The Reggiana cattle breed, native to the Emilia-Romagna region in the North of Italy, holds cultural and economic value due to its exclusive production of mono-branded PDO Parmigiano-Reggiano cheese. The conservation of this genetic resource is crucial for the sustainability of the value chain linked to this breed. The selection of animals in breeding management is a key factor in preventing inbreeding depression and the emerging disadvantageous alleles. High-throughput genotyping technologies offer a cost-effective solution for analysing livestock populations at a genome-wide level. This study aimed to identify potentially disadvantageous alleles or haplotypes in the Reggiana breed population combing different genomic information. A total of 4,000 Reggiana cattle, representing nearly the entire breed, and including 280 sires, was genotyped using the GeneSeek GGP Bovine 150k SNP chip and the genome of approximately 100 cattle was sequenced at 20X. Through the use of PLINK 1.9, SHAPEIT and ad-hoc scripts, several low-frequency alleles or haplotypes, which were never identified in homozygous state and located in genomic regions known to harbour reproduction relevant genes, were detected to be potentially associated with reduced fertility, stillbirths, and postnatal mortality. The study revealed up to 143 carriers of undesirable alleles, underscoring the importance for careful breeding strategies. These findings highlight the need of targeted breeding practices to mitigate the risks posed by these alleles while preserving diversity. The results could play a key role ensuring the long-term sustainability of the Reggiana breed and serve as a model for other local livestock conservation efforts. Funded within the Agritech National Research Center (Spoke 1) and 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
Schiavo, G., Bovo, S., Bertolini, F., Bolner, M., Ribani, A., Taurisano, V., et al. (2025). Mining genomic data in Reggiana cattle genetic resource to identify and manage potential deleterious alleles.
Mining genomic data in Reggiana cattle genetic resource to identify and manage potential deleterious alleles
G. Schiavo
;S. Bovo;F. Bertolini;M. Bolner;A. Ribani;V. Taurisano;S. Dall'Olio;L. Fontanesi
2025
Abstract
The Reggiana cattle breed, native to the Emilia-Romagna region in the North of Italy, holds cultural and economic value due to its exclusive production of mono-branded PDO Parmigiano-Reggiano cheese. The conservation of this genetic resource is crucial for the sustainability of the value chain linked to this breed. The selection of animals in breeding management is a key factor in preventing inbreeding depression and the emerging disadvantageous alleles. High-throughput genotyping technologies offer a cost-effective solution for analysing livestock populations at a genome-wide level. This study aimed to identify potentially disadvantageous alleles or haplotypes in the Reggiana breed population combing different genomic information. A total of 4,000 Reggiana cattle, representing nearly the entire breed, and including 280 sires, was genotyped using the GeneSeek GGP Bovine 150k SNP chip and the genome of approximately 100 cattle was sequenced at 20X. Through the use of PLINK 1.9, SHAPEIT and ad-hoc scripts, several low-frequency alleles or haplotypes, which were never identified in homozygous state and located in genomic regions known to harbour reproduction relevant genes, were detected to be potentially associated with reduced fertility, stillbirths, and postnatal mortality. The study revealed up to 143 carriers of undesirable alleles, underscoring the importance for careful breeding strategies. These findings highlight the need of targeted breeding practices to mitigate the risks posed by these alleles while preserving diversity. The results could play a key role ensuring the long-term sustainability of the Reggiana breed and serve as a model for other local livestock conservation efforts. Funded within the Agritech National Research Center (Spoke 1) and 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 J33C22001150008I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
