Table 1.
Summary statistics for the studied breeds calculated on the basis of the high-density SNP genotypes.
Fig 1.
The effective population size (NE) across generations from approximately 50 generations ago based on linkage disequilibrium (LD) calculations (a) and NE slope (b). Note: Breed: YRSL, Yaroslavl; KHLM, Kholmogor; HOL, Holsteins.
Fig 2.
Descriptive statistics of runs of homozygosity (ROH) by ROH length class.
Note: Breed: YRSL, Yaroslavl; KHLM, Kholmogor; HOL, Holsteins. (A). Number of ROHs by ROH length class: axis X, ROH classes (1–2 Mb, 2–4 Mb, 4–8 Mb, 8–16 Mb, and >16 Mb); axis Y, mean number of ROHs; (B). Length of ROHs by ROH length class: axis X, ROH classes (>1 Mb, >2 Mb, >4 Mb, >8 Mb, and >16 Mb); axis Y, mean length of ROHs.
Fig 3.
Genomic distribution of FST values estimated between pairs of breeds.
(A). Yaroslavl and Kholmogor breeds. (B). Yaroslavl and Holstein breeds. (C). Kholmogor and Holstein breeds. Note: Axis X, cattle autosomes (the breadth of autosomes corresponds to their length); axis Y, FST values. SNPs were plotted relative to their positions within each autosome. The horizontal line on each plot indicates the threshold, which was estimated as the top 0.1% for FST values. The SNPs with FST beyond the cut-off value were considered to be under selection pressure.
Fig 4.
Venn diagram illustrating the distribution of the top 0.1% of SNPs by FST value between pairs of breeds.
Note: Breed: YRSL, Yaroslavl; KHLM, Kholmogor; HOL, Holsteins.
Fig 5.
Genome-wide scan for the signature of selection based on the hapFLK statistics.
Note: Each dot corresponds to a single SNP; axis X, genomic coordinates by chromosome; axis Y, statistical significance (−log10 P-values); the red and blue lines indicate the thresholds of significance: 10−5 and 10−3, respectively; the figures above and below the plot present the magnified plots of the chromosome areas containing the hapFLK regions.
Table 2.
Genomic regions under putative selection in the two old Russian cattle breeds compared to those in Holsteins identified at least by two different methods.
Table 3.
Genes localised within the genomic regions affected by putative selection in Yaroslavl and Kholmogor cattle breeds.