Sustainable breeding and conservation of an autochthonous cattle breed: managing undesirable alleles and inbreeding in the Reggiana population

The Reggiana breed, an Italian autochthonous cattle genetic resource mainly reared in the Emilia Romagna region, holds a great cultural and economic importance due to the production of the exclusive mono-breed Protected Designation of Origin (PDO) Parmigiano-Reggiano cheese. Maintaining the integrity of this breed is essential for both economic and cultural reasons. The conservation of its genetic diversity provides a significant source of income for farmers in the Emilia Romagna region. Analysing allele frequencies across the population can identify the presence of potential disadvantageous alleles or alleles that may confer non-breed specific characteristics, carried by few heterozygous animals. Although these alleles exist at low frequencies, their potential impact on herd health, breed identity and economic losses could be substantial if not properly managed. For instance, if allele frequencies increase due to genetic drift or inappropriate breeding choices, homozygous animals may exhibit harmful phenotypes or undesirable traits. In this study, a population of approximately 4,000 Reggiana cattle, covering almost the entire breed and all the active sires, using the GeneSeek GGP Bovine 150k SNP chip to identify and manage undesirable alleles that could represent a risk to the breed's health, productivity, and long-term sustainability. Genotyping data were filtered and analysed using PLINK 1.9 software and ad-hoc Python and R scripts. Haplotypes were estimated with SHAPEIT software and the Ghap R package. The study revealedthe presence of several undesirable alleles in heterozygous carriers, already characterised in other cosmopolitan cattle breeds such as Brown Swiss and Holstein. Potential disadvantageous alleles and haplotypes were identified in a few animals, ranging from a minimum of 3 to a maximum of 143 carriers. These alleles, including BH2, HH1, HH3, and JH1, are associated with reproductive issues such as reduced fertility, stillbirths, and postnatal mortality if found in a homozygous state. Additionally, genomic inbreeding in the breed was monitored using runs of homozygosity. The findings highlight the necessity of implementing targeted breeding strategies, such as limiting pairings between carriers of undesirable alleles to eliminate these alleles and their potential impact on population health, without compromising the breed diversity. Inbreeding should also be controlled by introducing optimum contribution selection. These strategies are crucial for the sustainability of this genetic resource and provide a model for the conservation of small autochthonous livestock breeds. This study was carried out within the Agritech National Research Center (Spoke 1) and received funding from the European Union Next-GenerationEU under the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4, Call D. D.3138 published on 12/16/2021 amended D.D. 3175 on 18/12/2021, CN00000022 – CUP J33C22001150008.