Latvian local goat breed genome-wide association with somatic cell count
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, yet its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. 5 mL of blood and milk samples from all living animals were acquired. DNA from the blood buffy coat was extracted using the phenol-chloroform method, whereas milk samples were analyzed for the presence of bacterial pathogens and SCC levels. Genomes were sequenced employing a DNBSEQ-G400 sequencer to acquire at least 35x or 10x coverage with 150 bp paired-end reads. Acquired data were analysed using BWA-MEM, SAMtools, vcftools, PLINK, VEP and the goat reference genome ARS1.2. Heterozygosity, nucleotide diversity, and LD analysis indicated that LVK exhibits relatively low levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, = 500 kb) with a median length of 25 kb. PCA, genetic distance tree and admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine and Saanen, which is in line with the breed's history. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13% to 12.2%. We identified 26 genetic variants associated with SCC levels, from which potentially relevant is SNP rs662053371 in gene OSBPL8, indicating a potential signal linked to the lipid metabolism in goats. This study demonstrated that the LVK population has a complex yet pronounced genetic structure. Although kinship of the animals might have largely influenced the association analysis, we were able to identify potential genetic traits associated with the level of SCC. Therefore, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.