Greater Genetic Diversity Research Articles

Variants of the PTPN11 Gene in Mexican Patients with Noonan Syndrome

Background/Objectives: Noonan syndrome (NS) is a genetic multisystem disease characterized by distinctive facial features, short stature, chest deformity, and congenital heart defects. NS is caused by gene variants of the RAS/MAPK pathway, with PTPN11 accounting for about 50% of cases. This study aimed to identify PTPN11 pathogenic variants in Mexican patients with NS to enhance our understanding of the disease in this population. Methods: This study included 91 probands and 60 relatives, all of which were clinically evaluated by a geneticist. Sanger sequencing was used to screen the entire PTPN11 gene. Results: Twenty-one previously reported pathogenic variants were identified in 47.3% of the probands. The most frequently occurring were p.Asn308Asp (16.3%) and p.Met504Val (16.3%). Variants p.Tyr279Cys and p.Thr468Met were found exclusively in patients with lentiginosis. Eighty-three percent of patients carried a variant in one of the three exons (3, 8, or 13) where the greatest genetic diversity was observed. Common clinical findings identified in probands included short stature (82%), cardiac anomalies (70.7%), short neck (68.4%), and pectus excavatum (63.2%), although features represented by only one patient each were also detected. Conclusions: This study confirmed the clinical diagnosis of NS in 43 probands and 11 relatives, and further genetic analysis of the remaining 48 probands is required to identify the causal variant. The genetic and clinical variability observed in our cohort was consistent with reports from other populations, underscoring the importance of comprehensive care for all patients. This research provides the most extensive clinical and molecular characterization of NS in Mexican patients, identifying pathogenic variants of PTPN11.

The Progression of Epitope-specific Antibody Responses toPlasmodium falciparum Circumsporozoite Protein Following Consecutive Malaria Infections in Naïve Adults: A Repetitive Controlled Human Malaria Infection Study

Abstract Background With an estimated 249 million cases and 608,000 deaths in 2022 malaria continues to cause substantial morbidity and mortality worldwide, mostly in children in Sub-Saharan Africa due to Plasmodium falciparum. Circumsporozoite protein (CSP) coats the surface of the P. falciparum sporozoite and is the target of the two vaccines approved by the World Health Organization (WHO). CSP has three major regions: the N-terminus, the central repeat region, and the C-terminus, which contains highly variable T cell epitopes; only a fragment of the central repeat region and the C-terminus are represented by the two approved vaccines. The junction between the N-terminal Region 1 and the NANP repeat region (“junctional region”) is not represented in the approved vaccines and was recently found to be a target of protective antibody responses. Methods We used a repetitive controlled human malaria infection (rCHMI) model in which eight malaria-naïve participants were infected with P. falciparum up to three times over two years to identify immune responses associated with acquisition of natural immunity. We evaluated samples from the day of each CHMI and 18 days after each CHMI. We measured antibody responses using a peptide microarray inclusive of hundreds of P. falciparum proteins and focused our current study on the response to CSP. The amino acid sequences of CSP from the NF54 strain and 4 additional CSP variants were represented as 16-amino acid peptides with 13-amino acid overlap. Signal intensities at each amino acid position were estimated using a sliding window approach that averaged signals from adjacent overlapping peptides. Participants who comprised a “delayed parasitemia group” (n = 5) had onset of PCR-confirmed parasitemia 13 or more days after the last CHMI, a sign of developing humoral immunity. A “non-delayed parasitemia group” (n = 3) was comprised of those had onset of parasitemia within 12 or fewer days after the last CHMI. Along each amino acid position, the median signal intensities for all CSP variants are presented to describe the participants’ antibody responses at each time point. Wilcoxon signed rank test was used to compare medians between timepoints; p-values < 0.05 without adjustment for multiple comparisons were considered statistically significant. Results After three rCHMIs, participants developed antibody responses to amino acids corresponding to the junctional region and the central repeat region (P<0.05). When participants are grouped by time to parasitemia, those who showed delayed parasitemia development had strong immune responses to the junctional region while the non-delayed group did not. Antibody responses to the C-terminal region were more variable among the 5 CSP variant sequences compared to other regions. Conclusion Our results showed higher junctional region antibody response in participants with delayed time to parasitemia. We also demonstrate variable antibody response to the C-terminal region, a region with known greater genetic variability that has been previously associated with allele-specific vaccine escape and concern for decreased efficacy of current WHO-approved vaccines. Taken together, our results support future vaccine development that focuses on the conserved junctional region over the polymorphic C-terminal region.

Assessment of Groundnut (Arachis hypogaea L.) Cultivars on Yield and Yield Contributing Traits using Principal Component Analysis

Background: The breeder’s ability to identify and exploit genetic diversity at the genotypic level is essential for the success of any breeding effort. It requires evaluating various treatments for a variety of traits in order to choose parents with the greatest genetic diversity. The purpose of this research is to characterize the genetic variation among 48 groundnut accessions with 6 checks. Methods: Experiment was conducted to study groundnut genotypes for 15 varied traits such as phenological, yield attributing and biochemical ones. Data analysis for principal component analysis (PCA) is done using R software. Result: Principal component analysis (PCA) was carried out to investigate the principal components of variance usingtraits of study. Total variance among characters are classified into 15 principal components. Out of which first five components have eigen value greater than 1 contributing to 65.9% total variance. PC 1 alone accounted for highest variance of 16.3%, followed by PC 2 with 12.6%. PC1 explained a large amount of variation in important traits as number of mature kernels per plant, total number of kernels per plant, pod yield per plant and kernel yield per plant. PC 2 have positive influence on days to 50% flowering, days to maturity, number of branches per plant, biological yield per plant, number of mature kernels per plant, total number of kernels per plant, sound mature kernel percentage, oil content and harvest index.

Мицелна съвместимост на изолати от Phomopsis helianthi (Munt.- Cvet. еt al.)

In the present study, the genetic diversity of 30 isolates of the pathogen Phomopsis helianthi was studied using the mycelial compatibility groups (MCGs) method. Mycelial compatibility tests were carried out on two media - PDA + 80 µl/L and PSA +80 µl/L, with added colorant (Christmas red - Sly Commerce OOD) and without added colorant. The use of PDA medium was found to be inadvisable due to the indistinct dividing line (groove) in isolates having an incompatible phenotypic response. Based on the tests done, 416 combinations were carried out and the four types of reaction were observed- NC-N – incompatible with necrosis, NC-Gincompatible, mycelium do not approach with a pronounced distance between them, NC-DL- both lines (black) are spaced, C-compatible. Their percentage ratio is presented. Isolates are grouped into 20 MCGs, with two of the groups containing only one isolate due to their incompatibility. The remaining isolates were found to occur in more than one MCG. The isolates originating from the region of Ruse were marked with the greatest genetic diversity, and the isolates from the area of Karnobat with the least.

Molecular Diversity Analysis of in vitro and Irradiated Tomato (Lycopersicon esculentum Mill) Grew Under Salt Stress Expressed by SCoT and ISSR Markers

Tomato buds of cv. Idkawy were cultured in vitro on solid MS medium with 0.2 mg-l BAP. The plantlets that were produced were exposed to different doses of gamma radiation, ranging from 100 to 200 Gy. Afterward, single pieces of nodes were cut and moved to a fresh MS medium with 0.2 mg-l of BAP. The gamma radiation caused a mortality rate of 18.75% to 52.5% among the explants. The surviving plantlets were then cut into single node pieces and transferred to an MS medium containing 0.2 mg-l of BAP, with added NaCl concentrations of either 50 or 100 mM. There was increased mortality of the vegetative buds on the explants with increased salt concentrations. It was shown that the all gamma radiation doses caused reduced the percentage of survival at saline levels. The genetic diversity was assessment by using ten primers for each SCoT and ISSR markers to six irradiated treatments grew under salt stress (100 Gy x 50 mM, 150 Gy x 50 mM, 200 Gy x 50 mM, 100 Gy x 100 mM, 150 Gy x 100 mM, 200 Gy x 100 mM). It was showed that the polymorphism percentage mean of SCoT marker (29.56%) is higher than the ISSR marker (26.78%). The average of PIC values for both markers SCoT and ISSR were 0.197 and 0.288 (PIC ˂0.5), as well as, MI values were 0.077 and 0.081, respectively. In contrast, when considering the number of alleles (Ne), Nei's genetic diversity (H), and Shannon's information index (I) parameters, it was observed that the greatest genetic variation was caused by the combined treatment of 200 Gy x 50 mM NaCl using the SCoT marker. On the other hand, with the ISSR marker, the highest induced genetic variation was seen with the combined treatment of 150 Gy x 50 mM NaCl. The obtained results demonstrate that SCoT marker was more accurate and efficient than ISSR marker for distinguishing and genetic variation analysis of irradiated tomato plantlets grew under salt stress. The relationships within treatments were estimated through cluster analysis (UPGMA) based on SCoT and ISSR analysis.

Dataspace Integration for Agrobiodiversity Digital Twins with RO-Crate

A severe impact of human-induced climate change is the global decrease in crop yields, threatening the United Nations sustainable development goal (SDG) to end hunger, achieve food security, improve nutrition, and promote sustainable agriculture (SDG 2: “Zero Hunger Goal”). Decision-making on appropriate mitigation strategies requires data integration from heterogeneous data-rich contexts including Earth observation (EO), biodiversity monitoring, gene banks as well as socio-economic data. Accordingly, large-scale initiatives for thematic data spaces, such as the European projects Destination Earth (DestinE) and the Green Deal Data Space, have been launched. Underutilized crops and crop wild relatives (CWR) can contribute to mitigating the impacts of climate change since their greater genetic diversity allows adaptation of agro-food sources to extreme weather events such as flooding and drought or emerging crop pests. Within the framework of Biodiversity Digital Twin (BioDT), a prototype digital twin for crop genetic resources modeling is under development. This prototype combines the scanning of genetic resources of CWRs and traditional cultivars for promising pest resistance and abiotic tolerance traits with advanced species distribution modeling and actual climate scenarios from EO. The aim is to generate habitat suitability maps and identify potential areas where relevant populations are potentially growing (Chala et al. 2024). The talk gives an overview of data models used to facilitate the required interoperability of both Earth models and environmental data within and across different data spaces such as the DestinE Data Lake (Duatis Juarez et al. 2023). Based on our findings from the use case of agrobiodiversity digital twins, we will discuss approaches for processing machine-actionable digital objects (Fig. 1) containing workflow information (i.e., in the Common Workflow Language format, Crusoe et al. 2022), and for sharing resulting research data in a FAIR (Findable, Accessible, Interoperable, and Reusable) manner by leveraging on so-called webby FAIR Digital Objects involving Research Object Crate (RO-Crate, Soiland-Reyes et al. 2022), FAIR Signposting (Soiland-Reyes et al. 2024) and schema.org and its Bioschemas extension respectively (Castro et al. 2020),

The Genetic Diversity of the Macrophyte Ceratophyllum demersum in Backwaters Reflects Differences in the Hydrological Connectivity and Water Flow Rate of Habitats.

Macrophytes often live in fluvial backwaters that have a variety of hydrological connections to a main river. Since the ability of these plants to adapt to changing environments may depend on the genetic diversity of the populations, it is important to know whether it can be influenced by habitat characteristics. We examined the microsatellite polymorphism of the submerged macrophyte Ceratophyllum demersum from various backwaters and showed that the genetic diversity of this plant clearly reflects habitat hydrological differences. The greatest genetic variability was found in a canal system where constant water flow maintained a direct connection between the habitats and the river. In contrast, an isolated backwater on the protected side of the river had the lowest plant genetic diversity. Oxbows permanently connected to the branch system with static or flowing water, and former river branches temporarily connected to the main bed contained populations with moderately high or low genetic variability. The results demonstrate that habitat fragmentation can be a result not only of the loss of direct water contact, but also of the lack of flowing water. Adverse hydrological changes can reduce the genetic diversity of populations and thus the ability of this macrophyte to adapt to changing environments.

Morphological Characterization and Diversity Analysis of Maize Inbred Lines (Zea mays L.)

To characterize Maize inbred lines in respect to morphological and physiological traits for its diversity and final utilization in the breeding programs, a study was conducted with twenty-five inbred lines at Tirhut college of Agriculture, Dholi Muzaffarpur Bihar. Genetic diversity among inbred lines may be used for promising hybrid combinations development in maize breeding programme. In the present investigation, these twenty-five inbred lines were sown in randomized block design with standard agronomical practices during Kharif, 2022. Analysis of variance revealed highly significant differences among the genotypes for all the parameters viz., Days to 50 percent Tasseling and Silking, 75% Brown husk, Plant Height (cn), Ear height (cm), Ear length (cm), Ear girth (cm), No. of Kernels per row, No. of kernel rows per ear, Iron and Zinc content (ppm), 100 grain weight (g), Harvest index and Grain yield (kg/ha.) showed presence of considerable variability among all the genotypes. Narrow deviation from genotypic and phenotypic variance evidenced that very less environmental influence on expression of almost all studied characters. According to the D2 analysis, the 25 maize inbred lines were divided into eight clusters, with cluster I having the largest number of inbred lines, while clusters II, V, VI, VII, and VIII have only one inbred line. Cluster VI (21-213-CML-401) and cluster VIII (HKI-1105) was the most distant cluster among inbred lines within the clusters, indicating the greatest genetic diversity.

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

BackgroundYaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{HOM}$$\\end{document}, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{L\\&H}$$\\end{document}, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{VR1}$$\\end{document}, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{VR2}$$\\end{document}, and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{YAN}$$\\end{document}), as well as two segment-based estimators of runs of homozygosity (ROH, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{ROH}$$\\end{document}) and homozygous-by-descent (HBD, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{HBD}$$\\end{document}). Functional implications were analyzed for the positional candidate genes located within the related genomic regions.ResultsA total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{HOM}$$\\end{document}), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{ROH}$$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:{F}_{HBD}$$\\end{document}, however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals.ConclusionsWe successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.

Genetic resources of the genus Prunus L. and their role in stone fruit breeding

Stone fruits such as apricot, cherry plum, cherry, peach, plum, and sweet cherry are highly popular in the Russian Federation. They are cultivated in the industrial gardens of large agricultural producers, as well as the plantings on farms and household plots. The fruits of these species can be consumed fresh for a considerable period of time. The application of some processing methods (cooling, freezing, and storage in a special atmosphere) significantly extends this period. Stone fruits are also suitable for producing a wide variety of processed products. The biochemical composition of fruits determines their high energy value and dietary properties. The representatives of the genus Prunus L. exhibit great genetic diversity. Due to their high polymorphy, they cover a large area. In regions with favorable weather and climatic growth conditions, stone fruits constitute the main industrial varieties. High requirements for industrial varieties determine the relevance of breeding improvement of available varieties. Representatives of the genus Prunus are characterized by a long juvenile period, different ploidy of species, high incompatibility, as well as heterozygosity for a large number of traits with a comparatively small number of identified genes. This fact significantly complicates genetic studies. The assortment of stone fruit crops in central Russia was renewed in several main directions. Most varieties were created through intervarietal crosses within a species. The current breeding work is aimed at creating new stone fruit species, as well as at improving the existing assortment. Along with the crossing of geographically distant varieties within a species, distant hybridization is one of the promising directions. In this way, new cultivated species were created, e.g., Russian plum (P. rossica Erem.), which is widely used in plantings. Such varieties are characterized by an attractive appearance, large size, pleasant aroma, and great flavor of fruits, as well as resistance to frost and rotting.

Metabolic and Transcriptional Analysis Reveals Flavonoid Involvement in the Drought Stress Response of Mulberry Leaves.

Abiotic stress, especially drought stress, poses a significant threat to terrestrial plant growth, development, and productivity. Although mulberry has great genetic diversity and extensive stress-tolerant traits in agroforestry systems, only a few reports offer preliminary insight into the biochemical responses of mulberry leaves under drought conditions. In this study, we performed a comparative metabolomic and transcriptomic analysis on the "drooping mulberry" (Morus alba var. pendula Dippel) under PEG-6000-simulated drought stress. Our research revealed that drought stress significantly enhanced flavonoid accumulation and upregulated the expression of phenylpropanoid biosynthetic genes. Furthermore, the activities of superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) content were elevated. In vitro enzyme assays and fermentation tests indicated the involvement of flavonol synthase/flavanone 3-hydroxylase (XM_010098126.2) and anthocyanidin 3-O-glucosyltransferase 5 (XM_010101521.2) in the biosynthesis of flavonol aglycones and glycosides, respectively. The recombinant MaF3GT5 protein was found to recognize kaempferol, quercetin, and UDP-glucose as substrates but not 3-/7-O-glucosylated flavonols and UDP-rhamnose. MaF3GT5 is capable of forming 3-O- and 7-O-monoglucoside, but not di-O-glucosides, from kaempferol. This implies its role as a flavonol 3, 7-O-glucosyltransferase. The findings from this study provided insights into the biosynthesis of flavonoids and could have substantial implications for the future diversified utilization of mulberry.

Explorando la genética de tres poblaciones de la raza Cerdo Pelón en México

The objective of this research was to carry out a molecular genetic characterization of three Hairless Pig (HP) breed populations located in México in the states of Nayarit, Oaxaca and Yucatán to identify variations, selection effects and population genetic relationships. From blood samples, a total of 163 animals from three populations of HP were successfully genotyped. Genotyped SNP data was employed to compute genetic diversity, population structure and landscape genetic analysis. The parameters of minor allele frequency (MAF), observed heterozygosity (Ho) and Wright’s fixation index (FIS) pointed out that the population of Nayarit is the one with the greatest genetic diversity (MAF: 0.362, Ho: 0.336, FIS: 0.061). Principal Component Analysis (PCA) and a Neighbor-joining phylogenetic tree analysis showed diversification among the three HP populations and pointed out a closer genetic relationship between the HP populations and the Iberian pig breed. The Admixture analysis showed as well common ancestry shared from commercial and Iberian breeds in the HP populations in different gradients. For the analysis of the relationships between geographic and genetic distances, Mantel test was computed and the results described a distribution pattern of the geographical locations along the genetic distances similar to the clustering pattern of the PCA and Neighbor-joining phylogenetic tree analysis. The results obtained manage to present the HP poor conservation state and the need to stablish a genetic conservation program meaning an effort to prevent the loss of a significant cultural, natural and genetic resource. Keywords: genetic diversity, landscape genetics, native breeds, genetic resources.

Improved Protoplast Production Protocol for Fungal Transformations Mediated by CRISPR/Cas9 in Botrytis cinerea Non-Sporulating Isolates.

Botrytis cinerea is a necrotrophic fungus that causes considerable economic losses in commercial crops. Fungi of the genus Botrytis exhibit great morphological and genetic variability, ranging from non-sporogenic and non-infective isolates to highly virulent sporogenic ones. There is growing interest in the different isolates in terms of their methodological applications aimed at gaining a deeper understanding of the biology of these fungal species for more efficient control of the infections they cause. This article describes an improvement in the protoplast production protocol from non-sporogenic isolates, resulting in viable protoplasts with regenerating capacity. The method improvements consist of a two-day incubation period with mycelium plugs and orbital shaking. Special mention is made of our preference for the VinoTaste Pro enzyme in the KC buffer as a replacement for Glucanex, as it enhances the efficacy of protoplast isolation in B459 and B371 isolates. The methodology described here has proven to be very useful for biotechnological applications such as genetic transformations mediated by the CRISPR/Cas9 tool.

Diversity and Genetic Structure of a Natural Population of Mauritia flexuosa L. f. in APA-Pandeiros, Using Microsatellite Markers

Genetic diversity is essential to ensure that species maintain high adaptive evolutionary potential to resist environmental stochasticity. Thus, this research aimed to estimate the genetic diversity and structure of a natural population of Mauritia flexuosa and its stages, using five microsatellite primers. DNA was extracted from leaves collected from individuals of the three classes (G1-adult, G2-juvenile and G3-regenerant). Genetic diversity estimates indicated an average of 7.8 alleles/locus and lower observed heterozygosity (Ho) than expected heterozygosity (He) in the population (0.272-0.395 and 0.275-0.401, respectively). The Shannon Index (I) indicated moderate genotypic diversity and richness in the analyzed population, and exclusive alleles were found at the different stages. Also found were a lower population index (FST = 0.019) and a higher individual fixation index (FIS = 0.169). Classes G1 and G2 exhibited greater genetic similarity to each other than to G3, which had more distant genetic characteristics. These results revealed lower genetic diversity among regenerating (G3) individuals and greater genetic diversity among adults (G1). Immediate strategies for in situ and ex situ genetic conservation of M. flexuosa are essential to preserve its genetic variability and assist future programs for the improvement.

Genetic characteristics of producing bulls of the Kholmogorsky breed, depending on their linear affiliation and the level of Holstein

Relevance. Genetic analysis using STR markers makes it possible to effectively use various techniques to control the breeding process in a population.Methods. The material for DNA research was the deep-frozen sperm of 103 bulls-producers of the Kholmogorsky breed, with different blood levels of Holstein cattle belonging to five main genealogical lines. Molecular genetic studies were conducted in the laboratory of DNA technologies at VNIIPlem.Results. The animals of the VBA (I = 1,557) and Nl (I = 1,556) lines had the maximum genetic diversity, and the Chl lines had the lowest (the indicator is lower by 0.229 (р ≤ 0.05) relative to VBA). A pronounced discrepancy between the observed and expected heterozygosity towards heterozygote deficiency was found among animals of the VBA line (F = 0.173), which is higher by 0.220–0262 relative to RS and Chl (р ≤ 0.01–0.001). The bulls of the Chl and RS lines have an equilibrium shift towards an excess of heterozygosity (F = -0.111 and F = -0.054 respectively). The most related lines are Nl and VBA (DN = 0.097), as well as Nl and Lm (DN = 0.101), and the least VBA and Chl (DN = 0.247), as well as VBA and RS (DN = 0.218). When differentiating the samples by the level of Holstein, it was found that the greatest genetic diversity was characterized by bulls with a blood density of 25–49% (1,633), and the minimum was animals with a degree of Holstein above 74% (which is lower by 0.299–0.334 relative to other samples, р ≤ 0.05–0.01). With an increase in the degree of Holstein, an increase in the level of genetic inbred was observed (in crossbreeds with a bloodline above 74%, the indicator was 0.142–0.229 more (р ≤ 0.05–0.001) compared with other samples).

Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes.

Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.

Familial combined hyperlipidemia: current status of the problem (literature review)

Among the various dyslipidemia types, familial combined hyperlipidemia (FCH) is the most common genetic disorder, which is characterized by at least two dif­ferent forms of lipid disorders: hypercholesterolemia and hypertriglyceridemia. In FCH, the risk of atherosclerotic cardiovascular diseases (CVDs), including at a young age, increases significantly. The aim was to analyze literature data on modern criteria for diagnosis, pathogenesis and data from molecular genetic studies of FCH. Future studies aimed at understanding the underlying genetic and metabolic mechanisms of FCH and developing effective treatment strategies should include larger cohort studies with greater genetic diversity, as well as inves­tigation of epigenetic and lifestyle factors.

Great genetic diversity of vector-borne bacteria and protozoan in wild rodents from Guangxi, China.

Rodents are recognized as the hosts of many vector-borne bacteria and protozoan parasites and play an important role in their transmission and maintenance. Intensive studies have focused on their infections in vectors, especially in ticks, however, vector-borne bacterial and protozoan infections in rodents are poorly understood although human cases presenting with fever may due to their infection have been found. From May to October 2019, 192 wild rodents were trapped in wild environment of Guangxi Province, and the spleen samples were collected to reveal the presence of vector-borne bacterial and protozoan infections in them. The microorganisms in rodents were identified by detecting their DNA using (semi-)nested PCR. All the PCR products of the expected size were subjected to sequencing, and then analyzed by BLASTn. Furthermore, all the recovered sequences were subjected to nucleotide identity and phylogenetic analyses. As a result, 192 rodents representing seven species were captured, and Bandicota indica were the dominant species, followed by Rattus andamanensis. Based on the (semi-)nested PCR, our results suggested that Anaplasma bovis, Anaplasma capra, Anaplasma ovis, Anaplasma phagocytophilum, "Candidatus Neoehrlichia mikurensis", "Candidatus E. hainanensis", "Candidatus E. zunyiensis", three uncultured Ehrlichia spp., Bartonella coopersplainsensis, Bartonella tribocorum, Bartonella rattimassiliensis, Bartonella silvatica, two uncultured Bartonella spp., Babesia microti and diverse Hepatozoon were identified in six rodent species. More importantly, six species (including two Anaplasma, two Bartonella, "Ca. N. mikurensis" and Bab. microti) are zoonotic pathogens except Anaplasma bovis and Anaplasma ovis with zoonotic potential. Furthermore, dual infection was observed between different microorganisms, and the most common type of co-infection is between "Ca. N. mikurensis" and other microorganisms. Additionally, potential novel Bartonella species and Hepatozoon species demonstrated the presence of more diverse rodent-associated Bartonella and Hepatozoon. The results in this work indicated great genetic diversity of vector-borne infections in wild rodents, and highlighted the potential risk of human pathogens transmitted from rodents to humans through vectors.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Lack of Genetic Variation in Low Heterozygosity and Clonal Animals Creates Lack of Physiological Variation

Data variability frequently complicates reproducibility and interpretation of experimental results. Such variability arises from numerous sources such as differences in procedures or not accounting for key biological factors (e.g. sex, biological rhythms, prandial state). Making the situation more problematic, variation in physiological performance is often viewed as highly labile, easily and rapidly influenced by environmental stressors, development, etc., making it diffcult to pin down a source for variation. Undeniably, however, unknown (or ignored) genetic variation among and within strains/lines can also be a significant source of data variability in published physiological measurements, though surprisingly this has not been extensively investigated as a specific source of physiological variation. We hypothesized that variation in physiological performance is correlated with the intrinsic degree of genetic variability of the subject animal. To test this hypothesis, we employed two animal models: 1) Inbred lines ( e.g., NHGRI-1) derived from wild type strains of the zebrafish ( Danio rerio), with an estimated 15% of the genetic heterozygosity of wild type AB zebrafish, and 2) the parthenogenetically reproducing marbled crayfish ( Procambarus virginalis), all specimens of which are genetically identical clones. For these two animal models, we measured both physiological variables (e.g. heart rate, stroke volume, cardiac output, oxygen consumption) and morphological variables (e.g. yolk-chorion ratio, body mass, embryo mass, total length, condition factor, specific growth rate) during development. We subjected the two animal models to environmental stress in the form of both temperature and hypoxia to stimulate physiological responses that could be compared and contrasted among populations. From these data we then calculated the resultant coeffcients of variation for measured variables for wild type and low/zero heterozygosity populations and/or species. In zebrafish, both the wildtype AB and NHRGI-1 lines showed similar developmental trajectories characterized by similar mean values for physiological and morphological variables. Additionally, similar mean values for physiological and morphological variables were recorded in the face of temperature and hypoxia challenge. Yet, importantly, the coeffcient of variation for each measured variable was significantly lower in NHGRI-1 than AB larvae for >90% of the assessed endpoints. In the clonal crayfish, genetically identical early stage marbled crayfish reared in different temperatures or oxygen levels show major acclimation responses, but generally showed less morphological and physiological variation about the mean than sexually-reproducing species crayfish with inherently much greater genetic variation, as evident from comparisons of calculated coeffcients of variation. A key question regarding the clonal crayfish is how can there be any morphological or physiological variation between individuals? We suggest that variability that persists may arise from microenvironmental differences during rearing (e.g. egg position during incubation on the mother’s pleon) and/or stochastic differences in gene expression (e.g. due to random epimutations) in this clonal species. In conclusion, genetic diversity clearly contributes to physiological variability. For future experiments, low heterozygosity lines and/or clonal species may be useful for decreasing inter-individual variation, thus aiding interpretation of results and enhancing reproducibility. In any event, scientific documentation of physiological studies should include as much information on (genetic) background of the experimental animals as possible. NSF IOS-2103499. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.