondi et al, 2020), Italian Heavy Draught horse (100) (Mancin et al, 2020), Persian Arabian Horses (113) (Sadeghi et al, 2019), Noriker-Carinthia (104.7), Croatian Coldblood (87.2) and Altmaerkisch Draught Horse (64) (Druml et al, 2007). In fact, many of these breeds are catalogued as endangered.…”

Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs

“…Ablondi et al [ 3 ] evaluated the loss of genetic variability in the Bardigiano breed, based on linkage disequilibrium and provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed, using the average inbreeding based on runs of homozygosity (ROH). Other work, completed by Mancin et al [ 4 ], investigated the genetic diversity in the Italian Heavy Horse breed by using pedigree and genomic data. Pedigree information allowed reliable estimations of inbreeding values, resulting in medium to high correlations with genomic inbreeding.…”

Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses

“…The use of robust pedigrees with completeness indices of around 80% have reported to allow reliable estimations of inbreeding values, resulting in medium to high correlations with genomic inbreeding in horse breeds [ 74 ]. Average values for PCI in PRá, PRE, and Há historical and current populations were 77.07%, 90.13%, 96.13%, 99.01%, 73.26%, and 74.71%, respectively.…”