Vavilovskii Zhurnal Genetiki i Selektsii最新文献

Flax is an important agricultural crop with multifunctional uses. Diversified breeding for oil content in seeds and fiber in stems has led to the emergence of two morphotypes - fiber flax and oilseed flax. Previously, using single nucleotide polymorphisms (SNPs), we characterized the genetic diversity of 306 flax samples from the collection of the Russian Federal Research Center for Bast Crops. However, larger structural variations, such as mobile genetic elements, also play a significant role in shaping agronomically important plant traits and can be used for further flax improvement. Here, we used the same flax collection to predict sites of new transposon insertions and to assess the role of such insertions in the formation of agronomically important traits, as well as in the process of flax domestication. We discovered 588,480 new transposon insertion sites not present in the reference flax genome (NCBI assembly ASM22429v2), the majority of which were attributed to retrotransposons of the Copia and Gypsy superfamilies, while among DNA transposons, insertion sites of the MULE-MuDR, hAT, and CMC-EnSpm superfamilies were most common. Unlike SNPs, which were significantly more numerous in oilseed flax than in fiber flax, we did not find such a substantial difference in the number of insertions of different transposon families per plant among samples of different morphotypes. Analysis of genomic regions affected by recent breeding efforts revealed a total of 61 candidate regions, of which 18 regions overlapped with QTLs associated with important agronomic traits. Interestingly, 5 regions of reduced genetic diversity in kryazhs and cultivars compared to landraces were also identified as regions of reduced diversity when using single nucleotide polymorphisms as markers. A genome-wide association study (GWAS) identified 50 TE insertions associated with different phenotypic traits, with many associations confirmed by multiple models or detected in data from multiple years. Thus, transposon insertion sites are an important source of genetic diversity in flax, alongside single nucleotide polymorphisms, making them suitable for further crop improvement in breeding.

Guar (Cyamopsis tetragonoloba (L.) Taub), is an important short-day legume crop, whose cultivation is limited at high latitudes due its photoperiod sensitivity, that negatively impacts flowering and maturation of this industrial-oriented crop. In its close relative, soybean, the E1 gene has been highly associated with the regulation of flowering time under long-day conditions. In this study we investigated the natural diversity of the E1 homologue gene (CtE1) in a panel of 144 guar accessions. For this purpose, the CtE1 gene was amplified and sequenced using Illumina. As a result, five novel SNPs were identified in the 5'-untranslated region, coding region, and 3'-untranslated region of the CtE1 gene. One non-synonymous SNP was located in the coding region causing a conservative Arg→Lys substitution. Based on the identified SNP, five KASP markers linked to polymorphism in the target gene were developed and tested in the guar collection. No significant associations were detected between discovered SNPs and available data on variability in flowering time or vegetation period length in the cohort of 144 accessions. These findings suggest that natural variation of the CtE1 gene in the studied germplasm collection has minimal effect on flowering or maturation. The limited functional allelic diversity observed in the CtE1 gene of guar compared to the E1 gene in soybean likely reflects differences in their evolutionary histories, domestication bottlenecks, and selection pressures.

The duration of the vegetation period significantly impacts yield formation and is one of the important characteristics of spring common wheat (Triticum aestivum L.) varieties. The primary developmental phases influencing the vegetation period include the time from seedling emergence to heading and from heading to maturity. To identify genes and loci associated with these traits under long-day conditions typical of Western Siberia and to assess their impact on yield components, we conducted QTL mapping followed by an evaluation of yield-related traits in lines carrying different alleles of key heading time genes. For mapping, we used an F2 population derived from a cross between the varieties Obskaya 2 and Tulun 15, which contrast in their heading and maturity times. QTL analysis identified a novel locus on the long arm of chromosome 7B associated with maturity time, as well as two loci on chromosome 2D and the short arm of chromosome 7B associated with heading time. Gene analysis within these loci revealed candidate genes for the "seedling-maturity" trait, with expression patterns corresponding to the known maturity time regulator NAM-1. The localization of loci for the "seedling-to-heading" trait suggested their correspondence to the well-known genes Ppd-D1 and Vrn-B3. Analysis of progeny carrying the Ppd-D1a and Vrn-B3a allele combination demonstrated that Ppd-D1a had a stronger effect on heading time than Vrn-B3a, and their combined presence resulted in the earliest heading - on average, five days earlier than in lines with the Ppd-D1b and vrn-B3 alleles. Evaluation of yield-related traits (number and weight of grains per main spike and per plant, and 1,000-grain weight) indicated that Ppd-D1 was significantly associated with all traits, with the Ppd-D1a allele generally exerting a negative effect on yield. In contrast, Vrn-B3 had a comparatively smaller effect on yield traits than Ppd-D1.

It typically takes 12 to 15 years to develop a new promising variety. One of the ways to reduce this time is through speed breeding. This method allows for up to six consecutive generations of spring cereals in a single year. Although far-red light is often overlooked in speed breeding protocols, it serves as a potent inducer of accelerated flowering in various plant species. In this study, we explored the advantages of far-red light as a means to optimize the speed breeding of spring triticale. Experimental plants were cultivated under three conditions with different red to far-red ratios at 660 nm (R - red) and 730 nm (FR - far red): 1) 3.75 (R > FR); 2) 0.8 (R = FR) and 3) 0.3 (R < FR). We found that the onset of triticale flowering occurred significantly earlier at the lowest red to far-red light ratio (R/FR 0.3). On average, plants bloomed 2.6 and 4.1 days earlier in a mineral wool and a soil mixture at R/FR 0.3, respectively, than those grown at R/FR 3.75. A negative effect of higher-intensity far-red light on the reproductive system of triticale was observed. Additionally, seeds obtained from plants grown under higher-intensity far-red light showed significantly lower germination energy and capacity. No differences were found in the regenerative capacity of isolated embryos in vitro obtained from plants grown under the different spectral compositions. Our results demonstrate that the accelerated triticale development requires not only the involvement of far-red light, but also a specific red to far-red light ratio close to 0.3. A modified speed breeding protocol relying on this ratio enabled flowering to commence as early as 33.9 ± 1.2 days after sowing. The same triticale variety grown under field conditions in the Krasnodar region and in traditional laboratory growing conditions with a photoperiod of 18/6 h day/night flowered 25 to 29 days later than those cultivated under the speed breeding conditions.

mRNA vaccine technologies have been actively developing since the beginning of the 21st century and have received a major boost from new findings about the functioning of the immune system and the development of efficient vehicles for nucleic acid delivery. The mRNA vaccine demonstrates superior properties compared to the DNA vaccine, primarily due to accelerated mRNA vaccine development, enhanced flexibility, and the absence of integration into the genome. Artificial mRNAs have biotechnological and medical applications, including the development of antiviral and anticancer mRNA therapeutics. The effective expression of therapeutic mRNA depends upon the appropriate selection of structural elements. Along with the addition of the 5'-cap, appropriate polyadenylation, and sequence codon optimization, 5'- and 3'-untranslated regions (UTRs) play an important role in the translation efficiency of therapeutic mRNAs. In this study, new plasmids containing a novel combination of UTR pairs, namely 5'-UTR-4 and 3'-UTR AES-mtRNR1, were constructed to obtain artificial mRNAs encoding green fluorescent protein (GFP) and firefly luciferase (FLuc) with new structural elements and properties. The novel combination of the UTRs, which is described in this article for the first time, in addition to sufficient polyadenylation and pseudouridinilation of mRNA, was demonstrated to strongly increase the translation of codon-optimized sequences of reporter mRNAs. We generated lipoplexes containing the aforementioned reporter mRNAs and liposomes composed of cationic lipid 2X3 (1,26-bis(cholest-5-en-3beta-yloxycarbonylamino)-7,11,16,20-tetraazahexacosane tetrahydrochloride) and helper lipid DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine). For in vivo experiments, the liposomes were decorated with 2 % of 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (DSPE- PEG2000). The translation efficiency of mRNAs was found to be superior for the novel UTR combination compared with HBB gene UTRs, both in vitro and in vivo. When mRNA is administered intramuscularly, the proposed combination of UTRs provides lasting expression for more than 4 days. The results demonstrated that the novel UTR pair combination could be useful in the development of artificial mRNAs with enhanced translation efficiency, potentially reducing the dose for mRNA-based therapeutics.

In spite of recent substantial progress in genomic approaches, there is still a need for molecular markers convenient for Sanger sequencing and providing good phylogenetic reconstructions at short evolutionary distances. A new molecular marker, the histone H3-H4 region, containing partial coding sequences of the genes for histones H3 and H4 and the non-coding spacer between them, is proposed. This marker is potentially useful for molecular phylogenetic studies at the generic, species, and even intra-species level in insects and some other organisms, even from other phyla. The highly conserved histone-coding sequences ensure the universality of primers and the ease of primary alignment, while the highly variable non-coding spacer provides enough variation for analyses at short evolutionary distances. In insects, the histone genes reside in the histone repeat which is tandemly repeated in dozens to hundred copies forming the so-called histone cluster. This ensures a high concentration of the template for the marker in genomic DNA preparations. However, the order and orientation of the histone genes in the histone repeat is variable among orders, which puts some limitations on the use of the proposed marker. The marker efficacy is hereby shown for Odonata (dragonflies and damselflies), where it provided good resolution at the family, genus and species levels. The new marker also provided an interesting pattern in the relationship of two Sympetrum species, S. croceolum and S. uniforme, showing the sequences of the latter as a branch nested among those of the former. The same combination of the proposed original primers should also work in Diptera.

The composition of wheat grain plays a key role in determining its nutritional value. In this work, a collection of 133 durum wheat varieties and breeding lines was assessed for the content of macroelements (Ca, Mg, K), microelements (Cu, Mn, Zn, Fe, Na) and toxic metals (Pb, Cd, and Cr) in grain under the environmental conditions of Samara and Novosibirsk regions in 2023. The results showed a wide range of variations in the concentration of all elements depending on genotypic differences between the samples as well as the growing region. Ca and Mg contents in the varieties grown in Samara region showed a significant excess of 3.1- and 1.5-fold, respectively. Zn, Pb, and Cr content in the varieties cultivated in Novosibirsk turned out to be two times as high. Statistical analysis of element concentrations in the varieties of different origin indicates that Russian breeding lines significantly outperform Russian cultivars in Mg content, while being inferior in K, Cu, and Mn. Compared to Russian cultivars and breeding lines, foreign varieties demonstrated higher contents of K and heavy metals Cd and Cr. Correlation analysis using mean values of indicators for two environments showed highly significant ( p < 0.001) positive relationships between the content of microelements Fe/Mn (r2 = 0.69), Fe/Zn (r2 = 0.49), and Zn/Mn (r2 = 0.46), which suggests a feasibility of selecting genotypes for several elements at once. Multivariate statistics divided the durum wheat collection into two groups, one of them including Russian cultivars and breeding lines as well as some foreign genotypes. A separate cluster included seven Russian breeding lines placed at a distance from the other varieties, which suggested their potential differences at the genetic level. Comparing these lines with respect to mineral composition showed that they were, on average, characterized by higher Mg, K, Zn, and Fe contents. The data obtained in this study can be used for genetic research and breeding to improve the grain mineral composition of the modern durum wheat varieties.

The assessment of intraspecific variability of wheat has been relevant for years. Although most modern wheat cultivars are considered to be pure lines, the heterogeneity of varietal populations is one of the mechanisms for maintaining population homeostasis. It is possible that the high evolutionary stability of constitutive heterochromatin and its stable distribution within chromosomes will allow us to use karyological analysis not only for studying the genesis and taxonomy of Triticum L., but also for studying the intraspecific diversity of wheat. In this regard, a classification of 87 Russian cultivars of common wheat differing in breeding status (landraces and modern cultivars) and growth habit (spring and winter) was carried out using two alternative approaches for assessing karyograms. The first approach uses the qualitative assessment of karyograms based on the distribution of C-bands on chromosomes. We also proposed that quantification of karyograms based on the size of C-bands would make the classification of cultivars more adequate. The variability, informative value and resolution of diagnostic features, trends in grouping cultivars, and their associations with the breeding status and growth habit were studied. A high potential of karyotyping with C-banding in discriminating modern cultivars by growth habit, as well as in separating winter cultivars from landraces has been revealed. In terms of the tested karyological features, the homogeneity of modern cultivars was higher than that of local cultivars, and the homogeneity of winter wheat was higher than that of spring wheat. The obtained classification reflects the preservation of high similarity in the karyograms of modern spring cultivars and landraces, as well as the low distinguishability between the karyograms of landraces differing in growth habit. A comparative analysis of the classifications of 20 cultivars using C-banding and SNP genotyping (3,126 polymorphic markers) suggests that studying the karyotypic variability allows us to infer a more accurate differentiation of wheat varietal populations based on the breeding status than using SNP markers that detect genetic variability, especially when the number of diagnostic features is limited.

Chronic obstructive pulmonary disease (COPD) is a multifactorial disease of the respiratory system and is the third leading cause of death worldwide. In the framework of the most relevant concepts of COPD pathogenesis, the key focus is on accelerated cellular senescence. FOXO family transcription factors are important hub components of cellular senescence signaling pathways. The objective of the study is to identify the association of FOXO1 (rs12585277, rs9549240), and FOXO3A (rs2253310, rs3800231) genes polymorphic variants with COPD and disease phenotypes. DNA samples from COPD patients (N = 710) and healthy individuals (N = 655) were used, polymorphic loci were analyzed by real-time PCR. For the first time, significant associations of FOXO1 (rs12585277) and FOXO3A (rs2253310) gene polymorphic loci with COPD and disease phenotypes were shown. Association with COPD was established with FOXO1 (rs12585277) (Padj = 0.0018, OR = 1.44 for the AG genotype) and FOXO3A (rs2253310) (Padj = 5.926 × 10-7, OR = 1.99 for the GG genotype). A significant genotype-dependent variation of smoking index (in pack/years), vital capacity and forced vital capacity was revealed for FOXO1 (rs9549240, rs12585277) and FOXO3A (rs2253310) loci. Multiple regression and ROC analysis identified highly informative COPD risk model, which included polymorphic variants of the FOXO1 (rs12585277) and FOXO3A (rs2253310) genes, smoking index and age (P = 5.25 × 10-93, AUC = 0.864). The multivariate regression model of the COPD "frequent exacerbator" phenotype included the AG genotype of FOXO1 (rs12585277), smoking index and age (AUC = 0.897, P = 4.1 × 10-86). FOXO family transcription factors involved in autophagy, oxidative stress and cellular homeostasis may provide a platform for a new diagnostic and treatment strategy for COPD as potential biomarkers and targets for therapy.

One of the main methods for obtaining transgenic plants is Agrobacterium-mediated transformation. This process relies on the ability of certain soil bacteria, specifically from the genera Agrobacterium and Rhizobium, to transfer and integrate a fragment of their plasmid into the chromosome of the recipient plant. This transferred DNA is referred to as T-DNA. Laboratory studies have demonstrated that whole plants can be regenerated from transgenic cells. It soon became evident that similar processes occur in nature, leading to the emergence of naturally transgenic plants, or natural GMOs. Thus, naturally transgenic plants possess homologues of the T-DNA genes from agrobacteria in their genomes (cellular T-DNA, or cT-DNA). These sequences are inherited through multiple sexual generations and retain their functionality. Furthermore, the potential for using newly acquired plant sequences in phylogenetic studies has been established, as cT-DNAs are clearly defined, highly specific, and recognizable DNA fragments that differ from typical plant DNA sequences. They are not found in untransformed ancestors, and their integration at specific chromosomal sites marks a monophyletic group of species. This review highlights the diversity of cellular T-DNAs and their potential use as phylogenetic markers. It includes a description of the main methodological approaches to such studies and discusses specific examples that clarify controversial points in the phylogeny of the genera Nicotiana, Camellia, Vaccinium, and Arachis. An important aspect of phylogenetic analysis based on cT-DNA is the assembly of individual alleles, which enables the tracking of interspecific hybridization events. This approach demonstrated the incomplete process of speciation within the Thea section of the genus Camellia and confirmed the role of interspecific hybridization in the breeding of North American blueberries. The review also addresses the dating of transformation events based on cT-DNA, which are organized in the form of imperfect repeats, as well as the application of phylogenetic studies to investigate the biodiversity of agrobacterial T-DNA genes.