Mixture Of Genotypes Research Articles

Evolutionary Agroecology: Individual fitness, population yield and resource availability in wheat

Evolutionary Agroecology theory predicts that the relationship between population yield and individual fitness among genotypes of a crop species is unimodal, and experimental evidence supports this. We test the theory further by investigating the role of resource availability on this relationship by comparing growth and reproductive output of three old and three modern cultivars of wheat (Triticum aestivum) in mixture and monocultures grown at three resource levels. The relationship between population grain yield and individual fitness (mean individual grain yield in mixture) of genotypes was resource dependent in a way that is consistent with the theory: when resource levels are low and limit individual growth directly, individual and population yield are positively correlated. When resource levels are high and the growth of individual plants is limited by competition for these resources, the relationship between individual fitness and population yield becomes negative. There was evidence for the unimodal relationship at the intermediate resource level. Old cultivars had higher fitness than newer cultivars at all three resource levels. Old cultivars had higher yields at low resource levels, but the newer cultivars yielded more when resource levels were high. Evaluating individual fitness and population yield in different environments may help wheat breeders to develop locally adapted, cooperative cultivars to increase production across large wheat-producing areas.

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana. To quantify neighbor interactions among 199 genotypes grown in a randomized block design, we employ a genome-wide association method named “Neighbor GWAS” and genomic prediction inspired by the Ising model of magnetics. These analyses predict that 823 of the 19,701 candidate pairs can reduce herbivory in mixed planting. We planted three pairs with the predicted effects in mixtures and monocultures, and detected 18–30% reductions in herbivore damage in the mixed planting treatment. Our study shows the power of genomic prediction to assemble genotype mixtures with positive biodiversity effects.

The genetics of plant-plant interactions and their cascading effects on agroecosystem - from model plants to application.

Plants are typically surrounded by neighboring individuals in agricultural fields or natural environments. In such circumstances, plant-plant interactions (PPI) are ubiquitous and represent not only important evolutionary forces but also have consequences on (agro-)ecosystem functioning, such as increased productivity and resistance. However, many mechanisms underlying these PPIs remain poorly understood. Recently, new genomic technologies and tools, such as genome-wide association studies, have facilitated genetic approaches to study PPIs, particularly among conspecific individuals. Here, we highlight emerging issues and advances in the field by focusing on three different aspects. First, we overview the current status of genetic mapping studies on PPIs and pinpoint that these studies open a new opportunity that is relevant to agriculture and breeding. Second, we introduce two proof-of-concept studies in Arabidopsis thaliana, in which genetic differences among plants improved the functioning of genotype mixtures. Both studies were able to predict effective mixtures with different experimental designs applied to different outcomes (productivity increase vs. herbivory mitigation). Third, we discuss implications from these case studies about how PPIs have cascading effects that propagate to higher levels of biological organization, such as populations or communities. At the population level, plant yield or resistance can be optimized through breeding that achieves reduced competition or push-pull protection systems, respectively. At the community level, these population-level changes may have further beneficial effects on plant-associated organisms. Overall, we suggest that the increasing availability of genomic resources will improve our understanding of PPIs and thereby contribute to the management of crops or semi-natural ecosystems.

Impact of genotypic mixture on soybean (Glycine max) pest population

An experiment was conducted during rainy (kharif) seasons of 2018 and 2019 at the ICAR-Indian Institute of Soybean Research, Indore, and Madhya Pradesh to study the impact of genotypic mixture on soybean [Glycine max (L.) Merr.] pest population. A total of 16 soybean genotypes and 4 genotypic mixtures were evaluated for relative efficacy in management of insect-pests of soybean. Among the 20 treatments, the plots with genotypic mixtures had lowest population of Spodoptera exigua Hubner and at par with each other. In case of Spodoptera litura Fabricius, tussock moth, blue beetle and grey weevil management, a mixture of the genotypes JS-9560, JS-20-34, MAUS-47 and MACS-1460 was found most effective treatment. The plots with the genotypic mixtures of NRC-37, JS-9752, RSC-1046 and RKS-113 supported the least population of semiloopers. However, lowest population of leaf miner and girdle beetle was recorded in plots of JS-20-34 while the least population of stem fly was recorded in RSC-1046. The differences observed due to the genotypic combinations may be used for developing inset-pest management programmes in soybean.

Investigation of the influence of milk protein genotype on the process of fermentation of milk curds by mesophilic lactic acid streptococci

The relevance of this study lies in the fact that the majority of commercial milk processed into fermented dairy products is a mixture of β-casein genotypes. The increasing use of A2 milk in the dairy industry necessitates the development of scientifically grounded technologies for the production of fermented products, as casein genotype modifications can affect the course of technological processes and require adjustments to production parameters. The study aimed to determine the impact of genetic modification of the β-casein protein in cow’s milk on the fermentation process of milk mixtures during the production of fermented dairy products. Research methods included chemical, physical, organoleptic, and microbiological methods (determination of the quality indicators of raw milk and fermented milk curds), and technological methods (determination of acid formation activity and viscosity). The initial characteristics of raw milk were investigated according to genotype, revealing no direct correlation. Changes in the physicochemical, microbiological, and organoleptic properties of fermented milk curds during biotechnological processing and storage were examined. Optimal technological process regimes were selected, and technological methods were chosen to minimise the influence of secondary factors on the experiment. A mixed culture preparation of mesophilic lactic acid lactococci, including L. Lactis ssp., was chosen as a starter culture. It was established that all 13 milk samples were suitable for biotechnological processing using mixed cultures of mesophilic lactic acid bacteria. As a result, it was concluded that the production of fermented dairy products from raw milk with the presented β-casein genetic modifications, A1A1, A1A2, and A2A2 – using L. lactis ssp. cultures – is possible using the classical technology and does not require adjustment of the technological conditions. The obtained results can be used in the dairy industry when developing technologies for fermented dairy products from A2 raw milk

Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation.

Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies.

Genetic and ecological differentiation of Caragana jubata (Pall.) Poir.

Caragana jubata (Pall.) Poir. is a cold-tolerant mountain shrub and important medicinal species of Fabaceae family with a disjunctive pan-Asian range. Sequences of the atpH-atpI and trnL-trnF intergenic spacers of chloroplast DNA and of the internal transcribed spacer region, ITS-1, of the nuclear ribosomal DNA were used to investigate the intraspecific evolution and phylogeography of this species. Eleven cpDNA haplotypes were identified. The population subdivision is very high (GST = 0.743, NST = 0.943), suggesting a distinct phylogeographic structure (NST > GST, P < 0.001). Phylogenetic analyses of the eleven haplotypes were clustered into four clades, consistent with their respective distributions in four separate regions: Tibet, Tien Shan, Buryatia and Magadan Region. This pronounced phylogeographic gap is also confirmed by nrITS data, however, there is some mixture of genotypes in the Magadan and Buryat populations. Genetic evidence suggests that the center of origin of C. jubata was Tibet and adjacent mountain systems, from where the species spread westwards along continuous mountain chains towards the Tien Shan and northeastwards to the coast of the Sea of Okhotsk and further northwards to Arctic. Divergence of Tien Shan populations of C. jubata may have been caused by climate change in the Pleistocene associated with increased aridity and expansion of deserts, while subsequent climate-induced cycles of range contraction/expansion increased geographic isolation and fragmentation of more northern populations. Marginal northern populations now occupy sites with the most favourable environmental conditions. Special attention is paid to the Okhotsk populations of this species preserved in Magadan Region.

Our current understanding of the biological impact of endometrial cancer mtDNA genome mutations and their potential use as a biomarker.

Endometrial cancer (EC) is a devastating and common disease affecting women's health. The NCI Surveillance, Epidemiology, and End Results Program predicted that there would be >66,000 new cases in the United States and >13,000 deaths from EC in 2023, and EC is the sixth most common cancer among women worldwide. Regulation of mitochondrial metabolism plays a role in tumorigenesis. In proliferating cancer cells, mitochondria provide the necessary building blocks for biosynthesis of amino acids, lipids, nucleotides, and glucose. One mechanism causing altered mitochondrial activity is mitochondrial DNA (mtDNA) mutation. The polyploid human mtDNA genome is a circular double-stranded molecule essential to vertebrate life that harbors genes critical for oxidative phosphorylation plus mitochondrial-derived peptide genes. Cancer cells display aerobic glycolysis, known as the Warburg effect, which arises from the needs of fast-dividing cells and is characterized by increased glucose uptake and conversion of glucose to lactate. Solid tumors often contain at least one mtDNA substitution. Furthermore, it is common for cancer cells to harbor mixtures of wild-type and mutant mtDNA genotypes, known as heteroplasmy. Considering the increase in cancer cell energy demand, the presence of functionally relevant carcinogenesis-inducing or environment-adapting mtDNA mutations in cancer seems plausible. We review 279 EC tumor-specific mtDNA single nucleotide variants from 111 individuals from different studies. Many transition mutations indicative of error-prone DNA polymerase γ replication and C to U deamination events were present. We examine the spectrum of mutations and their heteroplasmy and discuss the potential biological impact of recurrent, non-synonymous, insertion, and deletion mutations. Lastly, we explore current EC treatments, exploiting cancer cell mitochondria for therapy and the prospect of using mtDNA variants as an EC biomarker.

A novel strategy to predict clonal composites by jointly modeling spatial variation and genetic competition

Biotic and abiotic stresses have been making it difficult to maintain the rates of genetic gains in forest tree breeding. Planting a mixture of genotypes or clonal composites can be an alternative to increase the security of forest plantations. The formation of clonal composites is complex due to inter-genotypic competition and indirect genotypic effects that can affect the efficiency of genetic selection. This study aims to understand how indirect genotypic effects can impact the response to selection and how the stand composition can be used to explore these effects and enhance forest yield. We used two clonal trials of eucalyptus hybrids implanted in a randomized complete block design with 24 replications, containing a single tree per plot evaluated for mean annual increment at 3 and 6 years. We focused on partitioning the genotypic variation into direct and indirect genotypic effects based on competition intensity factors. We identified aggressive, homeostatic, and sensitive clones based on the magnitude of indirect genotypic effects. Considering indirect genotypic effects, for mean annual increment, the total heritability decreased from 0.25 to 0.10 for 3 years and from 0.30 to 0.14 for 6 years, respectively. We proposed a workflow that uses the direct and indirect genotypic effects to predict the mean values for clonal composite combinations and to select the one with the highest yield. Our methodology considered spatial variation and interplot competition that can affect the total heritable estimates and response to selection in forest trials. The clones were classified as aggressive, homeostatic, and sensitive, according to their deviation from the indirect genotypic effects means. Our methodology enabled the extraction of useful information and predict many clonal composites' performance, which can be used in recommending genotypes to be planted in mixtures.

The genetic identity of neighboring plants in intraspecific mixtures modulates disease susceptibility of both wheat and rice.

Mixing crop cultivars has long been considered as a way to control epidemics at the field level and is experiencing a revival of interest in agriculture. Yet, the ability of mixing to control pests is highly variable and often unpredictable in the field. Beyond classical diversity effects such as dispersal barrier generated by genotypic diversity, several understudied processes are involved. Among them is the recently discovered neighbor-modulated susceptibility (NMS), which depicts the phenomenon that susceptibility in a given plant is affected by the presence of another healthy neighboring plant. Despite the putative tremendous importance of NMS for crop science, its occurrence and quantitative contribution to modulating susceptibility in cultivated species remains unknown. Here, in both rice and wheat inoculated in greenhouse conditions with foliar fungal pathogens considered as major threats, using more than 200 pairs of intraspecific genotype mixtures, we experimentally demonstrate the occurrence of NMS in 11% of the mixtures grown in experimental conditions that precluded any epidemics. Thus, the susceptibility of these 2 major crops results from indirect effects originating from neighboring plants. Quite remarkably, the levels of susceptibility modulated by plant-plant interactions can reach those conferred by intrinsic basal immunity. These findings open new avenues to develop more sustainable agricultural practices by engineering less susceptible crop mixtures thanks to emergent but now predictable properties of mixtures.

Techniques for Identifying and Sorting Transgenic Mosquito Larvae.

Transgenic mosquitoes are used in many aspects of mosquito research. First, they can help answer biological questions to advance scientific knowledge-for example, in the fields of mosquito-pathogen interactions, insect immunity, or olfaction. Second, transgenic technologies may be used to develop much needed novel vector control strategies, such as mosquitoes that are unable to transmit disease or transgenes that sterilize mosquito females to suppress vector populations. Here, we introduce how researchers use various selection markers to screen for transgenic mosquito larvae following a transgenesis experiment. Common procedures include using a binocular fluorescence microscope for initial screening. For higher-throughput screening, a flow cytometer known as Complex Object Parametric Analyzer and Sorter (COPAS) can be used to stabilize transgenic lines through the purification of homozygous individuals or to manage transgene frequency in established transgenic lines. In particular, COPAS sorting allows the production of mosquito larval cultures composed of a mixture of genotypes (control and genetically modified larvae) with the goal of raising both groups of mosquitoes under the same environmental conditions in preparation for a controlled phenotype assessment. It can also be used to produce large populations of male mosquitoes, which should facilitate the development of mosquito control intervention strategies similar to the sterile insect technique (SIT), which aims to release large numbers of sterile males that will mate with and sterilize wild females to suppress mosquito populations. Finally, the utilization of a puromycin resistance marker cassette to screen for transgenic Anopheles larvae is also introduced.

Beyond trait distances: Functional distinctiveness captures the outcome of plant competition

Abstract Functional trait distances between coexisting organisms reflect not only complementarity in the way they use resources, but also differences in their competitive abilities. Accordingly, absolute and relative trait distances have been widely used to capture the effects of niche dissimilarity and competitive hierarchies, respectively, on the performance of plants in competition. However, multiple dimensions of the plant phenotype are involved in these plant–plant interactions (PPI), challenging the use of relative trait distances to predict their outcomes. Furthermore, estimating the effects of competitive hierarchy on the performance of a group of coexisting plants remains particularly difficult since relative trait distances relate to the effects of a focal plant on another. We argue that trait distinctiveness, an emerging facet of functional diversity that characterizes the eccentric position of a species (or genotype) in a phenotypic space, can reveal the unique role played by a given individual plant in a group of competing plants. We used the model crop species Oryza sativa spp. japonica to evaluate the ability of trait distances and trait distinctiveness to predict the outcome of intraspecific PPI on the performance of single genotype and genotype mixtures. We performed a screening experiment to characterize the phenotypic space of 49 rice genotypes based on 11 above‐ground and root traits. We selected nine genotypes with contrasting positions in the phenotypic space and grew them in pots following a complete pairwise interaction design. Relative distances and distinctiveness based on traits associated with light competition were by far the best predictors of the performance of single genotypes—taller genotypes that acquired resource faster being the best competitors—while absolute trait distances had no effect. These results indicate that competitive hierarchy for light dominates PPI in this experiment. Consistently, trait distinctiveness in plant height and age at flowering had the strongest, positive effects on mixture performance, confirming that functional distinctiveness captures the effects of trait hierarchies and asymmetric PPI at this scale. Our findings shed new light on the role of trait diversity in regulating PPI and ecosystem processes and call for a greater consideration of functional distinctiveness in studies of coexistence mechanisms. Read the free Plain Language Summary for this article on the Journal blog.

Single-gene resolution of diversity-driven overyielding in plant genotype mixtures

In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.

A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L.

Root chicory (Cichorium intybus L. var. sativum) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic. However, bitter tasting sesquiterpene lactones, giving chicory its known flavour, need to be removed during inulin extraction. To avoid this extraction and associated costs, recently chicory variants with a lower sesquiterpene lactone content were created by inactivating the four copies of the germacrene A synthase gene (CiGAS-S1, -S2, -S3, -L) which encode the enzyme initiating bitter sesquiterpene lactone biosynthesis in chicory. In this study, different delivery methods for CRISPR/Cas9 reagents have been compared regarding their efficiency to induce mutations in the CiGAS genes, the frequency of off-target mutations as well as their environmental and economic impacts. CRISPR/Cas9 reagents were delivered by Agrobacterium-mediated stable transformation or transient delivery by plasmid or preassembled ribonucleic complexes (RNPs) using the same sgRNA. All methods used lead to a high number of INDEL mutations within the CiGAS-S1 and CiGAS-S2 genes, which match the used sgRNA perfectly; additionally, the CiGAS-S3 and CiGAS-L genes, which have a single mismatch with the sgRNA, were mutated but with a lower mutation efficiency. While using both RNPs and plasmids delivery resulted in biallelic, heterozygous or homozygous mutations, plasmid delivery resulted in 30% of unwanted integration of plasmid fragments in the genome. Plants transformed via Agrobacteria often showed chimerism and a mixture of CiGAS genotypes. This genetic mosaic becomes more diverse when plants were grown over a prolonged period. While the genotype of the on-targets varied between the transient and stable delivery methods, no off-target activity in six identified potential off-targets with two to four mismatches was found. The environmental impacts (greenhouse gas (GHG) emissions and primary energy demand) of the methods are highly dependent on their individual electricity demand. From an economic view - like for most research and development activities - employment and value-added multiplier effects are high; particularly when compared to industrial or manufacturing processes. Considering all aspects, we conclude that using RNPs is the most suitable method for genome editing in chicory since it led to a high efficiency of editing, no off-target mutations, non-transgenic plants with no risk of unwanted integration of plasmid DNA and without needed segregation of transgenes.

Mapping hepatitis B virus genotypes on the African continent from 1997 to 2021: a systematic review with meta-analysis

Hepatitis B virus (HBV) has ten genotypes (A–J) and over 40 sub-genotypes based on the divergence of ≥ 8% and 4 to < 8% in the complete genome respectively. These genotypes and sub-genotypes influence the disease prognosis, response to therapy and route of viral transmission. Besides, infection with mixed genotypes and recombinant genotypes has also been reported. This study aimed at mapping the de novo genotypes and correlate them with the immigration trends in order to inform future research on the underlying reasons for the relative distribution of HBV genotypes from a large sample size pooled from many primary studies. Data was extracted from 59 full research articles obtained from Scopus, PubMed, EMBASE, Willy library, African Journal Online (AJOL) and Google Scholar. Studies that investigated the genotypes, sub-genotypes, mixed genotypes and recombinant were included. The Z-test and regression were used for the analysis. The study protocol is registered with PROSPERO under the registration number CRD42022300220. Overall, genotype E had the highest pooled prevalence significantly higher than all the other genotypes (P < 0.001). By region, genotype A posted the highest pooled prevalence in eastern and southern Africa, E in west Africa and D in north Africa (P < 0.0001). Regarding the emerging genotypes B and C on the African continent, genotype B was significantly higher in south Africa than C (P < 0.001). In contrast, genotype C was significantly higher in east Africa than west Africa (P < 0.0001). The A1 and D/E were the most diverse sub-genotypes and genotype mixtures respectively. Finally, we observed a general progressive decrease in the prevalence of predominant genotypes but a progressive increase in the less dominant by region. Historical and recent continental and intercontinental migrations can provide a plausible explanation for the HBV genotype distribution pattern on the African continent.

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

Mixtures of genotypes increase disease resistance in a coral nursery

Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef building corals have been particularly devastated by disease and continue to experience catastrophic population declines. We show that mixtures of genotypes (i.e., diversity) increased disease resistance in the critically endangered Acropora cervicornis, a species that is frequently targeted for restoration of degraded reefs in the broader Caribbean region. This finding suggests a more generalized relationship between diversity and disease and offers a viable strategy for mitigating the spread of infectious diseases in corals that likely applies to other foundation species targeted for restoration.

Next-generation sequencing sheds light on the interaction between virus and cell during foot-and-mouth disease virus persistent infection

Foot-and-mouth disease virus (FMDV) infection can be either persistent or acute in susceptible animals. The mechanisms involved in FMDV replication and clearance during persistent infection remain unclear. To identify host factors that are critical for FMDV replication during persistent infection, we used RNA-seq to compare the transcriptomes of infected (BHK-Op) cells and bystander (BHK-VEC) cells, which are exposed to FMDV but not infected. In total, 1917 genes were differentially expressed between BHK-Op cells and BHK-VEC cells, which were involved in ribosome biogenesis, cell cycle, and dilated cardiomyopathy. We further identified host genes potentially involved in viral clearance during persistent FMDV infection by comprehensive crossover analysis of differentially expressed genes in ancestral host cells, evolved infected host cells, and evolved bystander cells, which are resistant to infection by wild-type FMDV and FMDV-Op that co-evolved with host cells during persistent infection. Among the identified genes were Cav1 and Ccnd1. Subsequent experiments showed that knockdown of Cav1 and Ccnd1 in host cells significantly promoted and inhibited FMDV replication, respectively, confirming that the overexpression of Cav1 and the downregulation of Ccnd1 contribute to virus clearance during persistent FMDV infection. In addition, we found that BHK-Op cells contained mixtures of multiple genotypes of FMDV viruses, shedding light on the diversity of FMDV genotypes during persistent infection. Our findings provide a detailed overview of the responses of infected cells and bystander cells to persistent FMDV infection.

Prevalence of hepatitis B virus genotypes among patients with liver disease in Eritrea

Eritrea is an East African multiethnic country with an intermediate endemicity for hepatitis B. Our aim was to establish the most prevalent genotypes of hepatitis B virus (HBV) among patients with liver disease. A total of 293 Eritrean patients with liver disease who were hepatitis B surface antigen (HBsAg) positive were enrolled. All sera were tested for liver transaminases, HBV DNA viral load, and hepatitis B seromarkers including HBsAg, anti-HBcAb (total), HBeAg, and anti-HBeAb. Those reactive for HBsAg and anti-HBc (total) were further tested for HBV genotyping. The median (interquartile range) of HBV DNA viral load and ALT levels were 3.47 (1.66) log IU/mL and 28 (15.3) IU/L, respectively. Using type-specific primer-based genotyping method, 122/293 (41.6%) could be genotyped. Irrespective of mode of occurrence, HBV genotype D (21.3%) was the predominant circulating genotype, followed by genotypes C (17.2%), E (15.6%), C/D (13.1%), and C/E (10.7%). Genotypes C/D/E (7.4%), A/D (4.9%), D/E (4.1%), A (2.5%), and B, A/E, B/E, and A/D/C (0.8%) were also present. HBV in Eritrea is comprised of a mixture of HBV genotypes. This is the first study of HBV genotyping among patients with liver disease in Eritrea.

Interpreting the effects of plant species diversity and genotypic diversity within a dominant species on above- and belowground overyielding

Biodiversity loss, either intraspecific or interspecific level, could alter community processes and ecosystem functioning. Exploring the mechanisms by which biodiversity at different levels influences ecosystem functioning is a major challenge in the field of ecology. In this study, by constructing plant communities with different diversity levels of both dominant species (Stipa grandis) genotype and common species in a mesocosm experiment, we analyzed the relative importance of dominant genotype diversity and common species diversity on biomass production through Fox's tripartite partition, and the relationships between community functional diversity and biomass production. For common species mixtures (G0S5), a significant positive net diversity effect on belowground biomass was found, and the net effect was contributed by a significant positive dominance effect and a significant negative trait-independent complementarity effect. For genotype mixtures of S. grandis (G5S0), a significant positive net diversity effect on aboveground biomass and a non-significant positive net diversity effect on belowground biomass were found, and both the effects were driven by positive trait-independent complementarity effects. The increases in both dominant genotype and common species diversity (G5S5) led to remarkable positive net diversity effects, with a significant positive trait-independent complementarity effect on belowground biomass and all the three biodiversity effect components on aboveground biomass being significantly positive. Only a small proportion (3/22) of relationships between community functional diversity and biomass were linear by a first order polynomial estimation. The significant positive trait-independent complementarity effect in G5S0 and trait-dependent complementarity effect in G5S5 could not be explained by the smaller intraspecific trait variation. These findings highlight the underestimated and overlooked roles of dominant genotypic diversity for ecosystem functioning, and are very important for grassland protection and management, especially in the semi-arid typical steppe.