Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses

Abstract

The Kushum is a relatively new breed of horses in Kazakhstan that was established in the middle of the 20th century through a cross between mares of Kazakhstan local horses and stallions of Thoroughbred, Trotter, and Russian Don breeds to supply military horses. To reveal the genetic characteristics of this breed, we investigated haplotypes of mitochondrial DNA (mtDNA) and single-nucleotide polymorphisms of the Y chromosome, as well as genotypes of five functional genes associated with coat color, body composition, and locomotion traits. We detected 10 mtDNA haplotypes that fell into 8 of the 17 major haplogroups of horse mtDNA, indicating a unique haplotype composition with high genetic diversity. We also found two Y-chromosomal haplotypes in Kushum horses, which likely originated from Trotter and/or Don breeds. The findings regarding the mtDNA and Y-chromosomal haplotypes are concordant with the documented maternal and paternal origins of the Kushum horses. The allele frequencies of ASIP, MC1R, and MATP associated with coat color were consistent with the coat color variations of Kushum horses. The allele frequencies of MSTN associated with endurance performance and those of DMRT3 associated with gait suggested that the observed allele frequencies of these genes were the result of selective breeding for these traits. As a result of this study, we were able to obtain useful information for a better understanding of the origin and breeding history of the Kushum horse breed using molecular markers.

Unlocking Horse Y Chromosome Diversity

“…The widespread presence of HT1 and HT2 is probably due to the Oriental wave, as Arabian horses carrying these MSY haplotypes were imported into Central European studs, while the frequency of HT3 in modern horses is attributable to the intensive use of English Thoroughbred in the improvement of other horse breeds. The SNPs and indels identifying the different haplotypes were further investigated in 42 breeds from different areas of Europe, Asia and America [ 136 ] and in 13 Chinese indigenous [ 138 ], 3 Sardinian [ 139 ] and 1 Kazach [ 140 ] horse breeds ( Figure 2 and Table S3 ).…”

“…The correlation between the genetic admixtures observed in European populations and the spread of the Yamnaya culture from the Pontic-Caspian steppe [ 21 ] initially suggested this area as the centre of horse domestication [ 91 ]. The loss of horse Y chromosome diversity originated from there, with one MSY lineage that gradually replaced all the other [ 118 ], except for the lineage found only among Yakutian horses [ 143 , 144 , 147 ] and a quite marked genetic diversity observed today in other Asian breeds [ 38 , 140 , 144 , 148 ]. In 2018, Wutke and colleagues conducted an analysis on the MSY polymorphic sites of 96 European ancient stallions dated back from Copper and Bronze Age to the Middle Ages, declaring that the loss of different Y chromosome lineages in modern horses is due to an artificial selection started in the Iron Age and not to a founder or demographic effect [ 118 ].…”

Refining the evolutionary tree of the horse Y chromosome

“…A maximum of 15 samples were taken per breed/population, while more samples were enclosed from East Asian populations due to a lack of pedigree information and expected population substructure. We included samples that were already used in previous Y studies 23 , 24 , 27 – 29 , 31 , 44 and in addition, we added samples collected for the purpose of diversity analysis in several different projects. If applicable, we selected samples from separate sample collections, with regard to region, timepoint and research groups.…”

Linebreeding as a system of stock breeding to improve the productive qualities of horses of the Kushum breed

“…Possessing high meat and dairy productivity and good reproductive and adaptive qualities to year‐round grazing, the Kushum breed plays an exceptional role as an improver of productive qualities in horse herding in Kazakhstan and the former Soviet republics (Nguyen et al, 2020). Describing the Kushum horse breed of Western Kazakhstan A.R.…”

“…The wide distribution of valuable lines with high genetic potential contributes to the progress of the breed and raises its general level (Folla et al, 2020). In addition, the selection of lines facilitates orientation in the breed and allows to maintain its optimal structure and to avoid unsystematic, inbred mating (Koveshnikov & Slotina, 2021; Nguyen et al, 2020; Toktabay & Nugumarova, 2022). Linebreeding theory was developed after clarifying the role of remarkable ancestors, possessing prepotency and producing excellent offspring.…”