PSIV-21 Feasibility of applying genomic selection to biopsied embryos of Nellore cattle.

Abstract This study had the objective of evaluating the feasibility of genomic prediction from biopsied bovine embryos. A total of 93 embryos were produced, derived from 28 donor cows and fertilized in vitro with semen from two bulls, all animals were of the Nellore breed. Embryo biopsies were performed, followed by DNA extraction and amplification, in addition to genotyping with the Illumina Bovine 50K v2 chip. FImpute software was used to check for Mendelian inconsistencies, correct genotyping errors and impute missing genotypes. Quality control of the genotype file was performed by eliminating non-autosomal SNPs and with the same position on the chromosome, based on the bovine reference genome ARS-UCD1.2. After quality control, analyses were performed using 34,900 SNPs from the 50K chip and 615,397 SNPs from the HD chip. The quality of genotyping was assessed by the call rate, which presented an average of 93%, ranging from 75.1% to 97.9%. It is worth noting that approximately 80% of the samples presented a call rate above 90%. After imputing the genotypes for the high-density panel, the call rate of the samples reached 100%, correcting all Mendelian inconsistencies. Heterozygosity increased from 11.7% in observed genotypes to 22.5% in imputed genotypes. The determination of the sex of the embryos was performed based on the heterozygosity of the X chromosome, identifying 41 males and 19 females, while 33 embryos did not show conclusive heterozygosity. The embryos were transferred, and the pregnancy rate of the recipient cows was 31%, similar to the control group of non-biopsied embryos, at 24%. All embryos had their genomic genetic values estimated, in addition to the selection index calculated according to the methodology used by the genetic breeding program of which the ranch participates. The average selection index calculated for all embryos was 11.25, with a minimum of 4.54 and a maximum of 20.06. Thus, the study showed that genotyping and genetic prediction from biopsied embryos can be feasible in Nellore cattle breeding programs. However, challenges related to DNA extraction and amplification still affect the quality of genotypes, making it essential to use techniques such as imputation to improve the accuracy of results.