Phenotypic Variation Research Articles

Chromosome-level genome assembly of American sweetgum (Liquidambar styraciflua, Altingiaceae)

The deciduous American sweetgum (Liquidambar styraciflua, Altingiaceae) is a popular ornamental and economically valuable tree renowned for its sweet-smelling bark resin, abundant volatile substances, and spectacular fall leaf color. However, the absence of a reference genome hinders thorough investigations into the mechanisms underlying phenotypic variation, secondary metabolite synthesis and adaptation, both in this species and other Liquidambar members. In this study, we sequenced and constructed a chromosome-level assembly of the L. styraciflua genome, covering 662.48 Mb with a scaffold N50 of 39.54 Mb, by integrating PacBio, Illumina and chromosome conformation capture data. We identified 58.83% of the genome sequences as repetitive elements and 25,713 protein-coding genes, 97.28% of which were functionally annotated. The genome sequencing reads, assembly and annotation data have been deposited in publicly available repositories. This high-quality genome assembly provides valuable resources for further evolutionary and functional genomic studies in American sweetgum and other Liquidambar species.

Gender, BMI, and Age-Related Variations in Lower Limb Alignment Parameters and CPAK Phenotypes in Chinese Patients with Knee Osteoarthritis.

Research on the distribution of and the variation in coronal plane alignment of the knee (CPAK) in the Chinese osteoarthritis population is limited. We aimed to establish the CPAK classification based on the characteristics of lower limb alignment in the Chinese osteoarthritis population. We also investigated variations in lower limb alignment parameters and CPAK phenotypes based on gender, body mass index (BMI), and age. A retrospective study was conducted on a total of 944 knees diagnosed with osteoarthritis in 479 patients from January 2017 to December 2023. A scatterplot was used to describe the distribution of the CPAK classification, and the differences in lower limb alignment parameters and the CPAK classification were compared across genders (male, female), ages (middle-aged/<65 years, elderly/≥65 years), and BMI categories (normal/<25 kg/m2, overweight and obese/≥25 kg/m2) using the chi-squared test or Fisher's exact test. The average arithmetic hip-knee-ankle angle and joint line obliquity (JLO) were -3.03° ± 5.69° and 174.45° ± 4.29°, respectively. There was a higher prevalence of constitutional varus alignment in males and the overweight or obese group, while constitutional valgus alignment was more common in females and the normal BMI group (p < 0.05). Additionally, females had a greater apex distal JLO than males (p < 0.05). There were no statistically significant differences in lower limb alignment parameters among different age groups (p > 0.05). Although there were variations in alignment parameters across different genders and BMI categories in the knee osteoarthritis population, the predominant CPAK classifications were type I (38.03%), followed by type II (20.02%) and type IV (17.06%). The most common CPAK types were I, II, and IV, and they were not influenced by gender, BMI, or age, indicating that the CPAK classification can reliably reflect constitutional alignment. A better understanding of native alignment variability can aid in providing patient-specific recommendations when considering orthopedic alignment strategies.

Intrafamilial neurological phenotypic variability due to either biallelic or monoallelic pathogenic variants in CACNA1A

Pathogenic heterozygous variants in CACNA1A are associated with familial hemiplegic migraine, episodic ataxia type 2 and spinocerebellar ataxia type 6, and more recently, neurodevelopmental disorders. We describe a severe, early-onset phenotype including severe muscular hypotonia, early-onset epileptic seizures, apnoea, optic atrophy and dysphagia in three siblings carrying compound heterozygous frameshift variants in CACNA1A. Two male patients died at the age of 5 or 14 months of suspected SIDS or severe developmental epileptic encephalopathy (DEE) with refractory seizures and apnoea. A male child (index patient) developed severe early-onset DEE including seizures and ictal apnoea at the age of 4 weeks. Another male child developed generalized epilepsy and mild intellectual impairment in late infancy, and his mother and his maternal uncle were identified as carriers of a known CACNA1A pathogenic variant [c.2602delG heterozygous, p. (Ala868Profs*24)] with a diagnosis of episodic ataxia type 2. This maternal pathogenic variant c.2602delG was detected in the index patient and child 2. Trio-Exome sequencing identified an additional heterozygous pathogenic variant in the CACNA1A gene, c.5476delC, p.(His1826Thrfs*30) in the index patient and child 2, which was inherited from the asymptomatic father. In conclusion, the novel compound heterozygosity for two frameshift pathogenic variants, maternally [c.2602delG, p.(Ala868Profs*24)] and paternally [c.5476delC, p.(His1826Thrfs*3)] is associated with a severe phenotype of early-onset DEE. This observation highlights the necessity of additional analyses to clarify unusual phenotypes even if a pathogenic variant has already been identified, and expands the clinical spectrum of CACNA1A-related disorders.

Classification of PTEN germline non-truncating variants: a new approach to interpretation

BackgroundPTEN hamartoma tumour syndrome (PHTS) encompasses distinct syndromes, including Cowden syndrome resulting from PTEN pathogenic variants. Missense variants account for 30% of PHTS cases, but their classification remains challenging. To...

Сравнительная оценка кормовой продуктивности чины посевной в различных эколого-географических условиях

Abstract. The article presents the results of studying the yield and quality of green mass of four varieties of domestic sowing varieties: Racheyka, Zhemchuzhina, Mramornaya and Elena. The purpose of the study is to assess the phenotypic variability of chinese varieties in terms of the duration of the growing season, yield and quality of green mass, to select genotypes that are resistant to limiting environmental factors and capable of forming consistently high feed productivity in different agroclimatic conditions. Methods. Laboratory and field research was carried out in 2022–2023 on the educational and experimental field of the Federal State Budgetary Educational Institution of Higher Education “Omsk State Agrarian University” (Omsk) and on the basis of the Federal State Budgetary Institution Russian Research and Design Technological Institute of Sorghum and Corn (Saratov). The conditions of the growing season are close to arid ones, HTC = 0.64…1.02. In the Omsk experimental plot, the soil is meadow-chernozem medium-thick (45 cm), low-humus (3.95 % humus), semi-loam (35 % physical clay), in Saratov – southern chernozem low-humus (3.80 % humus), medium-thick (42 cm), clayed loam (43 % physical clay). The predecessor is grain crops. When conducting research, we followed the same methodology – sowing in the first ten days of May, seeding rate – 700 thousand pieces grains per hectare, plot area – 5 m2, seed placement depth – 5 cm. Results. Growing conditions have a significant impact on the variability of the duration of the growing season – 65.8 % and the level of green mass yield – 54.2 %. The variation in the parameters of the biochemical composition is largely due to the genotype of the variety – 62.1 %. Evaluation of varieties according to adaptability indicators made it possible to distribute them into groups: 1 – extensive form with very low phenotypic stability (Mramornaya); 2 – form with high phenotypic stability (Zhemchuzhina); 3 – intensive form with reduced phenotypic stability (Elena); 4 – intensive phenotypically highly stable form (Racheyka). Scientific novelty. Varieties with high phenotypic stability of feed productivity, weakly responsive to fluctuations in climatic conditions and showing low rates of yield decline under unfavorable weather factors in various regions of the country were selected.

Challenging boundaries: is cross-protection evaluation necessary for African swine fever vaccine development? A case of oral vaccination in wild boar

African swine fever (ASF) poses a significant threat to domestic pigs and wild boar (Sus scrofa) populations, with the current epidemiological situation more critical than ever. The disease has spread across five continents, causing devastating losses in the swine industry. Although extensive research efforts are ongoing to develop an effective and safe vaccine, this goal remains difficult to achieve. Among the potential vaccine candidates, live attenuated viruses (LAVs) have emerged as the most promising option due to their ability to provide strong protection against experimental challenges. However, ASF virus (ASFV) is highly diverse, with genetic and phenotypic variations across different isolates, which differ in virulence. This study highlights the limitations of a natural LAV strain (Lv17/WB/Rie1), which showed partial efficacy against a highly virulent and partially heterologous isolate (Arm07; genotype II). However, the LAV's effectiveness was incomplete when tested against a more phylogenetically distant virus (Ken06.Bus; genotype IX). These findings raise concerns about the feasibility of developing a universal vaccine for ASFV in the near future, emphasizing the urgent need to assess the protective scope of LAV candidates across different ASFV isolates to better define their limitations.

Developmental noise, entropy, and biological system condition.

Developmental noise is considered as a permissible level of entropy, as a compromise between the cost and needed precision of the realization of genetic information. In terms of entropy, noise is a measure of acceptable level of disorder to ensure a reliable system operation. Developmental noise plays a role in the observed phenotypic diversity and is associated with other indicators of the biological system condition. The thermodynamic characteristic of entropy by the energy metabolism also turns out to be related to the developmental noise. Phenotypic variability is largely determined by developmental homeostasis, including both canalization (an ability to form a similar phenotype under different conditions) and developmental stability (a capability for perfect development measured by noise level). It is shown that the change in the noise level, as an expression of the certain entropy level, unlike other forms of phenotypic variability, is a reflection of a change in the system condition. Although the entropy indices of ontogeny and community under certain conditions can change simultaneously, the entropy index at the level of developmental noise proves to be a more unambiguous and universal measure of the disorder of a biological system, compared to biodiversity indices at the community level.

Multiparametric Cranberry (Vaccinium macrocarpon Ait.) Fruit Textural Trait Development for Harvest and Postharvest Evaluation in Representative Cultivars.

Fruit texture is a priority trait that guarantees the long-term economic sustainability of the cranberry industry through value-added products such as sweetened dried cranberries (SDCs). To develop a standard methodology to measure texture, we conducted a comparative analysis of 22 textural traits using five different methods under both harvest and postharvest conditions in 10 representative cranberry cultivars. A set of textural traits from the 10%-strain compression and puncture methods were identified that differentiate between cultivars primarily based on hardness/stiffness and elasticity properties. The complementary use of both methodologies allowed for a detailed evaluation by capturing the effect of key texture-determining factors such as structure, flesh, and skin. Furthermore, the high effectiveness of this approach in different conditions and its ability to capture high phenotypic variation in cultivars highlights its great potential for applicability in various areas of the value chain and research. Therefore, this study provides an informed reference for unifying future efforts to enhance cranberry fruit texture and quality.

Genetic dissection of flour whiteness through genome-wide association analysis in common wheat (Triticum aestivum L.)

The color of flour products has an important influence on consumer acceptance. Flour color is largely determined and measured by the index of flour whiteness (FW) in China. In this study, an association population comprising 207 wheat (Triticum aestivum) accessions originating from seven countries was used for dissection of FW-related genetic loci through genome-wide association analysis. Six quantitative trait loci (QTLs) significantly associated with FW were identified, accounting for 7.87%–16.53% of the total phenotypic variation. Four KASP markers were developed from single-nucleotide polymorphisms associated with the QTLs QFW.HAAS-1AS, QFW.HAAS-1BL, QFW.HAAS-5AL, and QFW.HAAS-7AL. The phytoene synthase-encoding gene TraesCS7A03G1357000 (TaPsyA1) was identified as a candidate gene for QFW.HAAS-7AL. Two allelic variants of TaPsyA1 (designated PsyA1-a and PsyA1-b) were differentiated on the basis of a 37bp insertion/deletion polymorphism in the second intron. PsyA1-b included the 37bp insertion, which led to a translational frameshift in the gene and was associated with higher FW. The PsyA1-a allele lacked the 37bp insertion and was classified into two haplotypes according to the number of repeated ‘TC’ units in a simple sequence repeat in the promoter region. Of the two PsyA1-a haplotypes, the Type 1 haplotype conferred higher FW, flour brightness, and flour redness, and lower yellow pigment content and flour yellowness. The KASP markers and PsyA1 polymorphic markers developed in the present study are suitable for use in molecular marker-assisted selection for improvement of wheat FW.

Identifying SSR/InDel loci related to tobacco bacterial wilt resistance using association mapping

Identifying molecular markers linked to tobacco bacterial wilt resistance is crucial for developing resistant tobacco varieties, thereby enhancing tobacco production and quality. In this two-year study, we evaluated the tobacco bacterial wilt disease index (TBWDI) in a mapping population of 78 tobacco accessions using SSR/InDel markers across 1377 marker loci. Two association models, GLM_Q and MLM_Q + Kinship, were used for association analysis. By considering multiple environments, selection thresholds, and phenotype values, we identified 19 reliable marker loci (P = 7.07-E05–4.98-E02) that explained 5.37–19.10 % of the phenotypic variation. Among these, we selected 11 accessions with high resistance to tobacco bacterial wilt, each containing at least one excellent locus. The models predicted five hybrid combinations whose offspring aggregated additional excellent loci. Additionally, one locus was identified during quantitative trait loci mapping, with accessions carrying this locus exhibiting significantly different TBWDI values from those without it, confirming its reliability and stability. A candidate gene (LOC107795335) was also identified downstream at 17.58 Kbp of the locus. Our study pinpointed reliable loci associated with bacterial wilt resistance, identified important materials for breeding resistant tobacco varieities, and predicted the best hybrid combinations for low disease indexes. The results of our study offer invaluable theoretical insights for breeding varieties with high and stable resistance.

Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study.

Sunflower (Helianthus annuus L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including the disc diameter. Over three consecutive years, 2019, 2020, and 2022, we assessed phenotypic variation in disc diameter across a diverse set of sunflower accessions (N = 342) in replicated field trials. Upon aggregating the phenotypic data from multiple years, we estimated the broad sense heritability (H 2) of the disc diameter trait to be 0.88. A subset of N = 274 accessions was genotyped by using the tunable genotyping-by-sequencing (tGBS) method, resulting in 226,779 high-quality SNPs. Using these SNPs and the disc diameter phenotype, we conducted a genome-wide association study (GWAS) employing two statistical approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU). The MLM and farmCPU GWAS approaches identified 106 and 8 significant SNPs located close to 53 and 21 genes, respectively. The MLM analysis identified two significant peaks: a prominent signal on chromosome 10 and a relatively weaker signal on chromosome 16, both of which were also detected by farmCPU. The genetic loci associated with disc diameter, as well as the related candidate genes, present promising avenues for further functional validation and serve as a basis for sunflower oil yield improvement.

Transcriptome-based prediction for polygenic traits in rice using different gene subsets

BackgroundTranscriptome-based prediction of complex phenotypes is a relatively new statistical method that links genetic variation to phenotypic variation. The selection of large-effect genes based on a priori biological knowledge is beneficial for predicting oligogenic traits; however, such a simple gene selection method is not applicable to polygenic traits because causal genes or large-effect loci are often unknown. Here, we used several gene-level features and tested whether it was possible to select a gene subset that resulted in better predictive ability than using all genes for predicting a polygenic trait.ResultsUsing the phenotypic values of shoot and root traits and transcript abundances in leaves and roots of 57 rice accessions, we evaluated the predictive abilities of the transcriptome-based prediction models. Leaf transcripts predicted shoot phenotypes, such as plant height, more accurately than root transcripts, whereas root transcripts predicted root phenotypes, such as crown root length, more accurately than leaf transcripts. Furthermore, we used the following three features to train the prediction model: (1) tissue specificity of the transcripts, (2) ontology annotations, and (3) co-expression modules for selecting gene subsets. Although models trained by a gene subset often resulted in lower predictive abilities than the model trained by all genes, some gene subsets showed improved predictive ability. For example, using genes expressed in roots but not in leaves, the predictive ability for crown root diameter was improved by more than 10% (R2 = 0.59 when using all genes; R2 = 0.66, using 1,554 root-specifically expressed genes). Similarly, genes annotated as “gibberellic acid sensitivity” showed higher predictive ability than using all genes for root dry weight.ConclusionsOur results highlight both the possibility and difficulty of selecting an appropriate gene subset to predict polygenic traits from transcript abundance, given the current biological knowledge and information. Further integration of multiple sources of information, as well as improvements in gene characterization, may enable the selection of an optimal gene set for the prediction of polygenic phenotypes.

Clinical characterization and founder effect analysis in Chinese amyotrophic lateral sclerosis patients with SOD1 common variants

Objective In the Asian population, SOD1 variants are the most common cause of amyotrophic lateral sclerosis (ALS). To date, more than 200 variants have been reported in SOD1. This study aimed to summarize the genotype–phenotype correlation and determine whether the patients carrying common variants derive from a common ancestor. Methods A total of 103 sporadic ALS (SALS) and 11 familial ALS (FALS) probands were included and variants were screened by whole exome sequencing. Functional analyses were performed on fibroblasts derived from patients with SOD1 p.V48A and control. Haplotype analysis was performed in the probands with p.H47R or p.V48A and their familial members. Results A total of 25 SOD1 variants were identified in 44 probands, in which p.H47R, p.V48A and p.C112Y variants were the most common variants. 94.3% and 60% of patients with p.H47R or p.V48A had lower limb onset with predominant lower motor neurons (LMNs) involvement. Patients with p.H47R had a slow progression and prolonged survival time, while patients with p.V48A exhibited a duration of 2–5 years. Patients with p.C112Y variant showed remarkable phenotypic variation in age at onset and disease course. SOD1V48A fibroblasts showed mutant SOD1 aggregate formation, enhanced intracellular reactive oxygen species level, and decreased mitochondrial membrane potential compared to the control fibroblast. Haplotype analysis showed that seven families had two different haplotypes. p.H47R and p.V48A variants did not originate from a common founder. Conclusions Our study expanded the understanding of the genotype–phenotype correlation of ALS with SOD1 variants and revealed that the common p.H47R or p.V48A variant did not have a founder effect.

341P Incidental DMD in-frame deletions identified by prenatal array CGH: inter and intra-familial phenotype variability

341P Incidental DMD in-frame deletions identified by prenatal array CGH: inter and intra-familial phenotype variability

588P Phenotype variability and natural history of X-linked myopathy with excessive autophagy running head: natural history of XMEA

588P Phenotype variability and natural history of X-linked myopathy with excessive autophagy running head: natural history of XMEA

Phenotypic variations in knee osteoarthritis: insights from MRI and radiographic comparisons.

To investigate the correlation between MRI-based phenotypes (cartilage-meniscus, subchondral bone, and inflammatory) and radiography-based atrophic and hypertrophic phenotypes, aiming to demonstrate MRI's diagnostic capability in identifying complex osteoarthritis phenotypes that radiography cannot fully capture. This single-center retrospective study examined knee radiographs and MRIs of patients from November 2021 to April 2023 to identify osteoarthritis phenotypes. Radiographs were staged by the Kellgren-Lawrence system, and both modalities were classified into atrophic or hypertrophic phenotypes. MRIs were further classified into three phenotypes: cartilage-meniscus, subchondral bone, and inflammatory. Associations between phenotypes, Kellgren-Lawrence stage, age, and gender were analyzed with Pearson chi-square test and student T-test. Reliability measurements were evaluated using kappa statistic. A total of 214 knees from 187 individuals (73.3% women, 26.7% men; mean age 57.1 ± 9.1years) were included. The hypertrophic MRI phenotype was significantly associated with cartilage-meniscus and subchondral bone phenotypes (p < 0.001). Cartilage-meniscus and subchondral bone phenotypes were less prevalent in Kellgren-Lawrence stage 2 than in stages 3 and 4 (p < 0.001 and p = 0.004, respectively). The subchondral bone phenotype was more common in men (p = 0.022), and the cartilage-meniscus phenotype in the elderly (p < 0.001). Radiography and MRI had substantial agreement (Kappa = 0.637, p < 0.001) in diagnosing hypertrophic and atrophic phenotypes. The hypertrophic phenotype was associated with cartilage-meniscus and subchondral bone phenotypes, with lower prevalences in Kellgren-Lawrence stage 2 knees. MRI offers enhanced phenotypic characterization, which facilitates more precise and individualized management in osteoarthritis care. Despite limitations compared to MRI, radiography remains valuable for the evaluation of hypertrophic and atrophic phenotypes.

Role of macrophages in aortic dissection pathogenesis: insights from preclinical studies to translational prospective.

Aortic dissection is a critical vascular disease that is characterized by a high mortality rate and inflammation significantly influences its onset and progression. Recent studies highlight the integral role of macrophages, key players in the immune system, in the pathological landscape of aortic dissection. These cells are involved in crucial processes, such as the remodeling of the extracellular matrix, immunocyte infiltration, and phenotypic switching of smooth muscle cells, which are essential for the structural integrity and functional dynamics of the aortic wall. Despite these insights, the specific contributions of macrophages to the development and progression of aortic dissection remains unclear. This review explores the pathogenesis of aortic dissection with a focus on macrophages and describes their origins, phenotypic variations, and potential roles based on the most recent research findings. Furthermore, we discuss key molecules related to macrophages during aortic dissection, their interactions with other cellular components within the aorta, and the implications of these interactions for future therapeutic strategies. This comprehensive analysis aimed to improve our understanding of macrophages in aortic dissection and promote the development of targeted interventions.

Identification of quantitative trait loci for lodging and related agronomic traits in soybean (Glycine max [L.] Merr.)

BackgroundLodging, a crucial agronomic trait linked to soybean yield, poses a significant challenge in soybean production. Nevertheless, there has been less research on soybean lodging compared to other important agronomic traits, hindering progress in breeding high-yield soybeans. Our goals were to investigate lodging, pinpoint quantitative trait loci (QTL) linked to lodging, and forecast potential candidate genes linked to this trait. To achieve this, we employed a recombinant inbred line (RIL) population derived from a cross between Guizao 1 and B13 (GB) across various environments.ResultsThe lodging score of the RIL population was found to be significantly positively correlated with flowering time, maturity time, plant height, number of main stem nodes, stem diameter, and internode length, with correlation coefficients ranging from 0.457 to 0.783. A total of 84 QTLs associated with soybean lodging and related traits were identified using the GB population. The contribution of phenotypic variance ranged from 1.26 to 66.87%, with LOD scores ranging from 2.52 to 69.22. Additionally, within these QTLs, a stable major QTL associated with lodging was newly discovered in the GB population. Out of the ten major QTLs associated with other related traits, nine of them were situated within the qLD-4-1 interval of the major lodging score locus, displaying phenotypic variations ranging from 12.10 to 66.87%. Specific alterations in gene expression were revealed through the analysis of resequencing data from the two parental lines, potentially indicating their significant roles in lodging. Subsequently, it was determined through qRT-PCR that four genes are likely to be the major genes controlling soybean lodging.ConclusionsThis study’s findings offer valuable insights into the genetic underpinnings of soybean lodging resistance traits. By comprehending the potential genetic factors associated with lodging, this research lays the groundwork for breeding high-yield soybeans with improved lodging resistance.

Just keep exploring: Genetics of fish niche adaptation.

Although the diversification of species has fascinated researchers for centuries, we know remarkably little about how behavior influences niche adaptation and the genetic mechanisms through which behavior evolves. In their recent study, Sommer-Trembo et al. (Science, 384, 470-475, 2024) demonstrate a critical role for the regulatory gene cacng5b in modulating phenotypic variation in exploratory behavior in one of the most exceptional adaptive radiations: the African cichlid fishes of Lake Tanganyika.

Polycystic Ovary Syndrome Markers and Mechanism

Polycystic ovary syndrome (PCOS) is a complex endocrine disorder characterized by hormonal imbalances, metabolic dysregulation, and reproductive abnormalities. This study aims to elucidate the significance of PCOS markers and their mechanisms while outlining the methodology employed. A comprehensive literature review was conducted from 2020 to 2023 using databases like PubMed, ScienceDirect, EMBASE, and Google Scholar. Key search terms included "pathophysiology," "pathogenesis," "PCOS," "marker," and "biomarker," aligned with the PICOT criteria. After removing duplicates, articles underwent a two-phase screening process based on predefined inclusion criteria. Additionally, a marker mechanism flowchart was created using the Biorender application. Results highlighted the pivotal role of various markers in understanding PCOS pathophysiology and guiding clinical management. Anthropometric, visual, metabolic, inflammatory, endocrine, and oxidative stress markers were analyzed for their diagnostic, prognostic, and therapeutic implications in PCOS. The study underscores the importance of marker interactions in personalized PCOS management. Limitations in marker interpretation warrant further research to refine diagnostic accuracy and optimize therapeutic interventions. Integrating marker mechanisms enhances understanding of PCOS heterogeneity and informs targeted treatment approaches tailored to individual phenotypic variations.