A breeding program has been developed for the Latvian warmblood heavy type horses in Latvia, with the aim to preserve this type, because the number of these horses is small and the status of the local endangered breed has been granted. The aim of the study was to analyse the genetic structure, inbreeding and effective population size of the Latvian warmblood heavy type (LSB) horse population. Horses that were living at the time of the study on January 1, 2023 were used for the study. A total of 374 genetic resources live horses were analysed. Population structure analysis, inbreeding and effective population size were investigated. Calculations were done by POPREP (v1.0) software. The effective population size (Ne) decreased, however, since 2018 the decline in the size of the effective population has not been so rapid. In 2000, the Ne was 316 animals, and in 2020, it was 101 animals. Over the years, changes in the average inbreeding level in the LSB population were observed from year to year. In 2000, inbreeding was 1.39%, and in 2020 it was 1.47% with the average inbreeding level of 1.12%. Over the last 20 years, large changes in Ne have been observed, thus, the loss of genetic diversity in the LSB breed should be controlled.

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.