American Genotype Research Articles

Cold Tolerance Assay Reveals Evidence of Climate Adaptation Among American Elm (Ulmus americana L.) Genotypes

T he American elm (Ulmus americana L.), once a dominant species in North American floodplain forests, has suffered significant population declines due to Dutch elm disease (DED). Despite this, some elms persist, potentially exhibiting disease resistance and climate-adaptive traits that could facilitate restoration. Understanding these traits is crucial for selecting genotypes suited to current and future climatic conditions, particularly in colder regions. This study evaluated the mid-winter cold tolerance of American elm genotypes across a climatic gradient to ascertain evidence of local climate adaptation. We used relative electrolyte leakage (REL) to assess mid-winter cold tolerance of current-year shoots on eleven survivor genotypes from New England and one susceptible, control genotype from Ohio. The lethal temperature, at which 50% of cellular leakage occurs (LT50), was determined and compared with 30-year climate data to identify potential climate adaptation. Genotypes from colder regions exhibited greater cold hardiness, indicating local adaptation to climate. Observed mid-winter LT50 values (−42.8 °C to −37.7 °C) were in excess of the 30-year minimum air temperature, even at the coldest source location. This calls into question whether mid-winter cold tolerance is the critical period for injury to American elm and more attention should be given to environmental conditions that cause de-acclimation to cold. By understanding the adaptive capacity of American elm, managers can better select mother trees for regional seed orchards, ensuring the long-term success of restoration initiatives.

Exploring genetic diversity of hepatitis D virus full-length genome in Brazil: Discovery of a novel HDV-8 subgenotype beyond African borders

Hepatitis D virus (HDV) is currently classified into 8 genotypes (1 to 8) and several subgenotypes, with distinct distribution worldwide. However, due to the scarcity of complete genome sequences in databases, this classification is constantly being updated and tends to be regularly revisited in upcoming years as more sequence data becomes available. Aiming to increase knowledge about the genetic variability of HDV, this study presents the full-length genomes of 11 HDV samples collected in Brazil in endemic and non-endemic regions, including the first complete genomes of the genotypes 5 and 8 obtained outside Africa. We also determined the co-infecting HBV genotypes to investigate their prevalence among the HDV-infected individuals throughout the country. Whole genome sequencing confirmed our previous findings based on a partial fragment of the HDV genome, in which HDV subgenoypes 3c (9/11; 81.8 %), 5b (1/11; 9.1 %) and one HDV-8 sequence (1/11; 9.1 %) were detected. As previously observed, HDV-8 formed a distinct branch apart from subgenotypes 8a and 8b, a monophyletic clade representing a novel HDV-8 subgenotype, designated as 8c. Among HDV-3 samples, the main co-infecting HBV genotype found was HBV-F (4/8; 50 %), reflecting the higher incidence of this native South American genotype in the endemic Amazon Basin. Both samples infected with HDV-5 and HDV-8 were coinfected with HBV genotype E, also a genotype with African origin. Our findings based on complete genome sequence of HDV corroborated our results based on a partial region of the HDV genome of a novel HDV-8 subgenotype and reinforced the need to use full-length genomes to properly subdivide genotypes with very low intragroup genetic variability, such as HDV-3. The provision of these complete genomes is expected to contribute to the enrichment of sequence databases for future molecular and evolutionary investigations of HDV.

Genome-wide association analysis of anthracnose resistance in the Yellow Bean Collection of Common Bean

Anthracnose caused by Colletotrichum lindemuthianum is a major disease of common bean (Phaseolus vulgaris) worldwide. Yellow beans are a major market class of common bean especially in eastern and southern Africa. The Yellow Bean Collection (YBC), which is comprised of 255 genotypes, and has not been used previously in genetic studies on anthracnose, is an excellent genetic resource for understanding the extent of anthracnose resistance and its genetic architecture in the yellow bean market class. The objectives of this study were i) evaluate the YBC for resistance to races 5, 19, 39, 51, 81, 183, 1050 and 1105 of C. lindemuthianum. and ii) conduct genome-wide association analysis to identify genomic regions and candidate genes associated with resistance to C. lindemuthianum. The YBC was genotyped with 72,866 SNPs, and genome-wide association analysis was conducted using Mixed Linear Model in TASSEL. Andean and Middle American genotypes with superior levels of resistance to the eight races were identified. YBC278 was the only one among 255 genotypes that was highly resistant to all eight races. Resistance to anthracnose in the YBC was controlled by major-effect loci on chromosomes Pv01, Pv03, Pv04, Pv05 and Pv07. The genomic region on Pv01, which overlapped with the Andean locus Co-1 provided resistance to races 81, 1050 and 1105. Significant SNPs for resistance to race 39 were identified on Pv02. The genomic region on Pv04, which overlapped with known major-effect loci Co-3, Co-15, Co-16, Co-y and Co-z, provided resistance to races 5, 19, 51 and 183. Novel genomic regions for resistance to race 39 were identified on Pv05 and Pv07. Plant resistance genes (R genes) with NB-ARC and LRR domains, which occurred in clusters, were identified as positional candidate genes for genomic regions on Pv02 and Pv04.

Circulation of Dengue Virus Serotype 1 Genotype V and Dengue Virus Serotype 2 Genotype III in Tocantins State, Northern Brazil, 2021-2022.

In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of cases of arboviral disease, particularly Dengue virus (DENV). This study aimed to deepen the knowledge on DENV circulation within that state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. There were a total of 8807 and 20,692 cases in 2021 and 2022, respectively, as reported by the state's Secretary of Health. Nucleotide sequencing confirmed the circulation of DENV serotype 1, genotype V and DENV serotype 2, genotype III in the State. Younger age groups (4 to 43 years old) were mostly affected; however, no significant differences were detected regarding the gender distribution of cases in humans. Phylogenetic analysis revealed that the circulating viruses belong to DENV-1 genotype V American and DENV-2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 genotype V genomes sequenced here are closely related to genomes previously sequenced in the state of São Paulo. Regarding the DENV-2 genotype III genomes, these clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. The findings reported here suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the importance of major population centers in Brazil on virus dispersion, such as those observed in other Latin American and North American countries. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here highlight the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of DENV and the relevance of surveillance efforts in supporting public health policies.

Response of Seed Yield and Its components of Several Genotypes of Vicia faba L. to Spraying of Zinc Nanoparticle Fertilizer

A field experiment was conducted at a College of Agriculture research station at - the University of Anbar during the winter season of 2021-2022 to study the response of seed yield and its components of several genotypes of Vicia faba L. to spraying of zinc nanoparticle fertilizer. The experiment was carried out by Split Plots arrangement according to the Randomized Complete Block Design (R.C.B.D.) at three replications. The main plots included four concentrations of zinc nanoparticle fertilizer (0, 60, 12 and 180mg L-1 ), whereas the sub-plots included four faba bean genotypes (Local, American, Dutch and Italian). The results showed that the American genotype was significantly superior in the number of pods per plant (21.40 pod plant-1 ), fertility percentage per pod (88.80%), seed yield (6.57 Mg ha-1 ) and biological yield (11.01 Mg ha-1 ). In contrast, the Dutch genotype achieved the highest mean of the number of seeds per pod (5.64 seed pod-1 ) and weight of 100 seeds (107.68 g). Also, the spraying of zinc nanoparticles at 180 mg L-1were significantly superior in the number of pods per plant (22.35 pod plant1 ), weight of 100 seeds (111.40 g), fertility percentage per pod (90.30%), seed yield (6.23 Mg ha-1 ) and biological yield (10.78 Mg ha-1 ), while the spraying of zinc nanoparticle at a 120 mg L-1 gave the highest mean of the number of seeds per pod (5.66 seed pod-1 ). The interaction between two factors had a significant effect on the most studied traits; the American genotype with the spraying of zinc nanoparticle at 180 mg L-1 gave the highest values of the number of pods per plant (25.23 pod plant-1 ), fertility percentage in a pod (91.14%) and seed yield (7.88 ton ha-1 ). Keywords: Viciafaba L., nano-zinc, seed yield, yield components.

Costa Rican Genotype of Ehrlichia canis: A Current Concern.

Canine monocytic ehrlichiosis (CME) is endemic to Brazil, and studies have verified that dogs have been exposed to different genotypes of Ehrlichia canis. This genetic divergence can influence the clinical response of the animals. We aimed to describe clinical and hematological changes in 125 dogs that reacted to BrTRP36, USTRP36, and CRTRP36 genotypes through enzyme immunoassays and to highlight the current concern regarding infection by the Costa Rican genotype. The results showed that 52.0% reacted to the Brazilian genotype, 22.4% reacted to the Costa Rican genotype, and 16.0% reacted to the American genotype, and some co-reactions were observed. Dogs reactive to BrTRP36 were 1.24% more likely to present with medullary regeneration in cases of anemia and 3% less likely to manifest hyperproteinemia, while dogs reactive to CRTRP36 were 0.7% less likely to present with medullary regeneration. Febrile illness and neurological alterations were also statistically associated, with an 85.7% and 231.2% increased likelihood, respectively, to occur in dogs that reacted to USTRP36. The dogs with the American genotype developed clinical manifestations related to systemic inflammation, while those with the Brazilian genotype of E. canis were more dispersed in the region studied, showing greater adaptation to the hosts. We highlight the significant serocurrence of the Costa Rican genotype, which has already been described to have zoonotic potential and which showed less adaptation.

Identification of donor parents containing favourable alleles for improving target American cotton hybrid (NA 1325 × L 604)

The present study was conducted during kharif 2013, kharif 2014 and kharif 2015 at Regional Agricultural Research Station, Lam, Guntur, Andhra Pradesh, India. The aim of the present investigation was to evaluate four American cotton genotypes and to determine which have the greatest relative values of favourable alleles for the improvement of number of bolls/plant, boll weight (g), 2.5% span length (mm), bundle strength (g/tex), seed cotton yield/plant (g) and lint yield/plant (g) in the elite single cross cotton hybrid (NA 1325 × L 604). Based on the estimates of μG’ values the genotype Surabhi was noted with positive high μG’ value and may be used as source of favourable alleles for improving elite hybrid with respect to quality traits like bundle strength (μG’=1.830*) and 2.5% span length (μG’=1.325*). This improvement may be possible by transferring favourable alleles from Surabhi to NA 1325 through back crossing as it had high genetic affinity with NA 1325. For number of bolls/plant RAH 1004 (μG’=3.230*) and HYPS 152 (μG’=0.302*) for boll weight and both the donors for seed cotton yield/plant (μG’ RAH 1004=13.915*and μG’ HYPS 152=23.972*) may be used as donors as they recorded significant and positive μG’ estimates.

Development of a Multiplex Crystal Digital RT-PCR for Differential Detection of Classical, Highly Pathogenic, and NADC30-like Porcine Reproductive and Respiratory Syndrome Virus

Porcine reproductive and respiratory syndrome virus (PRRSV) type 1 (European genotype) and PRRSV type 2 (North American genotype) are prevalent all over the world. Nowadays, the North American genotype PRRSV (NA-PRRSV) has been widely circulating in China and has caused huge economic losses to the pig industry. In recent years, classical PRRSV (C-PRRSV), highly pathogenic PRRSV (HP-PRRSV), and NADC30-like PRRSV (NL-PRRSV) have been the most common circulating strains in China. In order to accurately differentiate the circulating strains of NA-PRRSV, three pairs of specific primers and corresponding probes were designed for the Nsp2 region of C-PRRSV, HP-PRRSV, and NL-PRRSV. After optimizing the annealing temperature, primer concentration, and probe concentration, a multiplex real-time quantitative RT-PCR (qRT-PCR) and a multiplex Crystal digital RT-PCR (cdRT-PCR) for the differential detection of C-PRRSV, HP-PRRSV, and NL-PRRSV were developed. The results showed that the two assays illustrated high sensitivity, with a limit of detection (LOD) of 3.20 × 100 copies/μL for the multiplex qRT-PCR and 3.20 × 10-1 copies/μL for the multiplex cdRT-PCR. Both assays specifically detected the targeted viruses, without cross-reaction with other swine viruses, and indicated excellent repeatability, with coefficients of variation (CVs) of less than 1.26% for the multiplex qRT-PCR and 2.68% for the multiplex cdRT-PCR. Then, a total of 320 clinical samples were used to evaluate the application of these assays, and the positive rates of C-PRRSV, HP-PRRSV, and NL-PRRSV by the multiplex qRT-PCR were 1.88%, 21.56%, and 9.69%, respectively, while the positive rates by the multiplex cdRT-PCR were 2.19%, 25.31%, and 11.56%, respectively. The high sensitivity, strong specificity, excellent repeatability, and reliability of these assays indicate that they could provide useful tools for the simultaneous and differential detection of the circulating strains of C-PRRSV, HP-PRRSV, and NL-PRRSV in the field.

Genetic structure analysis and genetic fingerprinting of pomegranate cultivars (Punica granatum L.) by using SCoT molecular markers

AbstractGenetic diversity and genetic relatedness among 50 genotypes from eight countries, including Iran, Afghanistan, Turkmenistan, Syria, Lebanon, India, Yemen, and the United States located in two continents of Asia and the America, were assessed using SCoT markers. A total of 213 bands were produced; 100% of them were polymorphic; the average polymorphism information content (PIC) was 0.39. The mean Nei's gene diversity and Shannon's index were 0.33 and 0.49, respectively. Analysis of molecular variance suggested significant genetic differences within pomegranate populations. 99% of variance occurs within the populations, whereas 1% of the variation was recorded among the populations of pomegranate. Cluster analysis using SCoT markers able to group genotypes based on their geographical origins. Based on cluster analysis, the genotypes studied were divided into two main groups. The first group included most Asian genotypes, while American genotypes along with some Asian genotypes were in the second group. In the first group, Iranian genotypes were grouped with genotypes from Afghanistan and India. In the second group, the genotypes belonging to the America were in the same group as most of the genotypes of Turkmenistan. According to the present study, SCoT markers can be used to evaluate genetic diversity, identification and DNA fingerprinting pomegranate genotypes of different origins. This information can be used in breeding programs and the management of pomegranate collections.

Modified screening method of middle american dry bean genotypes reveals new genomic regions on Pv10 associated with anthracnose resistance.

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is one of the most devastating diseases in dry bean (Phaseolus vulgaris L.) with seed yield losses up to 100%. Most anthracnose resistance genes thus far identified behave in a dominant manner and were identified by seedling screening. The Middle American Diversity Panel (MDP; n=266) was screened with a modified greenhouse screening method to evaluate the response to anthracnose race 73. Thirty MDP genotypes exhibited resistance to the race of which 16 genotypes were not known to contain anthracnose resistance genes to race 73. GWAS with ~93,000 SNP markers identified four genomic regions, two each on Pv01 and Pv10, associated race 73 resistance. A likelihood-ratio-based R2 analysis indicated the peak four SNP markers are responsible for 26% of the observed phenotypic variation, where one SNP, S10_072250, explains 23% of the total variation. SNP S10_072250 is associated with a new region of anthracnose resistance and is in an intron of a ZPR1-like gene. Further greenhouse testing of the 16 resistant lines without previously known resistance to race 73 revealed various levels of resistance under various levels of disease pressure. Disease resistance was further characterized in the field using four representative genotypes. GTS-900 and Remington exhibited field resistance while Merlot and Maverick were susceptible. Field testing with two different fungicide regimes revealed the resistant genotypes had no significant disease differences. The results suggest resistance to anthracnose may differ at various growth stages and that breeders have been selecting for major genes at early seedling stages while ignoring the effect of alternative genes that may be active at later stages. The newly identified resistant lines may be related to Age Related Resistance (ARR) and could be exploited as parental sources of anthracnose resistance in addition to already known major genes. The physical localization of the multiple regions of resistance confirms the presence of two clusters of disease resistance genes on Pv01 and identifies two new regions of anthracnose resistance on Pv10 possibly associated with ARR. Future research should look at the mode of inheritance of this resistance and its effect when combined with other anthracnose resistance loci.

The use of amino acids as anti-browning agents in rice parboiling: Effects on quality attributes of three South American genotypes

The parboiling process improves the physical and nutritional quality of rice, but promotes browning, mainly due to the occurrence of the Maillard reaction (MR). Five different amino acids (glycine, methionine, glutamine, sodium glutamate, and aspartate) were studied as limiting agents of the MR in the parboiling process of two pure lines (Guri Inta CL and Irga 424 RI) and a hybrid (Titan CL) genotype. Samples were hydrated under two concentrations of those amino acids (1.5% and 3.0%) during the first step of parboiling. Methionine, glutamine, and aspartate were less effective in preventing the browning of parboiled rice. Glycine (26.63–28.48 GBZ) and sodium glutamate (26.88–28.12 GBZ) were able to provide lighter color to parboiled rice in comparison to control treatment (23.68 GBZ). Parboiled rice treated with amino acids had a lower degree of gelatinization when compared to the control treatment. The extent of gelatinization in parboiled rice produced by using amino acids as anti-browning agents may vary as a function of the applied amino acid molecule and its concentration as well as a result of the characteristics of the selected rice genotype. The percentage of broken grains only increased for the Irga 424 RI genotype, which exhibited shorter cooking time due to the greater ability of the grains to soften during cooking.

Phylogeographic patterns of the yellow fever virus around the metropolitan region of São Paulo, Brazil, 2016-2019.

From 2016 to 2019, the largest outbreak caused by the Yellow Fever virus (YFV) in the 21st century in the Americas occurred in southeastern Brazil. A sylvatic cycle of transmission was reported near densely populated areas, such as the large metropolitan area of the city of São Paulo. Here, we describe the origin, spread, and movement of the YFV throughout the state of São Paulo. Whole-genome sequences were obtained from tissues of two patients who died due to severe yellow fever, during 2018–2019. Molecular analysis indicated that all analyzed tissues were positive for YFV RNA, with the liver being the organ with the highest amount of viral RNA. Sequence analysis indicates that genomes belonged to the South American genotype I and were grouped in the epidemic clade II, which includes sequences from the states of Goiás, Minas Gerais, and São Paulo of previous years. The analysis of viral dispersion indicates that the outbreak originated in Goiás at the end of 2014 and reached the state of São Paulo through the state of Minas Gerais after 2016. When the virus reached near the urban area, it spread towards both the east and south regions of the state, not establishing an urban transmission cycle in the metropolitan region of São Paulo. The virus that moved towards the east met with YFV coming from the south of the state of Rio de Janeiro, and the YFV that was carried to the south reached the Brazilian states located in the south region of the country.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R=0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N= 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R= 0.87) and are closer to each other than expected under random mating (p<10-6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

Effect of Phosphate Fertilization on the Growth and Yield of Three Genotypes of Faba Bean( Vicia faba L.)

A field experiment was carried out in the winter season 2020-2021 in Al- Bualwan area of Fallujah District - Anbar Governorate to study the effect of phosphate fertilization on the growth and yield traits of the faba bean crop. The experiment was applied using a randomized complete block design (RCBD) according to the split-plot arrangement with three replications. The main plots included three levels of phosphate fertilization (0, 60, 120) kg P2O5 h-1, while the sub plots included three faba bean genotypes (American, Italian, and Dutch). According to the study levels, phosphate fertilizer was added in one batch before planting. The most important results were the following: The American genotype superiority in growth and yield traits, giving the highest average for each plant height( 95.63) cm, number of branches (10.11 ) branch plan-1 , leaf area per plant( 1053) cm2 plant-1, number of pods( 17.50 )pod plant-1, number of seeds per pod (6.11) seed pod-1, the weight of 100 seed (96.06) g and the total seed yield is( 4.168) tons ha-1. The effect of phosphate fertilizer was significantly in most of the studied traits. The level 120 kg P2O5 ha-1 gave the highest average for each of the plant height( 94.00) cm, number of branches( 9.83) branch plant-1, leaf area of the plant (2342) cm 2 plant-1, number of pods (17.83) pod plant-1, weight of 100 seed( 95.44) g and total seeds yield( 4.078) tons ha-1. There was a significant interaction between the American genotype and the level of 120 kg P2O5 ha-1 of phosphate fertilizer in plant height, number of branches per plant, leaf area, number of pods per plant and weight of 100 seeds.

Chemotaxonomic characterization of hop genotypes based on profiling of proanthocyanidins using liquid chromatography coupled with high-resolution accurate mass spectrometry

To determine the varietal specificity of the composition of proanthocyanidins (PACs) in hops, a fast and simple method of liquid chromatography coupled with high-resolution accurate mass spectrometry for qualitative profiling of PACs was developed. A total of 140 samples of 19 hop varieties were analysed. Three (epi)catechin-(epi)afzelechin dimers, six (epi)catechin-(epi)catechin dimers, four (epi)gallocatechin-(epi)gallocatechin dimers, seven (epi) catechin-(epi)gallocatechin dimers, and seven trimers consisting of (epi)catechin building blocks were detected in the hop samples. The cluster analysis of PAC varietal profiles showed their close link with the genetic origin of the hops. The main marker distinguishing the American and European genotypes is the representation of catechin and epicatechin in the PAC profile. The varieties in both of these genotype groups are further subdivided based on their low or high proportion of (epi)gallocatechin building blocks in the PAC profile. Knowledge of the composition of proanthocyanidins in hops can be important for the selection of hop varieties in brewing, pharmacy or food supplement production. The developed PAC profiling method can be easily adapted to other plant materials.

Deciphering the Genome-Wide Transcriptomic Changes during Interactions of Resistant and Susceptible Genotypes of American Elm with Ophiostoma novo-ulmi.

Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (Onu), is a destructive disease of American elm (Ulmus americana L.). The molecular mechanisms of resistance and susceptibility against DED in American elm are still largely uncharacterized. In the present study, we performed a de novo transcriptome (RNA-sequencing; RNA-Seq) assembly of U. americana and compared the gene expression in a resistant genotype, ’Valley Forge’, and a susceptible (S) elm genotype at 0 and 96 h post-inoculation of Onu. A total of 85,863 non-redundant unigenes were identified. Compared to the previously characterized U. minor transcriptome, U. americana has 35,290 similar and 55,499 unique genes. The transcriptomic variations between ‘Valley Forge’ and ‘S’ were found primarily in the photosynthesis and primary metabolism, which were highly upregulated in the susceptible genotype irrespective of the Onu inoculation. The resistance to DED was associated with the activation of RPM1-mediated effector-triggered immunity that was demonstrated by the upregulation of genes involved in the phenylpropanoids biosynthesis and PR genes. The most significantly enriched gene ontology (GO) terms in response to Onu were response to stimulus (GO:0006950), response to stress (GO:0050896), and secondary metabolic process (GO:0008152) in both genotypes. However, only in the resistant genotype, the defense response (GO:0006952) was among the topmost significantly enriched GO terms. Our findings revealed the molecular regulations of DED resistance and susceptibility and provide a platform for marker-assisted breeding of resistant American elm genotypes.

Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil.

In Brazil, the yellow fever virus (YFV) is maintained in a sylvatic cycle involving wild mosquitoes and non-human primates (NHPs). The virus is endemic to the Amazon region; however, waves of epidemic expansion reaching other Brazilian states sporadically occur, eventually causing spillovers to humans. To report a surveillance effort that led to the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021. A surveillance network was created, encompassing the technology of smartphone applications and coordinated actions of several research institutions and health services to monitor and investigate NHP epizootics. When alerts were spread through the network, samples from NHPs were collected and YFV infection confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and genome sequencing at an interval of only 10 days. Near-complete genomes were generated using the Nanopore MinION sequencer. Phylogenetic analysis indicated that viral genomes were related to the South American genotype I, clustering with a genome detected in the Amazon region (state of Pará) in 2017, named YFVPA/MG sub-lineage. Fast YFV confirmation potentialised vaccination campaigns. A new YFV introduction was detected in MG 6 years after the beginning of the major outbreak reported in the state (2015-2018). The YFV strain was not related to the sub-lineages previously reported in MG. No human cases have been reported, suggesting the importance of coordinated surveillance of NHPs using available technologies and supporting laboratories to ensure a quick response and implementation of contingency measures to avoid YFV spillover to humans.

Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions

Abstract Hops is a new culture in Brazil. Tissue culture can be an important technique for rapid hop propagation. This paper aims to characterize responses from different genotypes under different growth regulators through the interrelationship of response variables important to hop in vitro growth. Three genotypes were cultivated in six culture media with different combinations of growth regulators, BAP (6-benzylaminopurine), IAA (3-indolacetic acid) and GA3 (gibberellic acid). The means were compared by orthogonal contrasts and the interrelationship of the response variables was performed by path analysis. American genotypes showed favorable root development under the BAP + IAA combination, while the use of IAA improved shoot development. The origin of genotypes was important for defining the best protocol for in vitro cultivation. The path coefficient showed that the variable number of shoots has stronger direct effect on the number of nodal segments. Additionally, in tissue culture assays, the use of a covariable and proper error distribution significantly increased experimental accuracy.

Toxoplasma gondii Genotypes Circulating in Serbia-Insight into the Population Structure and Diversity of the Species in Southeastern Europe, a Region of Intercontinental Strain Exchange.

In Europe, Toxoplasma gondii lineage II is dominant, and ToxoDB#1 the most frequently occurring genotype. The abundance of lineage III genotypes varies geographically and lineage I are rare, yet present in several regions of the continent. Data on the T. gondii population structure in southeastern Europe (SEE) are scarce, yet necessary to appreciate the diversity of the species in Europe. To help fill this gap, we genotyped 67 strains from nine species of intermediate hosts in Serbia by MnPCR-RFLP, determined the population structure, and identified the genotypes using ToxoDB. A neighbor-joining tree was also constructed from the isolates genotyped on nine loci. While 42% of the total genotype population consisted of ToxoDB#1 and ToxoDB#2, variant genotypes of both lineages comprised 46% of the population in wildlife and 28% in domestic animals and humans. One genotype of Africa 4 lineage was detected in a human sample. Interestingly, the findings include one lineage III variant and one II/III recombinant isolate with intercontinental distribution, which appear to be moderately related to South American genotypes. Based on these findings, SEE is a region of underappreciated T. gondii genetic diversity and possible strain exchange between Europe and Africa.

Biological Characterization of Hepatitis B virus Genotypes: Their Role in Viral Replication and Antigen Expression.

Hepatitis B virus (HBV) inter-host evolution has resulted in genomic diversification reflected in the existence of nine genotypes (A-I) and numerous subgenotypes. There is growing evidence that genotypes influence HBV natural history, clinical outcomes, and treatment response. However, the biological characteristics underlying these differences have not yet been established. By transfecting HuH-7 cells with unit-length constructs of genotypes A2, B2, C1, D1, and F1b, we identified major differences in HBV replicative capacity and antigen expression across genotypes. Genotypes B2 and F1b showed a 2-fold increase in cccDNA levels compared to the other genotypes (p<0.005). Genotype A2 expressed the lowest pgRNA levels, with a 70-fold decrease in relation to the other genotypes (p<0.0001), while genotype B2 showed the lowest Precore RNA levels, with a 100-fold reduction compared to genotype A2 (p<0.0001). The highest intracellular HBV DNA levels were observed for genotype B2 and the lowest for genotypes A2 and C1 (p<0.0001). Regarding antigen expression, genotype F1b secreted the highest HBsAg levels and genotype D1 the lowest (p<0.0001), while genotypes A2 and B2 showed the highest intracellular HBsAg levels (p<0.0001). Interestingly, genotype C1 secreted the highest HBeAg levels, while genotype A2 showed the highest intracellular levels (p<0.0001). Finally, the analysis of the intra/extracellular antigen ratios revealed that most genotypes retained intracellularly 5–20% of the antigens, except the genotype A2 that retained 50% of the total expressed antigens. In conclusion, this study provides new insights into the biological characteristics of HBV genotypes, being the first study to comparatively analyze European (A and D) and Asian (B and C) genotypes with the Latin American (F) genotype. The differences in HBV replication and antigen expression might contribute to understand the differential role of genotypes in pathogenesis.