Evaluation of current gene pool of Kholmogor and Black-and-white cattle breeds based on whole genome SNP analysis

Abstract

Conservation of local cattle genetic resources is an important strategy for achieving Russia’s food security. During last decades, in the Russian Federation, local livestock populations were either crossbred or replaced by highly productive imported breeds, which led to a loss of the major part of original breeds identities. The objective of our study was to identify genetic differences between the populations of Kholmogor and Black-and-white cattle with varying degrees of admixture with the Holstein breed. The aforementioned breeds were studied using their whole-genome single nucleotide polymorphism (SNP) genotypes. The Kholmogor breed was subdivided into three groups: purebred (KHLM, n = 3), admixed with Holsteins (KHLM-HLST, n = 4) and representatives of old-type breed (KHLM-INTA, n = 15). Blackand-white was subdivided into four groups: purebred (BLWT, n = 9), with a low (BLWT-75, n = 8) and a high (BLWT-HLST, n = 10) level of admixture with Holstein, and represented by archival samples from the 1970s and 1980s (BLWT-OLD, n = 15). The Holsteins genetic profiles (HLST, n = 27) were taken as a comparison group. PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 and R package StAMPP were used to infer genetic relationship between the studied groups. After quality control, 29 688 SNPs were selected for analysis. Multidimensional scaling (MDS), Admixture analysis and a dendrogram constructed using the Neighbor-Net method, revealed the presence of three clusters belonging to the Kholmogor, Black-and-white and Holstein breeds. The first one included KHLM and KHLM-INTA, the second – BLWT and BLWT-OLD, and the third – HLST, KHLM-HLST and BLWT-HLST. The BLWT-75 samples were placed between HLST and BLWT. Thus, our results showed that currently the populations of native cattle breeds with valuable genotypes still exist. The populations with a high level of admixture with Holsteins could be considered neither as the Kholmogor nor as Blackand-white breeds, and would rather be referred as the Holstein breed of local breeding.

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

“…Nine cattle microsatellite loci were selected from the list of microsatellite markers recommended by the International Society of Animal Genetics (ISAG) [41]; the selected loci were: BM2113, BM1824 [42], ETH10 [43], ETH225 [44], INRA023 [45], SPS115 [46], TGLA122, TGLA126, and TGLA227 [47]. These loci are high-polymorphic, carrying 12,8,9,11,16,11,18,11, and 16 alleles, respectively [22]. The multiplex (9-plex) PCRs were conducted in a final volume of 10 mL in a PCR buffer with 200 mM dNTPs, 1.0 mM MgCl 2 , a 0.5 mM primer mix, 1 unit of Taq polymerase (Dialat Ltd., Moscow, Russia), and 1 µL of genomic DNA.…”

“…Yaroslavl cattle were highly demanded by peasants and small cattle holders owing to their adaptability, high feed efficiency, and good reproductive ability even in poor forage conditions during winter [ 7 ]. The origin of Kholmogor cattle remains questionable: numerous studies have highlighted a high contribution of Holland (Dutch) cattle [ 3 , 8 ], whereas other sources have highlighted only a limited participation of Holland bulls [ 9 , 10 , 11 , 12 , 13 ]. Kholmogor cattle, mainly bulls, were used to improve several other Russian cattle breeds, including Yaroslavl and Novgorod cattle (local cattle population of the Novgorod province of old Russia).…”

Evaluation of meat productivity of Limousin breed cattle in biogeochemical conditions of Voronezh region

“…The territorial development of beef cattle breeding must be provided with a solid genetic platform that provides both the prescience of the most desirable traits and properties, and the genetic diversity that determines the potential for evolutionary movement. Highly productive purebred and crossbred herds created on this basis should be selected in the direction of increasing the adaptive capabilities under traditional and intensive technology, as well as under specific natural, climatic and economic conditions [1,22,23,24].…”

Comparison of miR-106b, miR-191, and miR-30d expression dynamics in milk with regard to its composition in Holstein and Ayrshire cows

“…It is well known that Holstein cattle have a high potential for milk productivity, whereas high milk fat content is a distinctive feature of Ayrshire cattle. Modern populations of Ayrshire and Holstein cattle are distinguished by their unique genomic architecture, formed as a result of long-term breeding and artificial selection [20,21]. In this regard, it is relevant to study in detail the contribution of some key milk miRNAs as epigenetic regulators of lactopoiesis and galactopoiesis.…”