Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

Abstract

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

“…The results of the PCA plot, Neighbor-Net analysis, and admixture clustering (S3 Fig) suggest a low contribution of Holstein ancestors (probably Holland cattle) in the formation of the architecture of the Yaroslavl and Kholmogor breeds, which has been proposed by several researchers [5,[9][10][11].…”

“…Whole-genome studies performed using medium-density SNP chips showed that Yaroslavl and Kholmogor cattle are valuable national genetic resources, which have been little influenced by introgression with non-Russian breeds [9,10]. The maintenance of a visible part of historical components in the modern populations both of Yaroslavl and Kholmogor breeds was confirmed by the study of historical specimens [11]. Further PLOS ONE signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis, Dryad, Dataset, https://doi.org/10.5061/dryad.vt4b8gtq9.…”

“…and maintained their historical genomic components [9,11]; thus, they may carry specific signatures of selection, reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. Adaptation to the changing environment is increasingly important [59]; thus, native cattle breeds might become valuable sources of genetic TICAM1, FEM1A, MIR7, DPP9, TNFAIP8L1, SEMA6B, PLIN5, LRG1, PLIN4, HDGF2UBX, N6, CHAF1A, SH3GL1, STAP2, MPND, FSD1, TMIGD2, SHD, CCDC94, EBI3, ANKRD24, SIRT6, CREB3L3 NME5, BRD8, MIR2459, GFRA3, KIF20A, CDC23, FAM53C, CDC25C, REEP2, EGR1, ETF1 MIIP, MFN2, PLOD1, KIAA2013, NPPB, NPPA, CLCN6, MTHFR, AGTRAP, MAD2L2, FBXO6, FBXO44, FBXO2, PTCHD2 42.7 -43.5 KHLM a ROH, DCMS NPPB, NPPA, CLCN6, MTHFR, AGTRAP, MAD2L2, FBXO6, FBXO44, FBXO2, PTCHD2, UBIAD1, MTOR, ANGPTL7, EXOSC10, SRM, MASP2…”

“…Most researchers suggested that foreign breeds, including Holsteins contributed little in the development of the Yaroslavl and Kholmogor cattle populations [6,7], which was subsequently confirmed by molecular genetics studies [8][9][10]. The studies of the historical specimens of Yaroslavl and Kholmogor cattle, dated from the end of 19 th to the first half of 20 th century using microsatellites, indicated that Russian breeds and Holsteins were developed from different ancestral populations [11]. In the 1960s, the number of Kholmogor and Yaroslavl cattle was close to million individuals (993 and 951 thousand, respectively) each; in contrast, in 2015, their census population size remarkably decreased to 222.9 and 50.5 thousand heads, respectively [12].…”

Analysis of Genetic Diversity of Kazakh White-Headed Cattle Breed by Microsatellites Compare with Ancestral Breeds <sup>†</sup>

“…The study of museum and archeological samples can help to shed the light on the history of the livestock breeds [9][10][11]. In this study, we were able to obtain the valid genotypes for 11 microsatellites loci for the historical specimens of native Kazakh cattle dated by the first quarter of 20th century.…”