Successful trio-based reverse genetic screen in an endangered local cattle breed

Häfliger, I. M.; Seefried, F. R.; Drögemüller, C. (9 February 2023). Successful trio-based reverse genetic screen in an endangered local cattle breed. In: Veerkamp, R. F.; de Haas, Y. (eds.) Proceedings of 12th World Congress on Genetics Applied to Livestock Production (pp. 1074-1077). The Netherlands: Wageningen Academic Publishers 10.3920/978-90-8686-940-4_254

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We scanned the genomic data of almost one thousand Evolèner cattle, representing the by far smallest local cattle population of Switzerland, whereof only pedigree records are available. A reverse genetic screen using 94k SNP markers in 585 trios mapped recessive deleterious loci using homozygous haplotype deficiency. We found two haplotypes, EH1 and EH2, with moderate allele frequencies of >0.10. Mining for candidate variants was carried out by linkage analysis of the predicted haplotype status and whole-genome sequencing variant catalogue of seven Evolèner bulls. This led to the detection of two perfectly linked missense variants affecting conserved residues: GBE1:p.Arg437Gln for EH1, and LRRC8A:p.Ala73Val for EH2. No homozygous animals were observed in >5,100 cattle of various breeds including Evolèner. The presented study showed that very limited data can lead to the identification of candidate variants and thereby help to improve reproduction success in an endangered indigenous breed of cattle.

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