Evaluation of single nucleotide polymorphisms identified through the use of SNP assay in Romanian and Chinese Holstein and Simmental cattle breeds

Daniela Elena Ilie; Yahui Gao; Ioana  Nicolae; Dongxiao Sun; Junya Li; Bo Han; Dinu Gavojdian

doi:10.18388/abp.2020_5080

Daniela Elena Ilie 1Research and Development Station for Bovine Arad, Arad, 310059, Romania; 2Research and Development Institute for Bovine Balotești, Balotești, 077015, Romania https://orcid.org/0000-0002-0464-3199
Yahui Gao China Agricultural University, College of Animal Science and Technology, Beijing, 100193, China https://orcid.org/0000-0003-0602-4823
Ioana Nicolae Research and Development Institute for Bovine Balotești, Balotești, 077015, Romania https://orcid.org/0000-0002-7756-6235
Dongxiao Sun China Agricultural University, College of Animal Science and Technology, Beijing, 100193, China
Junya Li Chinese Academy of Agricultural Sciences, Beijing Institute of Animal Sciences, Beijing, 100193, China
Bo Han China Agricultural University, College of Animal Science and Technology, Beijing, 100193, China https://orcid.org/0000-0002-8679-6534
Dinu Gavojdian Research and Development Institute for Bovine Balotești, Balotești, 077015, Romania https://orcid.org/0000-0001-9603-881X

DOI: https://doi.org/10.18388/abp.2020_5080

Abstract

Simmental and Holstein cattle, being among the most widely distributed breeds worldwide, have been subjected to continuous selection for distinct purposes. In the current study, we evaluated the levels of SNPs identified through the use of SNP assay in Romanian Holstein and Romanian Simmental cattle, which then were compared to the data from Chinese Holstein and Chinese Simmental cattle. In total, 282 animals were genotyped: Romanian Holstein (n=30), Romanian Simmental (n=22), Chinese Holstein (n=96) and Chinese Simmental cattle (n=136), using 39,724 common SNPs to analyze minor allele frequency, genetic variability and level of SNPs. Among studied breeds, the average percentage of polymorphic markers was 90.84%, with the highest value in Chinese Simmental (91.37%) and lowest in Romanian Simmental cattle (90.31%). The average HO ranged from 0.426 in Romanian Holstein to 0.416 in Romanian Simmental, and from 0.425 in Chinese Holstein to 0.422 in Chinese Simmental. The distribution of SNPs was homogenous across the breeds, except the Romanian Simmental which displayed the lowest percentage of polymorphic markers (24,66 and 32,48%) from higher MAF category (0.3 to <0.4 and 0.4 to <0.5) and the highest percentage (3.82 and 12.00%) for SNPs from low and intermediate MAF categories (0.05 to <0.1 and 0.1 to <0.2). In the current study, the SNP assay was successfully used to analyze the level of SNP sites of Romanian cattle breeds, however, a higher number of samples and production data are needed for future applications of the results in genomic selection, genome-wide association studies and genetic diversity analysis.