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The aim of the work was a comparative assessment of the genetic diversity of Nenets reindeer depending on their gender. The object of research was animals of the Nenets breed of the Yamal experimental station of the Tyumen Scientific Research Center SB RAS (Salekhard). A total of 49 samples of auricle tissues obtained from males and 253 samples from females were subjected to DNA analysis. It was found that there are 24 microsatellites among the important ones, which are absent from the choirs. Private alleles were identified for all 9 analyzed loci, the average frequency of which was 0.073. A half-focus analysis of the correspondence of the observed and expected genotypes showed that the greatest similarity, regardless of gender, was observed at the NVHRT24 locus, and the maximum discrepancy was seen in RT6 in choirs, and RT30 in vazhenok. A significant discrepancy in the prevalence of observed and expected genotypes in males was typical for NVHRT76, RT27 and NV21 (PЈ0.001), and in females for all 9 analyzed loci (PЈ0.05...0.001). The analysis of the main genetic parameters indicates that the average number of observed microsatellite variants among the vazhenki was 2.24 more (PЈ0.05) compared with the choruses. The greatest discrepancy between the observed and effective microsatellites in males was characterized by the RT30 locus (a difference of 3.88 times), in females - RT9 (a difference of 3.75 times). A polocus analysis of the level of inbredity showed that the greatest correspondence between the observed and expected heterozygosity in choirs is characterized by the RT9 locus (-0.017), and RT6 locus (-0.020) in females. A noticeable deficiency of heterozygosity, regardless of gender, was observed in NV21 (choruses - 0.693; vazhenki - 0.511), whereas a pronounced shift towards an excess of heterozygotes was observed only among males at the RT6 locus (-0.272). The RT6 locus (DN=0.006) was characterized by the closest possible structure between the vazhenki and choruses, and the RT9 loci (DN=0.152) and RT30 (DN=0.299) had the greatest genetic difference. However, the average genetic divergence between males and females was not significant (DN=0.073). The data obtained predict a further narrowing of the genetic diversity of the analyzed population in the absence of choral exchange.

Abstract Aedes aegypti and Aedes albopictus mosquitoes spread major vector-borne viral diseases in tropical and sub-tropical regions of the globe. In this study, we sequenced the genome of Indian Ae. aegypti and Ae. albopictus and mapped to their reference genomes. Comparative genomics were performed between our strain and the reference strains. A total of 14,416,484 single nucleotide polymorphisms (SNPs) and 156,487 insertions and deletions (InDels) were found in Ae. aegypti, and 28,940,433 SNPs and 188,987 InDels in Ae. albopictus. Particular emphasis was given to gene families involved in mosquito digestion, development, and innate immunity, which could be putative candidates for vector control. Serine protease cascades and their inhibitors called serpins, play a central role in these processes. We extracted high-impact variants in genes associated with serine proteases and serpins. This study reports for the first time a high coverage genome sequence data of an Indian Ae. albopictus mosquito. The results from this study will provide insights into Indian Aedes specific polymorphisms and the evolution of immune related genes in mosquitoes, which can serve as a resource for future comparative genomics and those pursuing the development of targeted biopesticides for effective mosquito control strategies.

Aedes aegypti and Aedes albopictus mosquitoes spread major vector-borne viral diseases in tropical and sub-tropical regions of the globe. In this study, we sequenced the genome of Indian Ae. aegypti and Ae. albopictus and mapped to their reference genomes. Comparative genomics were performed between our strain and the reference strains. A total of 14,416,484 single nucleotide polymorphisms (SNPs) and 156,487 insertions and deletions (InDels) were found in Ae. aegypti, and 28,940,433 SNPs and 188,987 InDels in Ae. albopictus. Particular emphasis was given to gene families involved in mosquito digestion, development, and innate immunity, which could be putative candidates for vector control. Serine protease cascades and their inhibitors called serpins, play a central role in these processes. We extracted high-impact variants in genes associated with serine proteases and serpins. This study reports for the first time a high coverage genome sequence data of an Indian Ae. albopictus mosquito. The results from this study will provide insights into Indian Aedes specific polymorphisms and the evolution of immune related genes in mosquitoes, which can serve as a resource for future comparative genomics and those pursuing the development of targeted biopesticides for effective mosquito control strategies. [ABSTRACT FROM AUTHOR]

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever‐growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large‐scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)—a user‐friendly multiplatform software for preparation and evolutionary genetic analyses of genome‐ or transcriptome‐scale sequence polymorphism datasets. The program has an easy‐to‐use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ‐phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/. [ABSTRACT FROM AUTHOR]

In the Triticeae tribe, several subgenomes (St, J, V and others) were described, and a subgenome-specific molecular marker development is an actual branch of studies. Non-transcribed spacers (NTS) of 5S rDNA are perspective to create species-specific or genome-specific molecular markers in closely related organisms. Early, the 5S rDNA NTS based CAPS marker (StJV-f/StJV-r primers with the SmiM1 enzyme digestion) was designed for identification of the St, J and V subgenomes. The V subgenome amplicons were differed from the St and J amplicons in length. The St amplicons were distinguishable from the J amplicons after the SmiM1 enzyme digestion (St fragments were digested, J fragments were not digested, which is a disadvantage, because a failure with the digestion of St amplicons can be mistaken for J amplicons). This article presents the results of the StJV marker improvement. Comparative analysis of restriction enzyme maps revealed that the Hpy166 II enzyme cuts the StJV amplicons of all studied subgenomes in such a way that different product patterns are obtained. Experimental testing confirmed this finding. Thus, the improved CAPS marker can serve as a promising tool for verifying samples in Triticeae plant collections, screening herbarium materials, as well as in the breeding process aimed at improving wheat by involving its wild relatives in traditional breeding programs efficiently. [ABSTRACT FROM AUTHOR]

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent.

Background. Current molecular and genetic approaches make it possible to accelerate ryegrass breeding, simplify source material evaluation, and increase its accuracy. The efficiency of PCR-based SSR and SCoT marker techniques was studied in the context of evaluating the genetic structure of annual and perennial ryegrass accessions and defining DNA-identifying markers.Materials and methods. Genomic DNA was isolated from the aggregate sample of 30 seedlings from each of the 15 analyzed cultivars according to the modified SDS DNA extraction protocol. In total, 20 SSR and 22 SCoT markers were used to assess genetic polymorphism. Basic parameters of the markers’ informative efficiency were identified. Genetic relationships among the studied cultivars were analyzed on the basis of the Neighbor-Joining dendrogram and Bayesian model.Results. To assess the genetic polymorphism of ryegrass species and varieties, 7 SSR loci were selected, for which 110 allelic variants were identified (34 alleles were unique for individual cultivars), and 9 SCoT loci, for which 78 polymorphic amplification fragments were identified, with 28 being cultivar-specific. The dendrogram of genetic similarity and modeling in the Structure v2.3.4 program according to the results of SSR and SCoT analyses distributed the cultivars by their traits according to their species, ploidy level, origin, and similarity. Based on PCoA, carried out using summarized data of SSR and SCoT analyses, a multidimensional diagram of genetic relationships among ryegrass cultivars was constructed.Conclusions. The systems of SSR and SCoT markers appeared to be an efficient tool to reveal genetic polymorphism and identify differences among ryegrass species and cultivars. We found unique DNA profiles that can be used for genetic identification. The results of the study have practical significance in cultivar-specific identification and selection of cultivars for various purposes.

In Syria, there are ancient wild, and cultivated mulberry trees, traditionally used to feed the silkworm Bombyx mori L., and cultivated for their edible fruits. Evaluating genetic relationships is imperative for the identification, conservation, and improvement of mulberry germplasm. The present study addresses the use of inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers to estimate genetic diversity within and between two different mulberry species (49 genotypes of Morus nigra cultivar. El-Shami) and (8 genotypes of Morus alba) from different regions of Syria (Al-Qunaitra, Tartus and Latakia). Fifteen ISSR primers and six SSR primer pairs were used in the analysis. Overall, genetic diversity within M. alba and M. nigra was low (0.22). The genetic distance between the two species (M. nigra and M. alba) was higher (0.72) than that within the species (0.3). A dendrogram based on SSR and ISSR results showed the clustering of samples according to the species and to their geographic collection sites. The level of polymorphism detected between samples using the ISSR marker (90.31%) was higher than that detected with SSR marker (68.05%). The genotypes collected from Al-Qunaitra were very similar as the coefficient of genetic distance -CGD- was less than 0.1, while genotypes from Latakia were more distant (CGD is 0.33). In general, the level of genetic diversity between the analyzed genotypes of M. nigra cv. El-Shami was lower than between the samples of M. alba.

Within the Bosnian Mountain Horse Registry (BMH), some specific coat colours are permitted. Accurate determination of coat colours can be challenging as there are variations in coat colour shades and several dun dilution variants occur. The previously found single nucleotide polymorphisms (SNPs) within two coat colour loci, T-box 3 (TBX3) and Agouti Signalling Protein (ASIP), were genotyped in 313 BMH individuals. The obtained genotypes were then compared to the predicted phenotypes by using the observed coat colour types from the International Association of Bosnian Mountain Horse Breeders (IABMHB) database. It was found that the dark bay and black coat colours were the most representative coat colours both phenotypically and genotypically. The frequency of the dominant Dun (D) dilution allele is (0.09), and this frequency is higher than the previously predicted frequency recorded in the available BMH registers, as also demonstrated. Among the identified alleles, there was a discrepancy or inconsistency between the predicted coat colour based on genotypes and the observed coat colour in 73 horses (23%). The most frequent error concerned the misclassification of horses with genotypes aa and Aa at the ASIP gene, non-dun1/non-dun1 (nd1/nd1) and non-dun2/non-dun1 (nd1/nd2) at the TBX3 gene, which can be associated with the occurrence of slight dilution phenotypes in these individuals. In contrast to the Konik and Hucul breeds, no homozygosity of the D allele was found in the BMH. The D allele can be easily overlooked or not recognised in different phenotypic groups, such as dark bay and black horses. Therefore, the hypothesis that Dun dilution effects itself is not as strongly epistatic in the BMH as described in other horse breeds. This could be the result of an additional genetic modifier suppressing the phenotypic effect of the D allele. It also suggests that there has been a persistent selection pressure in favour of dark base colours, which may have contributed to the observed differences in BMH. Finally, a significant proportion (35%) of BMH individuals with genetically black coat colour were officially classified as dark bay. We hypothesise that the difficulty in visually distinguishing these two phenotypes is due to an independent locus upstream of the ASIP gene. This locus was recently identified as a factor that darkens the typical pigmentation in dark bay horses. The results of the study confirm the importance of molecular testing in accurately determining the coat colour of horses. This would help to avoid errors in coat colour descriptions in official breeding records and provide valuable information for selective breeding programmes aimed at producing specific and desired coat colours. Variabilnost genov ASIP in DUN, odgovornih za barvo dlake pri bosanskem planinskem konju Določanje barv dlake pri bosanskem planinskem konju (BPK) je lahko izziv, ker obstajajo razlike v barvnih odtenkih dlake in več oblik redčenja barve dlake (plavci). Pri 313 konjih pasme BPK smo genotipizirali polimorfizme posameznih nukleotidov (SNP) znotraj dveh lokusov za barvo dlake T-box 3 (TBX3) in polimorfizma 11-bp indel znotraj Agouti signalnega proteina (ASIP). Posamezne genotipe smo nato primerjali z vpisanimi fenotipi barv dlake iz baze podatkov MZRBPK (Mednarodno združenje rejcev bosanskega planinskega konja). Ugotovljeno je bilo, da sta bili temna rjava in črna najbolj reprezentativni barvi dlake pri BPK. Pogostnost prevladujočega alela za redčenje Dun (D) v študiji je višja (0,09) od predhodno zabeležene v razpoložljivem registru BPK. Med ugotovljenimi aleli je prišlo do neskladja ali nedoslednosti med predvideno barvo dlake na podlagi genotipov in opazovano barvo dlake pri 73 konjih (23%). Najpogostejša napaka se je nanašala na napačno razvrstitev konjev z genotipoma aa in Aa v genu ASIP, non-dun1/non-dun1 (nd1/nd1) in non-dun1/non-dun2 (nd1/nd2) pri genu TBX3, kar je lahko povezano s pojavom redčenja barve dlake pri teh fenotipih.V nasprotju s pasmami Konik in Hucul pri BPK ni bila ugotovljena homozigotnost alela D. Alel D je mogoče zlahka spregledati ali ga ne prepoznati v različnih fenotipskih skupinah, kot so temni rjavci in vranci. Zato hipoteza, da učinki redčenja Dun (plavci) pri BPK sami po sebi niso tako močno epistatični, kot je to opisano pri drugih pasmah konj. Rezultati študije potrjujejo pomen molekularnega testiranja pri natančnem določanju barve dlake konj. To bi pripomoglo k preprečevanju napak pri opisih barve dlak v uradnih rejskih evidencah in pomembna informacija pri selekciji na posebne in želene barve dlake pri konjih. Ključne besede: barva dlake konj; dun redčenje barve dlake; polimorfizem DNK; frekvenca alelov; frekvenca genotipa; bosanski planinski konj

Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (An) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψwl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na+ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (gs, E, An) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress. [ABSTRACT FROM AUTHOR]

Accurate determination of coat colours in Bosnian Mountain Horse (BMH) can be challenging as there are variations in coat colour shades and several dun dilution variants occur. In other studies found single nucleotide polymorphisms (SNPs) within two colour loci T-box 3 (TBX3) and 11-bp indel polymorphism within Agouti Signalling Protein gene (ASIP), were genotyped in 313 BMH individuals. The obtained genotypes were then compared to the identified phenotypes by using the observed coat colour types from the International Association of Bosnian Mountain Horse Breeders (IABMHB) database. It was found that the dark bay and black were the most representative coat colours in BMH. The frequency of the dominant Dun (D) dilution allele in the study is higher (0.09) than the previously predicted frequency recorded in the available BMH register. Among the identified alleles, there was a discrepancy or inconsistency between the predicted coat colour based on genotypes and the observed coat colour in 73 horses (23%). The most frequent error concerned the misclassification of horses with genotypes aa and Aa at the ASIP gene, non-dun1/non-dun1 (nd1/nd1) and non-dun2/non-dun1 (nd1/nd2) at the TBX3 gene, which can be associated with the occurrence of slight dilution phenotypes in these individuals. In contrast to the Konik and Hucul breeds, no homozygosity of the D allele was found in the BMH. The D allele can be easily overlooked or not recognised in different phenotypic groups, such as dark bay and black horses. Therefore, the hypothesis that Dun dilution effects itself is not as strongly epistatic in the BMH as described in other horse breeds. The results of the study confirm the importance of molecular testing in accurately determining the coat colour of horses. This would help to avoid errors in coat colour descriptions in official breeding records and provide valuable information for selective breeding programmes aimed at producing specific and desired coat colours. [ABSTRACT FROM AUTHOR]

Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study was to evaluate the patterns of genetic diversity in common reed stands located in habitats that are differently affected by anthropogenic factors. We studied whether riverbed modifications, land cover in the neighborhood of the stand and the chemical and physical parameters of the river water affect the genetic diversity of P. australis at the studied sites. Using DNA fingerprinting, we genotyped 747 plants from 42 sites located in 16 small Lithuanian rivers. Bayesian clustering and principal coordinate analysis revealed two main gene pools at the population (river) level. At the site level (i.e., considering all sites independently of their rivers), polymorphism was high even between sites in the same river. Our study revealed a negative relationship between the concentration of nitrogen compounds and the genotypic richness of P. australis populations. We did not find any correlations between the other chemical parameters of the water and the parameters of the genetic diversity. Additionally, there were no genetic differences between sites in modified and unmodified river sections or between sites that differed in land cover type in the neighborhood of the stand. [ABSTRACT FROM AUTHOR]

The main source of vegetable protein in the world are leguminous crops, among which peas are the most common in Russia. Dozens and even hundreds of genes are involved in the regulation of biological processes associated with the maturation of seeds and the accumulation of reserve nutrients in them, including proteins. The study conducted on legume species related to peas indicate that one of the genes at the highest hierarchical level in this regulatory chain is the ABI3 transcription factor gene; however, its role in the biosynthesis and accumulation of seed storage proteins remains poorly studied. The purpose of the current work is to identify high-protein pea genotypes and analyze the nucleotide sequences of the coding region of the ABI3 gene to search for possible DNA polymorphisms associated with protein percentage in their seeds. The study was carried out in 2020–2021. The objects of the study were 37 pea varieties from the collection of genetic resources of leguminous crops of VIR. Protein percentage in seeds was determined by the Bradford method. Selection of primers and comparative analysis of nucleotide sequences were performed using the PrimerSelect and MegAlign programs. Sequencing was performed according to the Sanger method. There were identified pea varieties with the highest (‘Aksaisky Usaty 55’, ‘Sakharny’) and low (‘K-8361’ (VIR), ‘Fregat’) seed protein percentage. In these variety samples, the coding region of the ABI3 gene was sequenced. Comparative analysis of their nucleotide sequences with the sequence of the ABI3 gene fragment annotated in the GenBank database revealed significant variability among them: nucleotide substitutions, deletion of 6 nucleotides. In the high protein variety ‘Sakharny’, there has been found a 9-nucleotide insertion, leading to the insertion of three additional amino acids, and in the low-protein variety Fregat, there has been found a single nucleotide insertion, causing a shift in the reading frame. The data obtained may indicate a correlation between mutations in the ABI3 gene and protein accumulation in pea seeds.

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations. [ABSTRACT FROM AUTHOR]

The genetic diversity of Pacific rainbow smelt Osmerus dentex from the seas of Okhotsk and Japan has been studied based on nine microsatellite loci and the control region of mitochondrial DNA (940 base pairs). The lowest values of all parameters of genetic diversity of mitochondrial DNA were observed in the group of samples from the northern coast of the Sea of Okhotsk. The highest value of the haplotype diversity was found in the sample from the Sakhalin Island and in rainbow smelt from the Sea of Japan. The star-shaped topology of the genealogical structures indicates a rapid expansion of the abundance and the origin of all populations of the species from a single common ancestor from the main refugium. Based on the results of analysis of nuclear markers, we have revealed a statistically significant genetic structuring of rainbow smelt within its Pacific range (the coefficient of genetic differentiation (FST) is 0.033), which is adequately described by the model of isolation by distance. The greatest genetic differences in two types of markers from the other samples have been found in rainbow smelt from the Shkotovka and Botchi rivers of the basin of the Sea of Japan and from the Naiba River (Sakhalin). The observed patterns of genetic differentiation of Pacific rainbow smelt by the nuclear and mitochondrial markers complement each other well and are most likely associated with differences in the distribution of smelt larvae from the spawning grounds, which are determined by the differentiation of oceanographic conditions. [ABSTRACT FROM AUTHOR]

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes. [ABSTRACT FROM AUTHOR]

Abstract Background Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species — perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. Results Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. Conclusions We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions.

The development of retinopathy of prematurity (ROP) may be influenced by anemia or a low fetal/adult hemoglobin ratio. We aimed to analyze the association between DNA methyltransferase 3 β (DNMT3B) (rs2424913), methylenetetrahydrofolate reductase (MTHFR) (rs1801133), and lysine-specific histone demethylase 1A (KDM1A) (rs7548692) polymorphisms, erythrocyte parameters during the first week of life, and ROP. In total, 396 infants (gestational age < 32 weeks or birth weight < 1500 g) were evaluated clinically and hematologically. Genotyping was performed using a MicroChip DNA on a platform employing iPlex MassARRAY®. Multivariate regression was performed after determining risk factors for ROP using univariate regression. In the group of infants who developed ROP red blood cell distribution width (RDW), erythroblasts, and mean corpuscular volume (MCV) were higher, while mean hemoglobin and mean corpuscular hemoglobin concentration (MCHC) were lower; higher RDW was associated with KDM1A (AA), MTHFR (CC and CC + TT), KDM1A (AA) + MTHFR (CC), and KDM1A (AA) + DNMT3B (allele C); KDM1A (AA) + MTHFR (CC) were associated with higher RDW, erythroblasts, MCV, and mean corpuscular hemoglobin (MCH); higher MCV and MCH were also associated with KDM1A (AA) + MTHFR (CC) + DNMT3B (allele C). We concluded that the polymorphisms studied may influence susceptibility to ROP by modulating erythropoiesis and gene expression of the fetal/adult hemoglobin ratio. [ABSTRACT FROM AUTHOR]

In Syria, there are ancient wild, and cultivated mulberry trees, traditionally used to feed the silkworm Bombyx mori L., and cultivated for their edible fruits. Evaluating genetic relationships is imperative for the identification, conservation, and improvement of mulberry germplasm. The present study addresses the use of inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers to estimate genetic diversity within and between two different mulberry species (49 genotypes of Morus nigra cultivar. El-Shami) and (8 genotypes of Morus alba) from different regions of Syria (Al-Qunaitra, Tartus and Latakia). Fifteen ISSR primers and six SSR primer pairs were used in the analysis. Overall, genetic diversity within M. alba and M. nigra was low (0.22). The genetic distance between the two species (M. nigra and M. alba) was higher (0.72) than that within the species (0.3). A dendrogram based on SSR and ISSR results showed the clustering of samples according to the species and to their geographic collection sites. The level of polymorphism detected between samples using the ISSR marker (90.31%) was higher than that detected with SSR marker (68.05%). The genotypes collected from Al-Qunaitra were very similar as the coefficient of genetic distance -CGD- was less than 0.1, while genotypes from Latakia were more distant (CGD is 0.33). In general, the level of genetic diversity between the analyzed genotypes of M. nigra cv. El-Shami was lower than between the samples of M. alba. [ABSTRACT FROM AUTHOR]

For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P. [ABSTRACT FROM AUTHOR]

Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (An) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψwl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na+ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (gs, E, An) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress.

Copyright of Chinese Journal of Oil Crop Sciences is the property of Oil Crops Research Institute of Chinese Academy of Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species — perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. Results: Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. Conclusions: We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions. [ABSTRACT FROM AUTHOR]

Background: Canine cryptorchidism, manifested by an abnormal testicular position, poses significant health risks and reproductive challenges in affected males. Despite a high prevalence, estimated at up to 10% in the canine population, a comprehensive understanding of its pathogenesis remains elusive. Studies in human cryptorchids and knockout mice have identified key factors involved in testicular descent, including INSL3, RXFP2, and AR. To date, only three DNA variants, found in the RXFP2, HMGA2, and KAT6A genes, have been associated with canine cryptorchidism., Summary: This review briefly summarizes current knowledge on testicular descent and the factors that regulate this process, based on cryptorchidism in humans and mice. It also highlights recent findings related to canine cryptorchidism, focusing on the INSL3, HMGA2, and KAT6A genes. The most significant results are discussed, with an emphasis on the role of the epididymis in testicular descent. This report presents insights that may facilitate further research aiming to broaden our understanding of canine cryptorchidism pathogenesis., Key Messages: DNA polymorphism in the KAT6A gene, associated with changes in global H3K9 acetylation, as well as the DNA methylation pattern in the INSL3 gene, suggest that further research should strongly focus on epigenetic modifications. In addition, the development of the epididymo-testicular junction and the link between cryptorchidism prevalence and dog size should be further investigated., (© 2024 S. Karger AG, Basel.)

Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study was to evaluate the patterns of genetic diversity in common reed stands located in habitats that are differently affected by anthropogenic factors. We studied whether riverbed modifications, land cover in the neighborhood of the stand and the chemical and physical parameters of the river water affect the genetic diversity of P. australis at the studied sites. Using DNA fingerprinting, we genotyped 747 plants from 42 sites located in 16 small Lithuanian rivers. Bayesian clustering and principal coordinate analysis revealed two main gene pools at the population (river) level. At the site level (i.e., considering all sites independently of their rivers), polymorphism was high even between sites in the same river. Our study revealed a negative relationship between the concentration of nitrogen compounds and the genotypic richness of P. australis populations. We did not find any correlations between the other chemical parameters of the water and the parameters of the genetic diversity. Additionally, there were no genetic differences between sites in modified and unmodified river sections or between sites that differed in land cover type in the neighborhood of the stand.

Currently, there is an increasing focus on understanding the interactions between genetic features of the invader and environmental factors that ensure the success of invasion. The objective of our study was to evaluate the genetic diversity of Lithuanian populations of highly invasive small balsam (Impatiens parviflora) by amplified fragment length polymorphism (AFLP) markers and to relate molecular data to biotope features defined by employing neighboring species of herbaceous plants. Low polymorphism of I. parviflora populations was observed at AFLP loci. Hierarchical analysis of molecular variance did not reveal differentiation of populations depending on biotope, geography, or road types. Bayesian analyses of AFLP data demonstrated many genetic clusters. Our results suggest multiple introductions of I. parviflora into Lithuania. The polymorphism of AFLP loci of populations significantly correlated with the total coverage by herbaceous plants in the sites. Defined by principal component analysis, the variability of study sites was most related to the coverage of herbaceous plants and least related to the molecular features of I. parviflora populations. The sites with I. parviflora were classified into agricultural scrubland, riparian forest, and urban forest biotopes. Of them, urban forest was distinguished by the highest coverage of I. parviflora and the lowest Ellenberg indicatory values for light, soil acidity, and richness in nutrients. [ABSTRACT FROM AUTHOR]

Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e. toll-like receptors) and direct pathogen inhibition (i.e. antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e. mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets. [ABSTRACT FROM AUTHOR]

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

Rice is one of staple food crops in the world. Improving the drought tolerance of rice has become an important issue for maintaining or increasing its grain production under water stress caused by the greenhouse effect. For achieving this goal, quantitative trait loci (QTL) mapping is considered to be useful in plant breeding. In this study, a doubled-haploid (DH) population was used as elite materials. Based on results of polymorphism detection, 108 polymorphic markers were identified. The mapping analysis results indicated that 40 QTLs putatively associated with seven traits were found in nine linkage groups. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

An efficacious and reproducible in vitro regeneration technique for safflower was established using varying concentrations and composition of plant growth regulators (PGRs) supplemented Murashige and Skoog (MS) medium. Successful in vitro seed germination in half strength MS (H-MS) with 1.4 µM GA3 resulted in procurement of sterile explants (cotyledons, apical meristems) for in vitro study. Callogenesis (2.2 µM BAP + 2.7 µM NAA), indirect organogenesis of shoot buds (0.54 µM NAA + 9.08 µM TDZ), somatic embryogenesis (2.2 µM BAP + 5.4 µM NAA) and somatic embryo germinated plantlets (H-MS + 1.4 µM GA3 + 2.2 µM BAP + 5.4 µM NAA) were successfully obtained. Histological study and scanning electron micrographs of embryogenic callus revealed pre-globular, heart-shaped and torpedo stages of dicot embryogeny. H-MS + 8 µM NAA showed maximum rhizogenic response with a mean root and shoot length of 17.5 mm and 48.50 mm respectively in 2.2 µM BAP + 0.54 µM NAA bearing an average of 9 capitula per plantlet with 70% post transplantation survival rate. True to type nature of the regenerates was confirmed using Start Codon Targeted (SCoT) marker, exhibiting 100% and 97.3% monomorphic bands for direct and somatic embryo regenerated plants respectively. Flow cytometry method (FCM) was employed for 2C DNA content analysis. The histogram peaks of 2C nuclear DNA content of in vitro regenerated safflower (direct and embryo derived) were similar to the peak of field grown donor plant. 2C nuclear DNA content of field grown, direct and somatic embryo regenerated C. tinctorius was 2.65 ± 0.04 pg, 2.62 ± 0.06 pg and 2.68 ± 0.04 pg respectively, further verifying genetic homogeneity. All things considered, the above protocol is insusceptible to genetic alteration and can be used for large scale production and sustainable utilization of desired genotype. Key message: An efficient, reproducible in vitro regeneration protocol was achieved for safflower via direct, callus mediated organogenesis and somatic embryogenesis. Histology and SEM study revealed typical dicot embryogenic stages. SCoT molecular marker and flow cytometric 2C genome size analysis were further applied for evaluating genetic fidelity of in vitro regenerated safflower. [ABSTRACT FROM AUTHOR]

An important area of crop development is the introduction of new vegetable plants, one of which is the sweet potato Ipomoea batatas (L.) Lam. The aim of our research was genetic, biological and economic assessment of sweet potato accessions held in the collection of the Plant Introduction and Acclimatization Dept., Udmurt Federal Research Center, Ural Branch of the RAS (UdmFRC UB RAS).Within this experiment, DNA polymorphism of 16 accessions of I. batatas was tested using ISSR markers. All accessions were found to represent different genotypes; the VM 17 accession obtained as a result of a bud mutation differed significantly from the original accession in its genotype.Evaluation of 16 accessions of sweet potato cultivars was carried out in a small-plot field experiment. The results of biological and economic assessment witnessed to the prospects of sweet potato cultivation within the territory of the Udmurt Republic for marketable tuber production. The productivity of the accessions was 140–2700 g of tubers per plant. According to their productivity, the accessions were divided into clusters: the low-productivity group (up to 500 g), with ‘Betty’, Fioletovy, ‘Beauregard’, ‘Covington’ and Bezhevy; medium-productivity group (500–1000 g), with ‘Jewel’, Fioletovy Sochi, Brazilsky, Afgansky, Vinnitsky rozovy, Lyubitelsky and ‘Bayou Bell’; and high-productivity group (more than 1000 g), with Pobeda 100, ВM 17, Druzhkovsky and Bely NBS. On the basis of the evaluation, 11 sweet potato accessions were recommended for cultivation in the Middle Urals: Afgansky, ‘Bayou Bell’, Bely NBS, ВM 17, Brazilsky, Druzhkovsky, Fioletovy Sochi, ‘Jewel’, Lyubitelsky, Pobeda 100, and Vinnitsky rozovy.

Background. Identification of crop varieties is presently one of the most important aspects due a significant annual increase in the number of newly developed cultivars. Application of molecular markers makes it possible to identify cultivars and secure protection of plant breeders’ rights. Marker techniques based on SSR loci and PawS markers were evaluated for their efficiency in revealing the DNA polymorphism in Russian red clover cultivars, and the research results are presented in this publication.Materials and Methods. The total genome DNA was extracted by a modified SDS method from 30 seedlings per each cultivar. Nine simple sequence repeats (SSR) and 4 PawS markers were used for genotyping. The basic genetic diversity parameters were measured and analyzed using the software resources GelAnalyzer 2010а, MStools v.3, and Statistica 7.0.Results and conclusion. The mean level of intervarietal DNA polymorphism in red clover was 38.6%. Cultivar-specific amplicons were obtained for 4 accessions (cvs. ‘Trifon’, ‘Topaz’, ‘Trio’ and ‘Mars’) with SSR loci RCS1307 and RCS3095. These loci were found appropriate for identification and certification of such cultivars. The tested PawS markers (individually and in combinations) proved non-informative for the analysis of intervarietal DNA polymorphism in red clover. The only primer pair PawS5+PawS16 generated reproducible PCR products, but unique amplicons were absent in the DNA profiles. The data obtained in this study may be helpful for further identification and certification of Russian red clover cultivars and promising breeding materials.

Abstract Background Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring, coupled with developing genomic resources, enables researchers to conduct linkage analysis studies to identify genomic loci associated with specific traits. Results We used available genomic data to identify DNA polymorphisms between P. maniculatus and P. polionotus and used the polymorphic data to identify the range of genetic complexity that underlies physiological and behavioral differences between the species, including cholesterol metabolism and genes associated with autism. In addition, we used the polymorphic data to conduct a candidate gene linkage analysis for the Dominant spot trait and determined that Dominant spot is linked to a region of chromosome 20 that contains a strong candidate gene, Sox10. During the linkage analysis, we found that the spot size varied quantitively in affected Peromyscus based on genetic background. Conclusions The expanding genomic resources for Peromyscus facilitate their use in linkage analysis studies, enabling the identification of loci associated with specific traits. More specifically, we have linked a coat color spotting phenotype, Dominant spot, with Sox10, a member the neural crest gene regulatory network, and that there are likely two genetic modifiers that interact with Dominant spot. These results establish Peromyscus as a model system for identifying new alleles of the neural crest gene regulatory network.

The use of DNA-fingerprinting of forest-forming woody plants is considered the most promising tool for genetic control of wood’s geographic origin, the formation of a reliable management system for harvesting and turnover of lumber. The purpose of this work was to search for identification markers, genotyping trees, and molecular genetic identification of previously not studied 2 populations of the Siberian larch Larix sibirica Ledeb. and 4 populations of Scots pine Pinus sylvestris L. of different regions of the Perm Krai. To DNA extraction, from each plant specimens wood were individually obtained and a modified method of extracting DNA from wood was used. In total, the analysis used the DNA of 114 Scots pine trees and 55 Siberian larch trees. For genetic testing, we used ISSR (Inter Simple Sequence Repeats)-method of DNA polymorphism analysis. Genetic identification was performed based on the original author’s method proposed by S. V. Boronnikova and I. V. Boboshina (2014). As a result of molecular genetic analysis, 74 ISSR markers were found and analyzed in populations of Scots pine, 85 ISSR markers were identified in populations of the Siberian larch, and the share of polymorphic loci in both species was high. As a result of molecular genetic identification, identification of species and polymorphic ISSR-markers and their combinations were found that characterize the belonging of trees to a species, as well as to a specific population. Molecular genetic formulas and barcodes for each individual population of two species have been compiled. The effectiveness, stability, and reproducibility of detected identification markers and their combinations have been proven through anonymous testing. The data obtained are the basis for determining the place of origin of wood, which will allow us to recommend measures to counter illegal logging and reduce the damage to the budget of logging regions of Russia, such as the Perm Krai.

Cannabis plants have been cultivated around the world for thousands of years and are widely used in the textile industry and medicine. From the point of view of analyses for the needs of the justice system, they can be divided into two categories – hemp of the fibrous type and the narcotic type, which differ in the content of the psychoactive compound THC. According to the guidelines, varieties with a content of active compounds above 0.2 % are considered to be the narcotic type. The standard approach used to distinguish between these two types of Cannabis is commonly used toxicological analysis. However, if the content of differentiating active compounds or the type of plant part sent to the laboratory is problematic, genetic identification may be a good solution. The subject of the study of the research consortium was the genetic analysis of Cannabis samples using STR markers. The collected population database of samples of Cannabis from fibrous and narcotic varieties was analyzed taking into account the basic statistical parameters describing the population. It was used to develop a method of genetic profiling of Cannabis on the basis of a selected set of 23 STR genetic markers, which were subjected to preliminary statistical analyses. The developed genetic models will be used to select the most useful genetic markers for the genetic identification of Cannabis and will enable the creation of an identification tool for forensic experts. [ABSTRACT FROM AUTHOR]

We analyzed the accumulation of population polymorphism in 2504 individuals - nuclear genomes (nDNA) of 26 populations (81 genes associated to extreme environments) and 3295 mitochondrial genomes (mtDNA) of 47 populations with the aim to found mitonuclear relationship associated an extremes environment as altitude. For that, we use an algorithm developed by us to determine the accumulation of polymorphisms by segments in the genome and thus be able to perform the multivariate analysis to found SNPs differences and similarities among populations. The results showed in Peruvian population a statistically significant mitonuclear relationship for 113/293970 nDNA SNPs in 16/81 genes. In the case of the mtDNA, we found a statistically significant mitonuclear relationship for 6/22 mtDNA positions – Gene. Additionally for the Peruvian population, the MRPP3 had the greatest polymorphism contribution with respect to other populations. Then, these nDNA and mtDNA SNPs in genetically close populations to Peru can be applied to forensic genomic phenotyping to identify groups likely adapted to extreme conditions (such as altitude) or make individualization between low and high altitude populations. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective: The AKR1B1 gene encodes an enzyme that catalyzes the reduction of glucose into sorbitol. Chronic hyperglycemia in patients with diabetes mellitus (DM) leads to increased AKR1B1 affinity for glucose and, consequently, sorbitol accumulation. Elevated sorbitol increases oxidative stress, which is one of the main pathways related to chronic complications of diabetes, including diabetic kidney disease (DKD). Accordingly, some studies have suggested the rs759853 polymorphism in the AKR1B1 gene is associated with DKD; however, findings are still contradictory. The aim was to investigate the association of the rs759853 polymorphism in the AKR1B1 gene and DKD. Materials and methods: The sample comprised 695 patients with type 2 DM (T2DM) and DKD (cases) and 310 patients with T2DM of more than 10 years’ duration, but no DKD (controls). The polymorphism was genotyped by real-time PCR. Results: Allelic and genotype frequencies of this polymorphism did not differ significantly between groups. However, the A/A genotype was associated with risk for DKD after adjustment for gender, triglycerides, BMI, presence of hypertension and diabetic retinopathy, and duration of DM, under both recessive (P = 0.048) and additive (P = 0.037) inheritance models. Conclusion: Our data suggest an association between the AKR1B1 rs759853A/A genotype and risk for DKD in Brazilians T2DM patients.

Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.

The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein‐coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability. [ABSTRACT FROM AUTHOR]