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

Abstract

International audienceChromosomal 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