Resequencing Composite Kazakh Whiteheaded Cattle: Insights into Ancestral Breed Contributions, Selection Signatures, and Candidate Genetic Variants.

Abstract

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. F_ST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). F_ST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point F_ST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions.