Genomic Analysis of Latvian Brown Old Type and Latvian Blue Local Dairy Cattle Breeds Using SNP Data

Conservation programmes for two local dairy cattle breeds-Latvian Brown old type (BV) and Latvian Blue (LZ)-commenced in 2004. The aim of this study was to evaluate genetic diversity in the BV and LZ local cattle populations using SNP data. This study was based on genotype data from 96 BV and 75 LZ cows and 20 BV and 18 LZ bulls. The SNPs were determined using the GGP 100K bovine SNP BeadChip. Quality control (QC) and genotype data analysis were performed using PLINK v1.9. The observed heterozygosity was moderate, at around 0.4, for both breeds. Inbreeding coefficients were estimated based on homozygosity runs (F_ROH) to compare recent and ancient inbreeding in the BV and LZ populations. Therefore, the ROH segments were divided into segments with the four classes (1-4 Mb, 4-8 Mb, 8-16 Mb, and above 16 Mb). Shorter ROH regions (ROH < 4 Mb) predominated in the genome. ROH regions with lengths above 16 Mb covers 4-6% of the genome in BV and 11% in LZ population. The average inbreeding coefficient for approximately three generations (F_ROH>16) was 2.30% and 4.87% for BV and LZ cows (p < 0.05), respectively, and 2.59% and 3.85% for BV and LZ bulls, respectively. This study demonstrates that inbreeding has increased from generation to generation (F_ROH>16 is higher compared with F_ROH<16) in both populations. The level of current inbreeding in LZ is higher compared with that in the BV breed. The overall level of inbreeding in the BV and LZ populations is low, but there is a high level of inbreeding among a few animals. The impact of inbreeding on cow productivity has been observed in the LZ and BV cow populations. As a result, breeding organisations need to monitor and control the level of inbreeding and prevent the loss of genetic diversity in these animal populations. Breeders should minimize mating among close relatives; introduce genetically unrelated animals, use pedigree, and genomic information in controlling rates of inbreeding.