Multiple Traits Research Articles

SCAMPI: A scalable statistical framework for genome-wide interaction testing harnessing cross-trait correlations.

Family-based heritability estimates of complex traits are often considerably larger than their single-nucleotide polymorphism (SNP) heritability estimates. This discrepancy may be due to non-additive effects of genetic variation, including variation that interacts with other genes or environmental factors to influence the trait. Variance-based procedures provide a computationally efficient strategy to screen for SNPs with potential interaction effects without requiring the specification of the interacting variable. While valuable, such variance-based tests consider only a single trait and ignore likely pleiotropy among related traits that, if present, could improve power to detect such interaction effects. To fill this gap, we propose SCAMPI (Scalable Cauchy Aggregate test using Multiple Phenotypes to test Interactions), which screens for variants with interaction effects across multiple traits. SCAMPI is motivated by the observation that SNPs with pleiotropic interaction effects induce genotypic differences in the patterns of correlation among traits. By studying such patterns across genotype categories among multiple traits, we show that SCAMPI has improved performance over traditional univariate variance-based methods. Like those traditional variance-based tests, SCAMPI permits the screening of interaction effects without requiring the specification of the interaction variable and is further computationally scalable to biobank data. We employed SCAMPI to screen for interacting SNPs associated with four lipid-related traits in the UK Biobank and identified multiple gene regions missed by existing univariate variance-based tests. SCAMPI is implemented in software for public use.

50 Awardee Talk: The role of non-traditional inheritance patterns among Bos indicus-Bos taurus crosses for global beef value chain considerations

Abstract Bos indicus-Bos taurus crosses have been effectively used in many production environments globally. Substantially higher amounts of hybrid vigor have been reported in these F1 crosses as compared with those involving only Bos taurus or only Bos indicus breeds. However, for many years, and in many environments, “unusual” aspects of calf growth have been documented among these crosses. Among F1 crosses, Bos indicus-sired calves (Bos indicus x Bos taurus) have birth weight 8 to 12 kg heavier than contemporary Bos taurus-sired calves (Bos taurus x Bos indicus); additionally, pronounced sexual dimorphism occurs where males may weigh 5 to 10 kg more than females from Bos indicus sires (Bos taurus dams) but 1 kg or less from Bos taurus sires (Bos indicus dams) in both natural service and embryo transfer calves. These reciprocal differences have been reported for fetal and placentome size mid gestation. Reciprocal differences in birth weight have also been reported among backcrosses and F2 calves, and also exist for longer gestation length from Bos indicus sires (Bos taurus dams). Increased birth weight and gestation length occur when more Bos indicus is present in the sire vs. the dam, and when Bos indicus influence is inherited through the sire vs. the dam. There is speculation that sex-specific genomic imprinting may be involved for reciprocal birth weight differences that are analogous to mouse interspecific crosses for litter weight. Reports of hybrid vigor retention among inter se matings after the F1 have been variable historically, and this variation may relate to how the foundational F1 parents were produced (Bos indicus- vs. Bos taurus-sired). Breed-of-origin haplotype on BTA5 has been shown to affect heifer pregnancy and rebreeding among F2 Nellore-Angus cows where Nellore-derived haplotypes had much lower performance compared with Angus-derived and hybrid haplotypes. Disproportionate calf sex has been reported among reciprocal F2 Nellore (Bos indicus)-Angus (Bos taurus) with 66.6% male calves from Nellore x Angus F1 sires. When retrospectively evaluating historical literature for reciprocal crosses, it appears that several instances occur with disproportionate calf sex percentage, and this phenomenon warrants further study. The extent that potential reciprocal differences may affect post-weaning growth and carcass traits has not been widely evaluated. Recent investigations have shown reciprocal F1 differences for some cell-mediated immune responses regarding T-lymphocyte proliferation, but no differences for humoral response. There needs to be additional research that completely characterizes the X chromosome of Bos indicus and Bos taurus origins and their roles for multiple production traits. There also needs to be more investigation of non-additive and parent-of-origin effects in genetic evaluations of Bos indicus-Bos taurus composites, particularly with desired first-generation breed percentage. Improved utilization of Bos indicus cattle and crosses will be instrumental in meeting global dietary protein demands.

161 Development, deployment, and calibration of genomic selection tools to improve performance traits for Canadian beef cattle

Abstract Genomic selection has the potential to accelerate the genetic improvement rate for difficult/expensive to measure traits such as feed efficiency and fertility traits in beef cattle. To develop genomic selection tools for Canadian beef cattle, we collected or sourced phenotypic data of feed efficiency along with other traits including carcass merit, female feed intake and fertility related traits, and their genotypes from both research and commercial herds. The phenotypic data were consolidated and recorded for contemporary groups, leading to the development of data sets including 11,292 beef cattle with residual feed intake, dry matter intake, average daily gain, metabolic body weight, 7,299 to 8,081 cattle with carcass merit traits, and 1,802 to 2,792 cows with feed intake and fertility traits after quality controls. Genotype data of the animals from various single nucleotide polymorphisms (SNP) panels were merged to the same allele format of 50K, and then imputed to 770K SNPs, and eventually to whole genome sequence variants. The refined Canadian beef cattle data sets have not only allowed us to investigate genetic architectures of the beef performance traits but also enabled the development of genomic selection tools including molecular breeding values and multiple trait selection indexes with a moderate to moderately high accuracy for the traits through a cross-validation of within reference data set. The genomic selection tools have been successfully deployed to over 10,415 breeding candidates submitted by Canadian beef producers through multiple demonstration projects. The average accuracy of the molecular breeding values and multiple trait selection index of the commercial beef cattle ranged from 0.38 to 0.49 for feed efficiency and carcass merit traits, and from 0.26 to 0.38 for female feed intake and fertility traits. Current research is focusing on calibrating the genomic selection tools with larger data sets and with more advanced genomic prediction methods.

Validation and identification of new QTLs for plant and fruit developmental and composition traits in eggplant under low N conditions

Enhancing plant adaptation to low input conditions is a fundamental goal for implementing sustainable agriculture. In the present study, two eggplant (Solanum melongena) accessions (MEL1 and MEL5), two introgression lines (ILs) derived from eggplant wild relatives S. dasyphyllum (IL-M1-D1) and S. insanum (IL-M5-I9), and a heterozygous version of this last IL (ILHet-M5-I9), along with hybrids among them were evaluated under low N (LN) conditions. IL-M1-D1 carries an introgressed fragment of 4.9 Mb in homozygosis from S. dasyphyllum on chromosome 2, while IL-M5-I9 and ILHet-M5-I9 carry an introgression of 21.5 Mb on chromosome 9 in homozygosis and heterozygosis, respectively, from S. insanum. Multiple quantitative trait loci (QTLs) for several traits of interest were associated with both introgressions under LN conditions in a previous study with segregating advanced backcrosses. Here we evaluated the performance of these materials for 22 agronomic and developmental traits under low N fertilization (LN) conditions. Hybrids with the ILs enabled the study of genetic background effects on QTLs expression. The materials evaluated showed a significant phenotypic variation, particularly within hybrids segregating for the introgression from S. insanum in chromosome 9. Statistical analysis revealed no significant differences among hybrids carrying or not the introgression on chromosome 2 of S. dasyphyllum, and only slight differences were observed between the IL-M1-D1 and its recurrent parent S. melongena MEL1, suggesting a limited impact of this introgression on chromosome 2 on the phenotype variation. However, the differences observed between IL-M5-I9 and its recurrent parent S. melongena MEL5, together with the association between genotypic and phenotypic variation in hybrids segregating for this introgression, allowed the identification of 13 QTLs on chromosome 9. These results successfully validated the previously identified QTLs for flavonol content in leaves, nitrogen balanced index, fruit mean weight, and nitrogen content in leaves and, also revealed nine new QTLs associated with the introgressed genomic region in chromosome 9. This study emphasizes the influence of environmental conditions, genotypes, and genetic backgrounds on the phenotypic expression of eggplant QTLs introgressed from wild relatives and highlights the importance of QTL validation. These findings contribute valuable insights for developing new eggplant cultivars for a more sustainable agriculture, particularly with adaptation to LN conditions.

Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots

Key message We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe.Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (n = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38–0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.

Sexual dimorphism and functional allometry in scorpions: A comparative study from a neotropical species

Sexual dimorphism (SD), the divergence of secondary sexual traits between males and females within a species, can arise from diverse evolutionary forces, such as natural selection, mate choice, and intrasexual competition. Allometric scaling patterns of dimorphic traits are related to their functional roles and the different selective pressures that affect each sex. Generally, traits that threaten rivals involved in intrasexual competition tend to exhibit the highest allometric slopes. Conversely, non-sexual traits often display isometric scaling, while genitalia and traits in direct contact between the sexes during courtship and copulation typically show hypoallometry. A good approach to study patterns of SD and allometry is to complement interspecific studies with analyzes of case studies, where the functional aspect is known in detail. Here, we review the occurrence of SD and evaluation of allometry in the Order Scorpiones, allowing us to compare general trends in a broader comparative framework within the group. In addition, we examined SD and allometric slopes of multiple traits (including somatic traits used in sexual and non-sexual interactions, as well as genitalia) in adult individuals of the scorpion Timogenes elegans (Scorpiones, Bothriuridae). We found that at an interspecific level there was a variation in SD between species and morphological traits, with most traits showing a male-biased SD, except for the chelicerae, which were found to be wider in females. Regarding SD studies, we found relatively few reports of functional allometry showing differences in allometric patterns between species. The results in T. elegans follow some of the general patterns found in other scorpions. We found hypoallometry in genital traits and hyperallometry in the pedipalps of both sexes, with steeper allometric slopes observed for pedipalp height in males. These results suggest that genital traits are under stabilizing selective pressure, while pedipalps in both sexes may be under natural and sexual selective pressure. Understanding allometric patterns and their relationship to function in scorpions provides significant insights into the evolutionary pressures driving the divergence of morphological traits used in both sexual and non-sexual contexts.

Pleiotropic Quantitative Trait Loci (QTL) Mining for Regulating Wheat Processing Quality- and Yield-Related Traits.

To investigate the genetic basis of processing quality- and yield-related traits in bread wheat (Triticum aestivum L., AABBDD), a systematic analysis of wheat processing quality- and yield-related traits based on genome-wide association studies (GWASs) of 285 regional test lines of wheat from Hebei province, China, was conducted. A total of 87 quantitative trait loci (QTL), including twenty-one for water absorption (WA), four for wet gluten content, eight for grain protein content, seventeen for dough stability time (DST), thirteen for extension area (EA), twelve for maximum resistance (MR), five for thousand-grain weight (TGW), one for grain length, and six for grain width were identified. These QTL harbored 188 significant single-nucleotide polymorphisms (SNPs). Twenty-five SNPs were simultaneously associated with multiple traits. Notably, the SNP AX-111015470 on chromosome 1A was associated with DST, EA, and MR. SNPs AX-111917292 and AX-109124553 on chromosome 5D were associated with wheat WA and TGW. Most processing quality-related QTL and seven grain yield-related QTL identified in this study were newly discovered. Among the surveyed accessions, 18 rare superior alleles were identified. This study identified significant QTL associated with quality-related and yield-related traits in wheat, and some of them showed pleiotropic effects. This study will facilitate molecular designs that seek to achieve synergistic improvements of wheat quality and yield.

The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution.

Complex traits are determined by many loci-mostly regulatory elements-that, through combinatorial interactions, can affect multiple traits. Such high levels of epistasis and pleiotropy have been proposed in the omnigenic model and may explain why such a large part of complex trait heritability is usually missed by genome-wide association studies while raising questions about the possibility for such traits to evolve in response to environmental constraints. To explore the molecular bases of complex traits and understand how they can adapt, we systematically analyzed the distribution of SNP heritability for ten traits across 29 tissue-specific Expression Quantitative Trait Locus (eQTL) networks. We find that heritability is clustered in a small number of tissue-specific, functionally relevant SNP-gene modules and that the greatest heritability occurs in local "hubs" that are both the cornerstone of the network's modules and tissue-specific regulatory elements. The network structure could thus both amplify the genotype-phenotype connection and buffer the deleterious effect of the genetic variations on other traits. We confirm that this structure has allowed complex traits to evolve in response to environmental constraints, with the local "hubs" being the preferential targets of past and ongoing directional selection. Together, these results provide a conceptual framework for understanding complex trait architecture and evolution.

A Genome-Wide Association Study Approach to Identify Novel Major-Effect Quantitative Trait Loci for End-Use Quality Traits in Soft Red Winter Wheat.

Wheat is used for making many food products due to its diverse quality profile among different wheat classes. Since laboratory analysis of these end-use quality traits is costly and time-consuming, genetic dissection of the traits is preferential. This study used a genome-wide association study (GWAS) of ten end-use quality traits, including kernel protein, flour protein, flour yield, softness equivalence, solvent's retention capacity, cookie diameter, and top-grain, in soft red winter wheat (SRWW) adapted to US southeast. The GWAS included 266 SRWW genotypes that were evaluated in two locations over two years (2020-2022). A total of 27,466 single nucleotide markers were used, and a total of 80 significant marker-trait associations were identified. There were 13 major-effect quantitative trait loci (QTLs) explaining >10% phenotypic variance, out of which, 12 were considered to be novel. Five of the major-effect QTLs were found to be stably expressed across multiple datasets, and four showed associations with multiple traits. Candidate genes were identified for eight of the major-effect QTLs, including genes associated with starch biosynthesis and nutritional homeostasis in plants. These findings increase genetic comprehension of these end-use quality traits and could potentially be used for improving the quality of SRWW.

Genomic-inferred cross-selection methods for multi-trait improvement in a recurrent selection breeding program

The major drawback to the implementation of genomic selection in a breeding program lies in long-term decrease in additive genetic variance, which is a trade-off for rapid genetic improvement in short term. Balancing increase in genetic gain with retention of additive genetic variance necessitates careful optimization of this trade-off. In this study, we proposed an integrated index selection approach within the genomic inferred cross-selection (GCS) framework to maximize genetic gain across multiple traits. With this method, we identified optimal crosses that simultaneously maximize progeny performance and maintain genetic variance for multiple traits. Using a stochastic simulated recurrent breeding program over a 40-years period, we evaluated different GCS methods along with other factors, such as the number of parents, crosses, and progeny per cross, that influence genetic gain in a pulse crop breeding program. Across all breeding scenarios, the posterior mean variance consistently enhances genetic gain when compared to other methods, such as the usefulness criterion, optimal haploid value, mean genomic estimated breeding value, and mean index selection value of the superior parents. In addition, we provide a detailed strategy to optimize the number of parents, crosses, and progeny per cross that can potentially maximize short- and long-term genetic gain in a public breeding program.

Coordination between water relations strategy and carbon investment in leaf and stem in six fruit tree species.

The water relation strategy is a key issue in climate change. Given the difficulty of determining water relations strategy, there is a need for simple traits with a solid theoretical basis to estimate it. Traits associated with resource allocation patterns along a 'fast-slow' plant economics spectrum are particularly compelling, reflecting trade-offs between growth rate and carbon allocation. Avocado (Persea americana ), fig tree (Ficus carica ), mandarin (Citrus reticulata ), olive (Olea europaea ), pomegranate (Punica granatum ), and grapevine (Vitis vinifera ) were characterised in terms of iso-anisohydric strategy through stomatal behaviour, water potential at the turgor loss point (TLP), and hydroscape area. Additionally, the association of these metrics with leaf mass per area (LMA) and wood density (WDen) was explored. We observed high coordination between LMA and WDen, and both traits were related to metrics of water relation strategy. More anisohydric species tended to invest more carbon per unit leaf area or unit stem volume, which has implications for hydraulic efficiency and water stress tolerance. WDen and TLP were the most powerful traits in estimating the water relation strategy for six fruit species. These traits are easy to measure, time-cost efficient, and appear central to coordinating multiple traits and behaviours along the water relations strategies.

Native arbuscular mycorrhizal fungi drive ecophysiology through phenotypic integration and functional plasticity under the Sonoran desert conditions.

Knowledge is scarce to what extent environmental drivers and native symbiotic fungi in soil induce abrupt (short-term), systemic (multiple traits), or specific (a subset of traits) shifts in C3 plants' ecophysiological/mycorrhizal responses. We cultivated an emblematic native C3 species (Capsicum annuum var. glabriusculum, "Chiltepín") to look at how the extreme heat of the Sonoran desert, sunlight regimes (low = 2, intermediate = 15, high = 46 mol m2 d-1) and density of native arbuscular mycorrhizal fungi in soil (low AMF = 1% v/v, high AMF = 100% v/v), drive shifts on mycorrhizal responses through multiple functional traits (106 traits). The warming thresholds were relentlessly harsh even under intensive shade (e.g. superheat maximum thresholds reached ranged between 47-63°C), and several pivotal traits were synergistically driven by AMF (e.g. photosynthetic capacity, biomass gain/allometry, and mycorrhizal colonization traits); whereas concurrently, sunlight regimes promoted most (76%) alterations in functional acclimation traits in the short-term and opposite directions (e.g. survival, phenology, photosynthetic, carbon/nitrogen economy). Multidimensional reduction analysis suggests that the AMF promotes a synergistic impact on plants' phenotypic integration and functional plasticity in response to sunlight regimes; however, complex relationships among traits suggest that phenotypic variation determines the robustness degree of ecophysiological/mycorrhizal phenotypes between/within environments. Photosynthetic canopy surface expansion, Rubisco activity, photosynthetic nitrogen allocation, carbon gain, and differential colonization traits could be central to plants' overall ecophysiological/mycorrhizal fitness strengthening. In conclusion, we found evidence that a strong combined effect among environmental factors in which AMF are key effectors could drive important trade-offs on plants' ecophysiological/mycorrhizal fitness in the short term.

Maize yields have stagnated in sub-Sahara Africa: a possible transgenic solution to weed, pathogen and insect constraints.

Despite major breeding efforts by various national and international agencies, yields for the ~40 million hectares of maize, the major food crop in sub-Saharan Africa, have stagnated at <2 tons/ha/year for the past decade, one-third the global average. Breeders have succeeded in breeding increased yield with a modicum of tolerance to some single-weed or pathogen stresses. There has been minimal adoption of these varieties because introgressing polygenic yield and tolerance traits into locally adapted material is very challenging. Multiple traits to deal with pests (weeds, pathogens, and insects) are needed for farmer acceptance, because African fields typically encounter multiple pest constraints. Also, maize has no inherent resistance to some of these pest constraints, rendering them intractable to traditional breeding. The proposed solution is to simultaneously engineer multiple traits into one genetic locus. The dominantly inherited multi-pest resistance trait single locus can be bred simply into locally adapted, elite high-yielding material, and would be valuable for farmers, vastly increasing maize yields, and allowing for more than regional maize sufficiency. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

AI can see you: Machiavellianism and extraversion are reflected in eye-movements.

Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms. Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron. Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.

Network Analysis of Brain and Bone Tissue Transcripts Reveals Shared Molecular Mechanisms Underlying Alzheimer's Disease and Related Dementias and Osteoporosis.

Alzheimer's disease and related dementias (ADRD) and osteoporosis (OP) are 2 prevalent diseases of aging with demonstrated epidemiological association, but the underlying molecular mechanisms contributing to this association are unknown. We used network analysis of bone and brain transcriptomes to discover common molecular mechanisms underlying these 2 diseases. Our study included RNA-sequencing data from the dorsolateral prefrontal cortex tissue of autopsied brains in 629 participants from ROSMAP (Religious Orders Study and the Rush Memory and Aging Project), with a subgroup of 298 meeting criteria for inclusion in 5 ADRD categories, and RNA array data from transiliac bone biopsies in 84 participants from the Oslo study of postmenopausal women. After developing each network within each tissue, we analyzed associations between modules (groups of coexpressed genes) with multiple bone and neurological traits, examined overlap in modules between networks, and performed pathway enrichment analysis to discover conserved mechanisms. We discovered 3 modules in ROSMAP that showed significant associations with ADRD and bone-related traits and 4 modules in Oslo that showed significant associations with multiple bone outcomes. We found significant module overlap between the 2 networks in modules linked to signaling, tissue homeostasis, and development, and Wingless-related integration site (Wnt) signaling was found to be highly enriched in OP and ADRD modules of interest. These results provide translational opportunities in the development of treatments and biomarkers for ADRD and OP.

Consistent signatures in the human gut microbiome of longevous populations

ABSTRACT Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.

Balancing the nutrient needs: Optimising growth in Malus sieversii seedlings through tailored nitrogen and phosphorus effects.

The impact of nitrogen (N) and phosphorus (P) on the physiological and biochemical processes crucial for tree seedling growth is substantial. Although the study of plant hydraulic traits in response to N and P is growing, comprehensive research on their combined effects remains limited. Malus sieversii, a key ancestral species of modern apples and a dominant species in Xinjiang's Tianshan wild fruit forest, is witnessing a decline due to climate change, pests and diseases, compounded by challenges in seedling regeneration. Addressing this, a 4-year study was conducted to determine the optimal fertilisation method for it. The experiment explored varying levels of N (N10, N20 and N40) and P (P2, P4 and P8), and their combined effects (N20Px: N20P2, N20P4, N20P8; NxP4: N10P4, N20P4 and N40P4), assessing their impact on gas exchange, hydraulic traits, and the interplay among functional traits in Tianshan Mountains' M. sieversii seedlings. Our study revealed that All N-inclusive fertilisers slightly promoted the net photosynthetic rate. N10 significantly increasing leaf hydraulic conductivity. All P-inclusive fertilisers adversely affected hydraulic conductivity. P8, N20P4 and N20P8 notably increased seedlings' vulnerability to embolism. Seedlings can adaptively adjust multiple functional traits in response to nutrient changes. The research suggests N10 and N20 as the most effective fertilisation treatments for M. sieversii seedlings in this region, while fertilisation involving phosphorus is less suitable. This study contributes valuable insights into the specific nutrient needs of it, vital for conservation and cultivation efforts in the Tianshan region.

Evaluating hydrologist specialist suitability applying the Holland’s RIASEC model using FIKR (facet, insight, knowledge, and resilience) profiling assessment tool

This study applies Holland's RIASEC model using FIKR (facet, insight, knowledge, and resilience) profiling assessment tool to evaluate the suitability of individuals for hydrologist specialist roles by focusing on the Investigative (I) and Realistic (R) traits, which are crucial for success in this field. The research analyzed data from 250 respondents to identify those with the highest alignment for hydrology careers, particularly regarding their analytical and practical abilities. The study found that only one individual possessed the ideal combination of high I and R scores with a lower Conventional (C) score, indicating strong potential for success in Hydrology. Additionally, 24 other individuals demonstrated high I and R traits but also exhibited high C scores, suggesting they may be better suited for roles that require a balance between investigative tasks and structured environments. These findings underscore the need for a comprehensive assessment of multiple RIASEC traits, a crucial strategy for ensuring proper career alignment and job satisfaction in environmental science roles.

Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus.

Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.

Characterization of bovine vaginal microbiota using 16S rRNA sequencing: associations with host fertility, longevity, health, and production

Due to their potential impact on the host’s phenotype, organ-specific microbiotas are receiving increasing attention in several animal species, including cattle. Specifically, the vaginal microbiota of ruminants is attracting growing interest, due to its predicted critical role on cows’ reproductive functions in livestock contexts. Notably, fertility disorders represent a leading cause for culling, and additional research would help to fill relevant knowledge gaps. In the present study, we aimed to characterize the vaginal microbiota of a large cohort of 1171 female dairy cattle from 19 commercial herds in Northern France. Vaginal samples were collected using a swab and the composition of the microbiota was determined through 16S rRNA sequencing targeting the V3–V4 hypervariable regions. Initial analyses allowed us to define the core bacterial vaginal microbiota, comprising all the taxa observed in more than 90% of the animals. Consequently, four phyla, 16 families, 14 genera and a single amplicon sequence variant (ASV) met the criteria, suggesting a high diversity of bacterial vaginal microbiota within the studied population. This variability was partially attributed to various environmental factors such as the herd, sampling season, parity, and lactation stage. Next, we identified numerous significant associations between the diversity and composition of the vaginal microbiota and several traits related to host’s production and reproduction performance, as well as reproductive tract health. Specifically, 169 genera were associated with at least one trait, with 69% of them significantly associated with multiple traits. Among these, the abundances of Negativibacillus and Ruminobacter were positively correlated with the cows’ performances (i.e., longevity, production performances). Other genera showed mixed relationships with the phenotypes, such as Leptotrichia being overabundant in cows with improved fertility records and reproductive tract health, but also in cows with lower production levels. Overall, the numerous associations underscored the complex interactions between the vaginal microbiota and its host. Given the large number of samples collected from commercial farms and the diversity of the phenotypes considered, this study marks an initial step towards a better understanding of the intimate relationship between the vaginal microbiota and the dairy cow’s phenotypes.