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 (f_a/f_e). 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 f_a/f_e 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.

Keywords: Italian Heavy Draught Horse; ROH; SNP; effective population size; genetic diversity; genomic; horse; inbreeding; pedigree; selection signatures.

Figure 1

Trend of average relatedness (AR), traditional (F_trad), and recursive (F_rec) inbreeding in the last 90 years.

Figure 2

Distribution of genomic inbreeding coefficients based on the comparison of observed and expected homozygous genotypes (F_het) and on ROH (F_roh) in genotyped individuals.

Figure 3

Comparison of inbreeding values obtained using different methods (definitions of methods in the text). The pie charts report the correlations (in red) between each pair of individual inbreeding values obtained with different methods.

Figure 4

Estimation of genomic effective population size (Ne) traced back to 18 generations ago.

Figure 5

Population structure of Italian Heavy Draught Horse breed. From the top to the bottom: (a) clustering output for K = 2 (subpop1 and subpop2) for genotyped individuals. Each individual is represented by one vertical line with the proportion of assignment to each cluster (ancestry proportion) on the y-axis; (b) population structure network for genotyped individuals, considering subpop1 and subpop2 resulted in (a). Individuals are nodes, and their relative genetic distances are represented by lines; (c) ancestors explaining 50% of the genetic diversity for subpop1 and subpop2. The same ancestors in the two groups have the same color and label, and the other ancestors are in a gray–black scale; (d) plot of individual genomic inbreeding (F_roh) in subpop1 and subpop2.