# Early Detection of Chromosomal Abnormalities in Cattle using SNP beadchip intensity data

Clémentine Escouflaire, Valentin Costes, M.C. Deloche, Aurélie Bonnet, Amélie Bonnet-Garnier, Didier Boichard, Aurélien Capitan, Sébastien Fritz, Daniel Lebourhis

► To cite this version:

Clémentine Escouflaire, Valentin Costes, M.C. Deloche, Aurélie Bonnet, Amélie Bonnet-Garnier, et al. Early Detection of Chromosomal Abnormalities in Cattle using SNP beadchip intensity data. 76th Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2025, Innsbrück, Austria. 39, pp.801, 2025, Book of abstracts of the 76th annual meeting of the european federation of animal science. hal-05238722

HAL Id: hal-05238722

https://hal.inrae.fr/hal-05238722v1

Submitted on 3 Sep 2025

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Early Detection of Chromosomal Abnormalities in Cattle using SNP beadchip intensity data

C. Escouflaire¹, V. Costes¹, M. C. Deloche¹, A. Bonnet¹, A. Bonnet-Garnier², D. Boichard³, A. Capitan³, S. Fritz¹, D. Le Bourhis¹

¹ Eliance, 149 rue de Bercy, 75012 Paris, France, ² Université Paris-Saclay, INRAE, BREED, UVSQ, 78350 Jouy-en-Josas, France, ³ Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France

Chromosomal abnormalities frequently induce high mortality rate during gestation or after birth. Their early detection is a major challenge for the industry and breeders. The AnEmBoV project aims to identify chromosomal abnormalities, both in in vitro produced embryos (IVP) within selection programs and in calves for herd renewal, to prevent genetic defects, improve fertility, and minimize economic losses and unproductive periods. To provide an early diagnosis solution, we developed a methodology for detecting chromosomal abnormalities based on intensity data from genotyping arrays used in genomic selection. This approach enables the identification of chromosomal anomalies in both embryos and calves, distinguishing individuals with aneuploidies or structural rearrangements. A total of 192 IVP blastocysts were produced and few cells from each embryo were biopsied for genotyping. Five embryos were excluded because of low call rates. By analyzing signal intensity (Log R Ratio or LRR) and B allele frequency (BAF) data, we identified aneuploidy for 26% of the IVP embryos with 1 haploid, 11 triploid, 25 monosomic, 8 trisomic, and 3 tetraploid. We then tested various indicators to estimate the status of each chromosome for each embryo. While genotyping quality can affect detection, we have adapted our approach to different types of aneuploidy and have been able to make reliable predictions. Based on these results, we are currently developing an aneuploidy detection pipeline for genotyped embryos within genomic selection programs. Additionally, we applied this methodology to known cases of bulls carrying chromosomal rearrangements that induce partial aneuploidy in their offspring. Through intensity data visualization, we confirmed the chromosomal status of their progeny, which had previously been predicted using haplotype analysis, even in cases involving genomic regions as small as 2Mb. An automated pipeline is in development for detecting partial aneuploidies and deletions in breeding candidates. The AnEmBoV project is funded by APIS-GENE.

Copy number variations among draught and milk type zebu cattle of South Asia by whole genome sequencing

T. K. Mavunga¹,², J. Sölkner², G. Mészáros², R. Pichler¹, Y. Ressaissi¹, M. B. Malima³, M. Barbato⁴, K. Periasamy⁵

¹ Animal Production and Health Section, Department of Nuclear Science Applications, International Atomic Energy Agency, Wagramer Strabe 5, 1220 Vienna, Austria, ² University of Natural Resources and Life Sciences, Department of Sustainable Agricultural Systems, Gregor Mendel Strasse 33, 1180 Vienna, Austria, ³ Agriculture Research Council, Department of Animal Production, 100 Old Soutpan Road (M35), Private Bag X5, Onderstepoort, 0110 Pretoria, South Africa, ⁴ Università degli Studi di Messina, Dipartimento di Scienze Veterinarie, Piazza Pugliatti, 1, 98122 Messina, Italy, ⁵ Indian Council of Agricultural Research, National Research Center on Mithun, Medziphema, 797106 Nagaland, India

Copy number variations (CNV) arise from losses or gains of DNA fragments and they significantly explain genetic and phenotypic diversity. This study aims to uncover CNV among draught and milk-type Zebu cattle breeds of South Asia that potentially contribute to differences in production potential and adaptation to local conditions. Asian Zebu is recognized for their ability to thrive in harsh environments, tolerance to tropical heat, and higher resistance to diseases and tropical vectors. We generated 40 short-read paired-end whole genome sequences on Asian Zebu cattle and used an additional 20 from publicly available sources. The samples comprised 12 breeds from five countries (Pakistan, India, Sri Lanka, Myanmar, and Cambodia) located in South Asia. An average coverage of 20x per raw sequence data was generated in addition to 20 publicly available sequences. Quality-controlled reads were aligned using the recently generated Bos indicus reference genome (NCBI Bioproject Accession No. PRJNA897888) and the output sequence was used as input for CNV analysis. The read-depth approach of CNVpytor software was used. A large number of deletions and insertions of different lengths were identified. We identified overlaps with genes, many of them related to metabolic pathways and tropical adaptation. In conclusion, we present the distribution and diversity of CNV in South Asian Zebu cattle populations and our results indicate their significance to genetic differences between draught and milk-type breeds.