Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets

Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

BACKGROUND

Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology.

RESULTS

We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates.

CONCLUSIONS

The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

Validated DNA isolation method ensuring successful long-read sequencing of cattle semen genome

Obtaining high-quality DNA suitable for long-read sequencing can be difficult for many types of tissues and cells, and it is a key step in current genomic studies. The challenge is even greater when it comes to isolating genomic DNA from mammalian spermatozoa, as DNA is tightly packed into a cell with a robust membrane rich in disulfide bonds. Here we describe a method for isolating high molecular weight DNA from Bovine commercial semen straws. This protocol includes a cleaning step to remove diluents and preservatives used for the long-term storage of the semen, which may affect long read sequencing. It is based on a simple salting-out method and avoid the use of spin columns, strong mixing or intensive centrifugation, in order to limit DNA fragmentation. However, we have adapted this protocol to facilitate the disruption of cell membranes and disulfide bonds with strong chaotropic and reducing agents. The average size of the fragments produced was approximately 49 kb, ranging from 25 to 85 kb, according to the femto pulse profiles.This method was used to isolate DNA from semen straws, more than 80 of them were successfully sequenced using the Continuous Long-Read (CLR) sequencing mode on the PacBio SequelII platform to study genome diversity and notably to detect large structural variations within genomes.

A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle

BACKGROUND

Nine male and eight female calves born to a Normande artificial insemination bull named "Ly" were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality.

RESULTS

Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes.

CONCLUSIONS

In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.

Identification of a common haplotype in carriers of rob(1;29) in 32 Italian cattle breeds

Robertsonian translocation 1;29 (rob(1;29)), a widespread chromosomal anomaly affecting cattle fertility, appears to have originated from a common ancestor. This study utilizes routine SNP data to investigate the chromosomal region associated with rob(1;29) and confirm the presence of a shared haplotype among carriers in diverse Italian breeds. Three datasets were employed: Dataset 1 included 151 subjects from 5 beef cattle breeds genotyped with the GGP Bovine 33 k SNP chip; Dataset 2 encompassed 800 subjects from 32 Italian breeds genotyped with the Illumina 50 k SNP chip, sourced from the BOVITA dataset; Dataset 3 combined Dataset 2 with 21 karyologically tested subjects from breeds with a high carrier frequency, genotyped using the Affymetrix 65 K SNP chip. FST analysis pinpointed a distinctive genomic region on the first six Mb of BTA29, the centromeric region involved in the translocation. Haplotype comparisons within this non-recombining region revealed a common haplotype shared among all carriers, supporting the theory of a common ancestor. Principal component and haplotype analysis allowed clear differentiation of rob(1;29) homozygous and heterozygous carriers. Expanding to Dataset 2 revealed rob(1;29) carriers in unexpected breeds, all sharing the same ancestral haplotype. Notably, previously untested breeds, including Cinisara, exhibited a high carrier prevalence (nearly 50%), confirmed by karyological analysis. This study validates the presence of a shared haplotype among all identified rob(1;29) carriers, reinforcing the common ancestor theory as the origin of this translocation's spread throughout the cattle population. Furthermore, it underscores the potential of SNP data analysis as a rapid, accurate, and cost-effective tool for broad rob(1;29) screening, given the translocation's consistent nature across all analyzed breeds.

Characterization of Robertsonian and Reciprocal Translocations in Cattle through NGS

This study presents a novel approach that combines next-generation sequencing (NGS) and cytogenetic technologies for identifying chromosomes involved in chromosomal anomalies. This research focuses on a chromosome anomaly discovered in male Alpine Grey cattle, as well as two previously reported cases of reciprocal translocations (rcps), namely rcp(9;11) and rcp(4;7). Abnormal chromosomes from Alpine Grey cattle were microdissected from conventional preparations, and the amplified products were sequenced using NGS. The sequencing reads were then mapped to the reference genome, and the leverage effect was calculated to identify abnormal reads/Mb values. The result revealed the presence of rob(26;29), which was further confirmed through traditional cytogenetic analyses such as Giemsa staining, CBA-banding, RBA-banding, and FISH techniques. Furthermore, the feasibility of this approach on preserved metaphases was demonstrated through analysis of old slides from previously characterized cases. The study highlights the challenges involved in identifying and characterizing chromosomal aberrations in bovine species and offers a potential solution for analyzing historical anomalies when fresh blood material is unavailable. The combination of NGS and cytogenetic techniques provides a cost-effective and reliable approach for characterizing chromosomal anomalies in various species, including those identified before the availability of modern banding technologies and FISH mapping using specific molecular markers.