Uncovering genetic diversity and adaptive candidate genes in the Mugalzhar horse breed using whole-genome sequencing data

Simple Summary

Mugalzhar horses are a native breed of Kazakhstan valued for their ability to produce milk and meat and adapt to harsh environments. This study explored the genetic diversity of these horses and identified regions of their DNA affected by natural selection using advanced genome analysis techniques. Using more than 21 million genetic variants, we found that most of them occurred in non-coding regions of the genome, with only a small fraction affecting certain genes directly as candidates for adaptation to a harsh climate. Despite the presence of rare genetic markers associated with traits like coat color and gait, no harmful segregating genetic mutations linked to diseases with Mendelian inheritance were identified. These results suggest that Mugalzhar horses have maintained a moderate genetic diversity, exhibiting traces of historical selection and no signs of inbreeding. This study provides useful insights into the genetic makeup of this breed, which can help to preserve and improve it in breeding programs.

Abstract

Mugalzhar horses are a relatively young native breed of Kazakhstan, prized for meat and milk production and adaptation. This study was conducted to investigate genetic diversity and pinpoint genomic regions associated with selection signatures in this breed using whole-genome sequence data. Variant calling yielded a total of 21,722,393 high-quality variants, including 19,495,163 SNPs and 2,227,230 indels. Most variants were located in introns and intergenic regions, while only 1.94% were exonic. Estimates of genetic diversity were moderate, with expected and observed heterozygosity and nucleotide diversity of 0.2325, 0.2402, and 0.0021, respectively. We identified nine adaptive candidate genes (SCAPER, FHAD1, MMP15, ADGRE1, CMKLR1, MRPL15, ZNF667, CCDC66, and LOC100055310), harboring high-impact exonic variants in the homozygote state for an alternative allele. No deleterious segregating variants associated with Mendelian traits were found in this population, while seven variants linked to coat color and gaitedness were detected in a low frequency heterozygous state. Our findings suggest that there are certain genomic regions subjected to ancient selection footprints during the ancestor breed formation and adaptation. The outcome of this study serves as a foundation for future genomic-driven strategies, a broader utilization of this breed, and a reference for genomic studies on other horse breeds.