Russian Journal of Genetics最新文献

Abstract—

Marker-assisted selection for improving reindeer meat production is at the early stages of development, which requires analysis of variation within the candidate genes for meat production. The calpastatin and androgen receptor genes were chosen as such genes to study their variability in reindeer. In different domesticated animal species, polymorphisms and indels in the androgen receptor gene were associated with growth and weight characteristics. Based on the results from many studies, sequence variation in the calpastatin CAST gene region was associated with meat quality and meat production of livestock. Principal component analysis of CAST variability grouped wild and domestic deer from Yakutia, as well as wild and domestic deer from Amur oblast, which implies gene flow between local breeds of domesticated deer and wild populations. At the same time, in the case of three microsatellite loci found in the present study in the intron of the androgen receptor gene, principal component analysis separated wild and domestic deer.

Abstract—The current stage of genetic certification of horses of cultural and local breeds based on microsatellite analysis makes it possible to quite effectively carry out identification and genetic examination of the origin of breeding animals, as well as solve the problem of assessing and preserving genetic resources. With a reduction in the number of breeding stock to 200–300 mares observed in a number of breeds, the threat of a decrease in the genetic diversity of populations and the accumulation of genetic load increases, which necessitates the need to study and monitor the genetic structure of horse breeds. In this regard, our comparative genetic analysis of polymorphism of 17 microsatellite loci in 20 541 horses of 29 cultural and local breeds allows us to certify the basic part of the genetic resources of the horse breeding of the Russian Federation. including riding, trotter, draft, and local breeds. During the genetic population analysis of the studied breeds, basic parameters were assessed: the total number of allele variants (N_a), the effective number of alleles (A_e), the average number of alleles per locus (MNA), the level of observed (H_o) and expected heterozygosity (H_e), as well as the coefficient of intrapopulation inbreeding F_is. Phylogenetic relationships of breeds were assessed using the R and R Studio software packages. Among horse breeds of different specializations, the highest values of all indicators of genetic diversity (A_e, H_o, H_e, and N_a) were determined in aboriginal populations. In the allele pool of local horse breeds, there were rare alleles ASB2T, HMS7S, HMS6J, HMS6H, HMS2T, HMS1O, HTG7L, HTG6L, HTG6H, VHL20S, ASB17Z, ASB17X, ASB17U, LEX3S, LEX3R, and CA425E, which were absent in horses of stud breeds. Among the riding horse breeds created in Russia, the Budennovskaya, Donskaya, and Kabardian horse breeds stood out due to the presence of rare alleles. Alleles ASB2G, ASB2F, HMS2F, HTG7Q, and ASB23O were found in trotter horses, which were not identified in the genetic structure of other breeds. The phylogenetic analysis showed the division of horse breeds into two clear subclusters, the first of which included only stud breeds. The second cluster united all the native breeds, as well as the Orlov Trotter and a group of draft breeds, which were used for many years as improvers of the local horse population. The analysis of the genetic structure of domestic horse breeds revealed a fairly high reserve of diversity even in small populations, which is an indispensable condition for successful selection in horse breeding.

Abstract

Nested within the vast genetic landscape of the major histocompatibility complex (MHC), a cluster of genes assumes a pivotal role in pathogen recognition and orchestrating mechanisms for disease resistance. This investigation successfully cloned and sequenced the complete 786 bp cDNA entity corresponding to the MHC-DQB gene in yaks. A comprehensive analysis of the sequence unveiled distinct features, including highly conserved peptide binding sites (PBS) spanning 8 amino acids and specific nucleotide-binding regions at designated positions (–1, –28, 2, 3, 29, 64, 93, and 108). The pronounced uniformity and remarkable preservation demonstrated by the yak MHC-DQB gene underscore its potential in providing protection against pathogens and the inherent stability within the DQB genetic framework. Moreover, a comparison across six distinct domains of the Yak-DQB gene revealed notable similarities with closely related species. Particularly significant is the identification of a conserved peptide-binding region consisting of 16 amino acids, alongside the detection of multiple conserved nucleotide-binding regions. When conducting a comparative analysis of amino acid lengths in the Yak-DQB orthologous sequence, a substantial homology with cattle was observed, registering at 91.2%. Interestingly, however, the DQB gene in yaks exhibited discrepancies in 23 amino acids compared to the bovine sequence. Specifically, a detailed examination revealed that 15 of these variable amino acids were clustered within the Beta 1 (в1) domain. These insights provide valuable information about the distinct characteristics of the MHC gene in both ruminant and non-ruminant species, unraveling the complexities of their comparative molecular genetics.

Abstract—The production of microorganisms that produce biologically active compounds for agriculture and the chemical, veterinary, and pharmaceutical industries, as well as for environmental protection, continues to be an important direction of microbial biotechnology. One of the most effective approaches to the production of producers is chemical mutagenesis, which, in combination with the correct breeding strategy, makes it possible to obtain highly productive strains. A significant disadvantage of chemical mutagenesis is the large number of induced mutations in the genomes of mutant strains, which makes it difficult to identify genes and, accordingly, biosynthetic pathways involved in the production of a given compound. The solution to this problem is modern technologies of genome sequencing and analysis, which make it possible to identify new genes and unknown biochemical pathways involved in the formation of biologically active compounds. The aim of the work was to analyze the genome of the mutant strain B-162/2 of the bacterium Pseudomonas chlororaphis subsp. aurantiaca, which is capable of increased production of biologically active compounds of the phenazine series and is resistant to hydrogen peroxide. When analyzing the genome of strain B-162/2 in full size, 6482 coding sequences and 64 coding RNA sequences were identified. Comparison of the genome of the B-162/2 strain with the genome of the wild type B-162 allowed the identification of 39 mutations, five of which are located in intergenic regions, and 34 affected coding sequences. Of the mutations detected, 14 led to a radical amino acid substitution in the proteins and two led to the formation of premature stop codons (methyl group sensor and MFS-type transporter). Several substitutions with high values of the Grantham coefficient were found, which could possibly lead to a change in the activity of the proteins. Three regions with phage genes in the genome of the B-162/2 strain were detected.

Abstract—

Triticum militinae Zhuk. et Migusch., a tetraploid wheat with the GAA genome, is considered a natural naked mutant of Triticum timopheevii Zhuk. Previously, the karyotype and crossing characteristics of this wheat were examined. To clarify the origin and relationships of T. militinae with other representatives of the wheat family, analysis of its chloroplast genome, which remained unexplored, is of great interest. In the present study, for the first time, sequencing and annotation of the complete chloroplast genome of T. militinae, the size of which was found to be 135 898 bp, was conducted. The plastome of this wheat is composed of two inverted repeats, each of 21 552 bp in length, the small single-copy (SSC) region of 12 791 bp, and the large single-copy (LSC) region of 80 003 bp. The chloroplast genome of T. militinae contains 132 annotated structural genes, of which 85 genes are protein-coding, 31 are tRNA genes, and four genes code for rRNA.

Abstract—Using the next-generation sequencing (NGS) technology, the nucleotide polymorphism in a fragment of the ND4 gene encoding NADH dehydrogenase subunit 4 was studied in 14 samples from three populations of the bird cherry-oat aphid (Rhopalosiphum padi L.) and the range of nucleotide polymorphism was determined. The insects were collected in 2021 and 2022 in the Northwest of Russia (in the vicinity of St. Petersburg) and in the northern Caucasus (Krasnodar Territory and Dagestan). Mitochondrial DNA haplotypes were identified, which have 97.95–99.80% sequence identity with the reference GenBank accession number KT447631.1. The level of intraspecific polymorphism of a 438 bp ND4 gene fragment in Rh. padi varied from 0.2 to 4.3%. In 2-year experiments, 33 polymorphic sites (17 transitions and 16 transversions) were found in the ND4 sequences, which made it possible to identify 30 mitochondrial DNA haplotypes. The Rh. padi populations collected simultaneously on different host plants or at different times on bird cherry (spring) and cereals (summer) differed in the proportion of the main haplotype, as well as in the composition of unique minor haplotypes. Analysis of the ratio of mitochondrial DNA haplotypes suggests the important role of the host plant genotype in the formation of the structure of Rh. padi populations.

Abstract—

Oxidative stress is one of the components of the pathological process leading to the development of obesity. The level of formation of free radical products is controlled by the antioxidant system. Antioxidant gene polymorphism influences the level and/or activity of the encoded enzymes. The purpose of this work was to investigate the association of SNP in the genes of the antioxidant system with the risk of overweight in children and adolescents. The material for the study were DNA samples from 279 overweight children and 131 children from the control group. Genotyping was performed for rs6721961 (–617G>T) NFE2L2, rs4998557 (7958G>A) SOD1, rs4880 (47C>T Ala16Val) SOD2, rs1001179 (–262C>T) CAT, rs713041 (718C>T) GPX4, rs662 (Gln192Arg) PON1. It has been shown that the –617GT genotype (rs6721961) NFE2L2 is associated with a decreased risk of overweight in children. An increased risk of developing overweight was detected for heterozygotes –262CT for rs1001179 CAT and the –262T allele. As a result of the analysis of intergenic interactions, a 6-locus genotype was identified that is associated with a reduced risk of overweight.

Abstract—

The widespread Palearctic rodent species gray hamster Nothocricetulus migratorius has a karyotype with a stable number of chromosomes 2n = 22 throughout the entire range of its habitat. We found gray hamsters with diploid number of chromosomes 2n = 24 locally distributed in the Qurama Ridge of the Tian Shan. A new karyotype and analysis of G- and NORs-bands of differentially stained chromosome sets were described for the first time. The described karyotype differs from the 22-chromosomal karyotype of gray hamsters by the Y-chromosome morphology and the presence of an additional pair of heteromorphic small chromosomes. Molecular genetic analysis revealed genetic divergence of 24- and 22-chromosomal forms of N. migratorius, and the differences between them in mitochondrial markers are comparable and in terms of nuclear markers exceed the differences between C. barabensis (2n = 20) and C. psevdogriseus (2n = 24). The data obtained give grounds to discuss the taxonomic status of the 24-chromosomal form of gray hamsters from the Qurama Ridge and consider the differentiation of N. migratorius karyomorphs as a stage of chromosomal speciation.

Abstract—

When combining imputed and sequenced data in a single gene-based association analysis, the problem of reconstructing genetic correlation matrices arises. It is related to the fact that the correlations between genotypes of all imputed variants and the correlations between genotypes of all sequenced variants are known for a gene but we do not know the correlations between genotypes of variants, one of which is imputed, and the other is sequenced. To recover these correlations, we propose an efficient method based on maximising the determinant of the matrix. This method has a number of useful properties and an analytical solution for our task. Approbation of the proposed method was performed by comparing reconstructed and real correlation matrices constructed on individual genotypes from the UK Biobank. Comparison of the results of gene-based association analysis performed by the SKAT, BT, and PCA methods on reconstructed and real matrices using modelled summary statistics and calculated summary statistics on real phenotypes showed high quality of reconstruction and robustness of the method to different gene structures.

Abstract—

Basic methods of population genetics and animal breeding and mathematical methods of machine learning used in animal breeding are analyzed. CatBoost library models were trained on the example of two domesticated species—horse (Equus caballus) and reindeer (Rangifer tarandus). Data from microsatellite panels of loci 16 and 17, respectively, were used to train the model using data on domesticated and wild reindeer, European and Russian horse breeds. The standard indicators (Accuracy, Precision, Recall, and F1) were calculated, and confusion matrices were constructed to assess the success of the model. New possibilities for identifying animal breed affiliation are shown.