Genetic position of Hungarian Grey among European cattle and identification of breed-specific markers

Abstract

Hungarian Grey is an indigenous cattle breed that is one of the national symbols of Hungary. However, genetic description of the Hungarian Grey cattle has not yet been conducted based on whole-genome screening. Using the GeneSeek high-density Bovine SNP (single nucleotide polymorphism) 150 K BeadChip, we sampled the genome of 36 Hungarian Grey, 12 Maremmana, 13 Hungarian Fleckvieh and 5 Holstein-Friesian cattle for population studies and used data of 139 other cattle from an additional dataset created on European cattle breeds (Upadhyay et al.2017. Heredity 118, 169–176). The performance of a multidimensional scaling plot showed that Hungarian Grey clustered independently from other European cattle. The number and total length of runs of homozygosity (ROH) is similar or slightly below the value of other European cattle; FROH coefficients (proportion of the autosomal genome covered by ROH) are similar to Maremmana and Maronesa. The frequency of ROH does not show increased values as it can be noticed in Heck and Maltese. These results indicate that the Hungarian Grey cattle have been successfully maintained avoiding negative genetic effects, and reflect the uniqueness among European cattle. The identification of breed-specific loci has been aimed at differentiating Hungarian Grey (n = 136 in this case) from other cattle breeds (n = 169). Ten loci (−log10P > 5) were identified as markers capable for differentiation of Hungarian Grey. These markers are located on chromosomes 6, 14, 15, 16, 20 and 24.

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

“…Multidimensional scaling analysis on IBS allele-sharing values revealed a clear separation between Maremmana and the other Podolian-derived Italian breeds along the first dimension (C1; Figure 2 ). This clustering trend was confirmed by the neighbor joining (NJ) tree of individuals, which revealed two major clades that coincide with Maremmana and the rest of the Podolian-derived populations ( Supplementary Figure S1 ), in agreement with previous studies ( Senczuk et al, 2020 ; Zsolnai et al, 2020 ). It is also noteworthy that, both MDS and NJ tree revealed additional substructure of Maremmana suggesting the presence of individuals from several sub-populations with different allele frequencies.…”

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

“…The estimates of H E and H O were not dissimilar, 0.261 and 0.274 respectively, which suggests that there are no major recent events pushing heterozygosity in either direction. On a smaller sample size (N = 12), H E were estimated at 0.369 and 0.381 from 150k SNP data [39]. More recently, from 48 k SNP data and sample size N = 25, estimates of H E = 0.319 and H O = 0.338 were obtained [40].…”

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

“…Moreover, our results contrast with those of the MDS plot reported by Zsolnai et al . [ 46 ] that showed that Hungarian Grey clustered independently from the other European Podolian cattle breeds.…”

“…Among the Balkan breeds, the Podolsko Serbian, Croatian Podolian and Hungarian Grey breeds are the most differentiated, which confirms the genetic differentiation of the Hungarian Grey breed with respect to other Podolian and non-Podolian European taurine found by Zsolnai et al . [ 46 ]. The observed distinctness of these Balkan breeds (including the Romanian Grey), might be the result of a strong genetic drift, as suggested by the low values obtained for the genetic diversity indices and effective population size (Table 1 ) and (see Additional file 4 : Figure S2) and the long branches in the TREEMIX graphs (Fig.…”