Parentage testing and looking for single nucleotide markers associated with antler quality in deer (Cervus elaphus)

Edith Elblinger; Julianna Bokor; Árpád Bokor; Vilmos Altbäcker; János Nagy; József Szabó; Bertalan Sárdi; Adrian Valentin Bâlteanu; Zsolt Rónai; László Rózsa; József Rátky; István Anton; Attila Zsolnai

doi:10.5194/aab-65-267-2022

Parentage testing and looking for single nucleotide markers associated with antler quality in deer (Cervus elaphus)

Arch Anim Breed. 2022 Jul 28;65(3):267-274. doi: 10.5194/aab-65-267-2022. eCollection 2022.

Authors

Affiliations

¹ Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary.
² Game Management Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary.
³ Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania.
⁴ Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Eötvös Loránd University, Budapest, 1053, Hungary.
⁵ Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary.
⁶ Department of Obstetrics and Food Animal Medicine Clinic, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary.
⁷ Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllő, 2100, Hungary.

Abstract

To provide a cost-efficient parentage testing kit for red deer (Cervus elaphus), a 63 SNP set has been developed from a high-density Illumina BovineHD BeadChip containing 777 962 SNPs after filtering of genotypes of 50 stags. The successful genotyping rate was 38.6 % on the chip. The ratio of polymorphic loci among effectively genotyped loci was 6.5 %. The selected 63 SNPs have been applied to 960 animals to perform parentage control. Thirty SNPs out of the 63 had worked on the OpenArray platform. Their combined value of the probability of identity and exclusion probability was $4.9 \times 10^{- 11}$ and 0.99803, respectively. A search for loci linked with antler quality was also performed on the genotypes of the above-mentioned stags. Association studies revealed 14 SNPs associated with antler quality, where low-quality antlers with short and thin main beam antlers had values from 1 to 2, while high-quality antlers with long and strong main beams had values between 4 and 5. The chance for a stag to be correctly identified as having high-value antlers is expected to be over 88 %.