Genomic Sequencing to Detect Cross-Breeding Quality in Dogs: An Example Studying Disorders in Sexual Development

Luciana de Gennaro; Matteo Burgio; Giovanni Michele Lacalandra; Francesco Petronella; Alberto L'Abbate; Francesco Ravasini; Beniamino Trombetta; Annalisa Rizzo; Mario Ventura; Vincenzo Cicirelli

doi:10.3390/ijms251910763

Genomic Sequencing to Detect Cross-Breeding Quality in Dogs: An Example Studying Disorders in Sexual Development

Int J Mol Sci. 2024 Oct 6;25(19):10763. doi: 10.3390/ijms251910763.

Affiliations

¹ Department of Biosciences, Biotechnology and Environment, University of Bari, Via Orabona 4, 70124 Bari, Italy.
² Department of Veterinary Medicine, University of Bari Aldo Moro, S.P. per Casamassima km. 3, 70010 Valenzano, Italy.
³ Institute of Biomembranes, Bioenergetics, and Molecular Biotechnology (IBIOM), 70125 Bari, Italy.
⁴ Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy.

Abstract

Disorders of sexual development (DSDs) in dogs, similar to humans, arise from genetic mutations, gonadal differentiation, or phenotypic sex development. The French Bulldog, a breed that has seen a surge in popularity and demand, has also shown a marked increase in DSD incidence. This study aims to characterize the genetic underpinnings of DSDs in a French Bulldog named Brutus, exhibiting ambiguous genitalia and internal sexual anatomy, and to explore the impact of breeding practices on genetic diversity within the breed. We utilized a comprehensive approach combining conventional cytogenetics, molecular techniques, and deep sequencing to investigate the genetic profile of Brutus. The sequence data were compared to three other male French Bulldogs' genome sequences with typical reproductive anatomy, including Brutus's father and the canine reference genome (CanFam6). We found a Robertsonian fusion involving chromosome 23 previously reported in dogs as a causative mutation responsible for sex reversal syndrome. Our findings revealed a 22% mosaicism (78,XX/77,XX), the absence of the sex-determining region (SRY) gene, and the presence of 43 unique Single Nucleotide Variants (SNVs) not inherited from the father. Notably, the run of homozygosity (ROH) analysis showed Brutus has a higher number of homozygous segments compared to other Bulldogs, with a total length of these fragments 50% greater than the average, strongly suggesting this dog is the product of the mating between siblings. Although no direct causative genes for the DSD phenotype were identified, four candidate loci warrant further investigation. Our study highlighted the need for a better annotated and curated reference dog genome to define genes causative of any specific phenotype, suggests a potential genetic basis for the DSD phenotype in dogs, and underscores the consequences of uncontrolled breeding practices in French Bulldogs. These findings highlight the importance of implementing strategic genetic management to preserve genetic health and diversity in canine populations.

Keywords: French Bulldog; breed; dogs; genomics; run of homozygosity.

MeSH terms

Animals
Breeding*
Disorders of Sex Development* / genetics
Disorders of Sex Development* / veterinary
Dog Diseases / genetics
Dogs
Female
Genome
Genomics / methods
High-Throughput Nucleotide Sequencing
Male
Phenotype
Polymorphism, Single Nucleotide

Grants and funding

We acknowledge financial support under the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.1, Call for tender No. 104 published on 2 February 2022 by the Italian Ministry of University and Research (MUR), funded by the European Union—NextGenerationEU—Project Title Telomere-to-telomere sequencing: the new era of Centromere and neocentromere eVolution (CenVolution)—CUP H53D23003260006—Grant Assignment Decree No. 1015 adopted on 7 July 2023 by the Italian Ministry of Ministry of University and Research (MUR) (M.V.).