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

Enrico Mancin,Roberto Mantovani,Alberto Sabbioni,Michela Ablondi,Cristina Sartori,Giuseppe Pigozzi

doi:10.3390/ani10081310

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.

Highlights

The conservation and management of domestic animal genetic diversity has become a key issue in modern livestock breeding since the globalization of breeding programs [1]
Pedigree completeness measured as pedigree completeness index (PC) index was 87.5%, increasing to 98.2% in the reference population defined as animals born from 2010
The pedigree completeness increased over time, but a quick reduction in completeness happened at the end of 1970s

Summary

Introduction

The conservation and management of domestic animal genetic diversity has become a key issue in modern livestock breeding since the globalization of breeding programs [1]. The increase in recessive allele frequency, and reduced performances in traits of breeding interest are the main consequences of mating among relatives [2]. The availability and completeness of population data are key aspects to assess genetic variability and develop strategic goals in biodiversity conservation [3]. The availability of high-density SNP chips has fostered the development of new tools to assess genetic diversity, offering a detailed picture of diversity across the genome [4]. The correlation between pedigree-based and molecular diversity depends on the completeness of pedigree information, as well as on the number and frequency of molecular markers

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Discussion

Conclusion