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

## TL;DR

This study analyzes the genetic diversity and inbreeding levels in two Latvian dairy cattle breeds using SNP data to support their conservation.

## Contribution

The study provides a genomic assessment of inbreeding and its impact on milk productivity in two local Latvian cattle breeds.

## Key findings

- Latvian Blue cattle show higher inbreeding levels compared to Latvian Brown old type despite fewer bulls.
- Genomic inbreeding negatively correlates with milk yield in both breeds.
- Inbreeding has increased over generations in both populations, with some animals showing high inbreeding.

## Abstract

In Latvia, there is only a small number of the native dairy cattle breeds: Latvian Brown old type and Latvian Blue. The protection and breeding of these breeds, which are genetically adapted to traditional production systems, are very important. Using genome-wide SNP data, breed diversity and genetic variation were analysed. Recent and ancient inbreeding in the BV and LZ populations were estimated based on homozygosity runs. Regardless of the lower number of bulls, the Latvian Blue breed had a much higher level of inbreeding than the Latvian Brown old type. The relationship between genomic inbreeding and milk productivity and a negative phenotypic correlation between genomic inbreeding and milk yield for both breeds was observed. The Latvian local cow breeds are not characterised by high milk yields, but they do have a high dry milk matter content.

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 (FROH) 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 (FROH>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 (FROH>16 is higher compared with FROH<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.