Biology subjects

Lin, M.

Publications and source records attributed to Lin, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Proteome Dynamics Across the Blastogenic Cycle of Botryllus schlosseri Reveals Targets for Cell Immortalization

The colonial tunicate Botryllus schlosseri regenerates weekly through a cyclical process in which adult zooids are replaced by a new generation of buds. While this dynamic asexual development is a hallmark of the species, its molecular regulation remains poorly understood. This study presents the first comprehensive proteomic analysis of B. schlosseri blastogenesis at the individual zooid level, using data-independent acquisition mass spectrometry to quantify protein abundance across developmental stages. The results reveal extensive proteome remodeling between proliferating buds and degenerating zooids. Co-expression analysis identified stage-specific protein modules enriched for biosynthesis and cell cycle pathways in buds, and for apoptosis, catabolism, and metabolic remodeling in zooids. A focused comparison between takeover buds and takeover zooids uncovered distinct regulatory programs controlling proliferation and senescence. Key proteins, including CDK1, CDK2, HDAC2, and PCNA, were identified as candidate regulators of cell cycle progression. These findings provide a molecular framework for understanding regeneration in a basal chordate and offer protein targets that may enable cell cycle re-entry and long-term culture of tunicate primary cells. Summary StatementThis study maps proteome dynamics during the blastogenic cycle in Botryllus schlosseri, identifying candidate proteins that regulate cell proliferation and offer targets for tunicate cell line development.

developmental biology↗

bioRxiv2025

Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana

Climate change is threatening species with extinction, and rapid evolutionary adaptation may be their only option for population rescue over short ecological timescales. However, direct observations of rapid genetic adaptation and population dynamics across climates are rare across species. To fill this gap, we conducted a replicated, globally synchronized evolution experiment with the plant Arabidopsis thaliana for 5 years in over 30 outdoor experimental gardens with distinct climates across Europe, the Levant, and North America. We performed whole-genome sequencing on [~]70,000 surviving reproductive individuals and directly observed rapid and repeatable adaptation across climates. Allele frequency changes over time were parallel in experimental evolution replicates within the same climates, while they diverged across contrasting climates--with some allele frequency shifts best explained by strong selection between -46% to +60%. Screening the genome for signals of rapid climate adaptation identified a polygenic architecture with both known and novel adaptive genetic variants connected to important ecological phenotypes including environmental stress responses, CAM5 and HEAT SHOCK FACTORs, and germination and spring flowering timing, CYTOCHROME P450s and TSF. We found evolutionary adaptation trends were often predictable, but variable across environments. In warm climates, high evolutionary predictability was associated with population survival up to 5 years, while erratic trends were an early warning for population extinction. Together, these results show rapid climate adaptation may be possible, but understanding its limits across species will be key for biodiversity forecasting.

evolutionary biology↗

bioRxiv2025

A resource and computational approach for quantifying gene editing allelism at single-cell resolution

CRISPR-Cas9-based gene editing is a powerful approach to developing gene and cell therapies for several diseases. Engineering cell therapies requires accurate assessment of gene editing allelism because editing patterns can vary across cells leading to genotypic heterogeneity. This can hinder development of robust cell therapies. Droplet-based targeted single-cell DNA sequencing (scDNAseq) has been used to genotype targeted loci across thousands of cells enabling high-throughput assessment of gene editing efficiency. Here, we constructed a "ground truth" gene editing single-cell DNAseq atlas, along with an artifact-aware computational workflow called GUMM (Genotyping Using Mixture Models) to systematically infer single-cell allelism from these data. This resource was created by expanding CRISPR-Cas9-edited HL-60 clones that harbored distinct insertion-deletion (indel) profiles in CLEC12A and mixing them at pre-defined ratios to create artificial cocktails that mimic the potential editing diversity of a CRISPR-Cas9 experiment. This enabled assessment of technical artifacts that confound interpretation of allelism in the readouts of gene edited cells. GUMM was able to accurately genotype cells and infer the original clonal composition of the artificial cocktails even in the presence of artifacts.

bioinformatics↗

bioRxiv2025

Disabling PSGL-1 abrogates immune suppression and resistance to PD-1 blockade in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer for which there is a critical need to identify novel therapeutic targets. Herein we define PSGL-1 as a checkpoint inhibitor using a syngeneic orthotopic model of PDAC. As with PDAC patients, CD8+ T cells within murine PDAC tumors expressed high levels of PSGL-1. PSGL-1-/- mice displayed striking T cell-dependent control of primary tumors and lung metastases. Extensive spatial remodeling within PDAC tumors occurred in PSGL-1-/- mice with a dramatic loss of proliferating tumor cells and an increase in CD8+ T cell engagement of antigen-presenting cells. The prominent CD8+ T cell infiltrates included subsets of pre-exhausted T cells retaining hallmarks of stemness and multifunctional effector capacity. These changes enabled a near complete response of PDAC to therapeutic PD-1 blockade. Our findings identify PSGL-1 as a key regulator of anti-tumor immunity in PDAC, highlighting its potential as a therapeutic target to limit CD8+ T cell exhaustion and enhance immunotherapy response. SummaryHope et al describe a pivotal function of PSGL-1 in CD8+ T cell responses to pancreatic ductal adenocarcinoma. Genetic deletion of PSGL-1 elicits tumor control by increasing T cell infiltration and maintaining functional subsets, thereby promoting sensitivity to PD-1 blockade.

immunology↗

bioRxiv2025

The distribution of fitness effects varies phylogenetically across animals

1The distribution of fitness effects (DFE) describes the selection coefficients (s) of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (Pagels{lambda} = 0.84, P = 0.01). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (PGLS{lambda}, P = 0.03), and the proportion of new beneficial mutations ([Formula], P < 0.001). These findings align with Fishers Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGMs predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals. 2 Significance StatementUnderstanding how mutations affect fitness is fundamental in evolution, but little is known about how and why the distribution of fitness effects (DFE) varies across species. In this study, we examine the DFE in diverse animal populations and show that closely related species exhibit similar patterns of mutation effects, with new mutations being more deleterious in mammals compared with birds and insects. Our findings corroborate Fishers Geometric Model, which explains the variation in the DFE across species as a function of organismal complexity and long-term population size. By connecting organismal complexity and population size with the DFE, we offer a phylogenetic view into the selective forces shaping species adaptation and evolution.

evolutionary biology↗

bioRxiv2025

Accelerated genome shuffling associated with rapid evolution of sexual conflict in seed beetles

Structural variation (SV) has an extensive impact on the evolution of the genome. The diverse SV provide a material basis for genome evolution, which can affect gene expression, 3D genome structure, and even changes in complex chromosomal features through regional recombination, copy number variation, and chromosome rearrangement. Here, we assemble and compare the chromosome-level assemblies of three species (Acanthoscelides obtectus, Callosobruchus chinensis, and C. maculatus) in Bruchinae, a clade of Coleoptera that is often used as models to study sexual conflict, to investigate the influence of SV on the changes of various genomic characteristics during species evolution. Through comparative genomic analysis of Coleoptera species, we reveal extensive structural variants (SVs) within the Bruchinae family, which is linked to the ongoing activity of LINE transposons. We show that SV drive the rapid evolution of sex chromosomes and correlated with dynamic evolution of sex-biased gene expression in seed beetle species. Our analysis highlights the acquisition of novel genes on the Y chromosome through frequent gene translocations, gradually shaping them into genes exhibiting male-biased expression patterns. This underscores the Y chromosomes role in promoting sexual dimorphism evolution. Our findings reveal the significant contributions of SV to genome evolution, specifically through their influence on sex chromosome evolution and the evolutionary dynamics of sex-biased genes.

evolutionary biology↗

bioRxiv2025

A Robust Fluorogenic Substrate for Chikungunya Virus Protease (nsP2) Activity

Chikungunya virus (CHIKV) is an emerging pathogen with pandemic potential. CHIKV infection in humans is transmitted by mosquitoes and induces common symptoms of high fever, arthralgia and myalgia. Because no specific antiviral drugs for treatment of CHIKV infection are available, drug development remains a central goal. The chikungunya virus protease nsP2 (CHIKVP) has emerged as a key drug target due to its indispensable role in viral replication via cleavage of the viral polyprotein. To date, effective tools for screening for CHIKVP inhibitors that reflect the most critical polyprotein cleavage sites have been lacking, hampering drug-development efforts. We found that the recognition ability of CHIKVP is sensitive to the length of peptide substrates. In this study, we report a robust fluorogenic substrate comprising a 15-mer peptide derived from the nsP3/4 junction from the CHIKV polyprotein. This peptide is flanked by an ACC-Lys(dnp) donor-quencher pair. Our new substrate acc-CHIK15-dnp shows a 20-fold improved signal-to-noise ratio as compared to the previously reported edab8 substrate, which is also based on the nsP3/4 junction. We found acc-CHIK15-dnp is recognized only by CHIKVP but not by other alphavirus proteases. This is surprising due to the high level of sequence conservation in the alpha virus polyprotein junctions and indicates that the P-side residues are more important than the P-side sequence for effective CHIKVP cleavage. The robust signal-to-noise ratio obtained using acc-CHIK15-dnp derived from the nsP3/4 cleavage site enabled much improved small molecule HTS on CHIKV relative to other fluorogenic reporters.

biochemistry↗

bioRxiv2025

A cholinergic spinal pathway for the adaptive control of breathing

The ability to amplify motor neuron (MN) output is essential for generating high intensity motor actions. This is critical for breathing that must be rapidly adjusted to accommodate changing metabolic demands. While brainstem circuits generate the breathing rhythm, the pathways that directly augment respiratory MN output are not well understood. Here, we mapped first-order inputs to phrenic motor neurons (PMNs), a key respiratory MN population that initiates diaphragm contraction to drive breathing. We identified a predominant spinal input from a distinct subset of genetically-defined V0C cholinergic interneurons. We found that these interneurons receive phasic excitation from brainstem respiratory centers, augment phrenic output through M2 muscarinic receptors, and are highly activated under a hypercapnia challenge. Specifically silencing cholinergic interneuron neurotransmission impairs the breathing response to hypercapnia. Collectively, our findings identify a novel spinal pathway that amplifies breathing, presenting a potential target for promoting recovery of breathing following spinal cord injury.

neuroscience↗

bioRxiv2024

Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River Basin, Mt. Everest

Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mount Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5{degrees}C and 15{degrees}C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15{degrees}C, with both methane and CO2 production rate negatively correlated with altitude. While temperature sensitivity of CO2 production but not CH4 showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15{degrees}C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae and Methanotrichaceae, respectively. Besides altitude, factors like phosphorus, C-to-N ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.

ecology↗

bioRxiv2024

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations. Significance StatementDomestication of dogs to live alongside humans resulted in a dramatic shift in the pressures of natural selection. Thus, comparing dogs and wolves offers a unique opportunity to assess how these shifts in selective pressures have impacted the fitness effects of individual mutations. In this project, we use patterns of genetic variation in dogs and wolves to estimate the distribution of fitness effects (DFE), or the proportions of amino acid changing mutations with varying fitness effects throughout the genome. Overall, we find that the DFE for amino acid changing mutations is similar between dogs and wolves. Even genes thought to be most affected by domestication show a similar DFE, suggesting that the DFE has remained stable over evolutionary time.

genetics↗

bioRxiv2024

Integrative cell bin segmentation on spatial transcriptomics by Voronoi

Spatial transcriptomics is undergoing rapid advancements and iterations. It is a beneficial tool to significantly enhance our understanding of tissue organization and relationships between cells. Recent technological advancements have achieved subcellular resolution, providing much denser spot placement for downstream analysis. A key challenge for this following analysis is accurate cell segmentation and the assignment of spots to individual cells. The primary objective of this study was to evaluate the effectiveness of a new cell segmentation approach based on subcellular level spatial transcriptomic data by confirming nuclei positions and using Voronoi diagrams, compared to direct clustering with cellbin data. Our findings demonstrate that the Voronoi method not only outperforms traditional methods in providing clearer boundaries and better separation of cell types but also excels in preserving the most transcripts, addressing the issue of low capture efficiency. This integrative methodology presents a substantial advancement in spatial transcriptomics, offering improved cell type classification and spatial pattern recognition. All codes in the paper are available at the GitHub repository: https://github.com/Charlottttttte/Cell_Segmentation_Voronoi

genetics↗

bioRxiv2024

Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors

Genome-wide association studies (GWAS) and polygenic score (PGS) development are typically constrained by the data available in biobank repositories in which European cohorts are vastly overrepresented. Here, we increase the utility of non-European participant data within the UK Biobank (UKB) by characterizing the genetic affinities of UKB participants who self-identify as Bangladeshi, Indian, Pakistani, "White and Asian" (WA), and "Any Other Asian" (AOA), towards creating a more robust South Asian sample size for future genetic analyses. We assess the relationships between genetic structure and self-selected ethnic identities and use consistent patterns of clustering in the dataset to train a support vector machine (SVM). The SVM was utilized to reassign n = 1,853 AOA and WA participants at the subcontinental level, and increase the sample size of the UKB South Asian group by 1,381 additional participants. We further leverage these samples to assess GWAS performance and PGS development. We include environmental covariates in the height GWAS by implementing a rigorous covariate selection procedure, and compare the outputs of two GWAS models: GWASnull and GWASenv. We show that PGS performance derived from both GWAS models yield comparable prediction to PGS models developed with an order of magnitude larger training, and environmentally-adjusted PGS models reduce the sex-bias in predictive performance. In summary, we demonstrate how GWAS performance can be improved by leveraging ambiguous ethnicity codes, ancestry matched imputation panels, and including environmental covariates.

genetics↗

bioRxiv2024

Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations Global Biodiversity Framework (GBF). However, we lack large-scale mathematical frameworks to quantify how much genetic diversity has already been lost, let alone to predict future losses under 21st century conservation scenarios. To fill this gap, we developed an area-based spatio-temporal predictive framework of genetic diversity calibrated with population-scale genomic data of 29 plant and animal species. To estimate present genetic diversity loss with our framework, we used species habitat area and population sizes losses reported in the Living Planet Index, the Red List, and new GBF indicators across 13,808 species for the last 5 decades. Applying our evolutionary framework across these species, we estimate genetic diversity loss lags behind population and habitat area declines, with an estimated current 13-22% {pi} genetic diversity loss. However, we forecast future genetic diversity losses will reach 41-76% even if populations are not further contracted. These results highlight that safeguarding existing habitats is insufficient to maintain the genetic health of species and relying solely on continuous genetic monitoring underestimates lagging long term impacts. Significance statementGenetic diversity is crucial for both species adaptation and survival. Recently, it has been included as a target for protection in the United Nations Global Biodiversity Framework. However, we lack large-scale predictive methods to quantify current and future losses of genetic diversity across species. Here, we develop an area-based spatio-temporal predictive framework trained with high-quality genome-wide data from 29 plant and animal species to enable quantitative predictions of genetic biodiversity at global scales. We infer global genetic diversity losses are beyond the preliminary UN targets to protect 90% of genetic diversity of species, evolutionary models dramatic genetic losses will occur in the future even with habitat protection if populations across species are not recovered.

genomics↗

bioRxiv2024

Multi-Modal CLIP-Informed Protein Editing

AO_SCPLOWBSTRACTC_SCPLOWProteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

bioinformatics↗

bioRxiv2024

Endothelial cell Piezo1 promotes vascular smooth muscle cell differentiation on large arteries

Vascular stabilization is a mechanosensitive process, in part driven by blood flow. Here, we demonstrate the involvement of the mechanosensitive ion channel, Piezo1, in promoting arterial accumulation of vascular smooth muscle cells (vSMCs) during zebrafish development. Using a series of small molecule antagonists or agonists to temporally regulate Piezo1 activity, we identified a role for the Piezo1 channel in regulating klf2a levels and altered targeting of vSMCs between arteries and veins. Increasing Piezo1 activity suppressed klf2a and increased vSMC association with the cardinal vein, while inhibition of Piezo1 activity increased klf2a levels and decreased vSMC association with arteries. We supported the small molecule data with in vivo genetic suppression of piezo1 and 2 in zebrafish, resulting in loss of transgelin+ vSMCs on the dorsal aorta. Further, endothelial cell (EC)-specific Piezo1 knockout in mice was sufficient to decrease vSMC accumulation along the descending dorsal aorta during development, thus phenocopying our zebrafish data, and supporting functional conservation of Piezo1 in mammals. To determine mechanism, we used in vitro modeling assays to demonstrate that differential sensing of pulsatile versus laminar flow forces across endothelial cells changes the expression of mural cell differentiation genes. Together, our findings suggest a crucial role for EC Piezo1 in sensing force within large arteries to mediate mural cell differentiation and stabilization of the arterial vasculature.

developmental biology↗

bioRxiv2024

c-di-GMP modulates ribosome assembly by inhibiting rRNA methylation

Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial secondary messenger, with diverse functions, many of which are yet to be uncovered. Stemming from an Escherichia coli proteome microarray, we found that c-di-GMP bound to 23S rRNA methyltransferases (RlmI and RlmE). rRNA methylation assays showed that c-di-GMP inhibits RlmI activity, thereby modulating ribosome assembly. Based on molecular dynamic simulation and mutagenesis studies, we found that c-di-GMP binds to RlmI at residues R64, R103, G114, and K201. Structural simulation revealed that c-di-GMP quenches RlmI activity by inducing the closure of the catalytic pocket. Furthermore, we revealed that c-di-GMP promotes antibiotic tolerance by regulating RlmI activity, which played a role in antibiotic-resistant strains. Finally, the binding and methylation assays showed that the effect of c-di-GMP on RlmI is conserved, at least in various pathogenic bacteria. This study discovered an unexpected functional role of c-di-GMP in regulating ribosome assembly by inhibiting rRNA methylases. This study identified an unexpected but crucial member among the c-di-GMP effectors. HighlightsO_LIc-di-GMP regulates ribosome assembly in Escherichia coli. C_LIO_LIc-di-GMP inhibits rRNA methylation activity of RlmI by inducing catalytic pocket closure. C_LIO_LIc-di-GMP promotes antibiotic resistance by regulating ribosome assembly. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/597503v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@52baforg.highwire.dtl.DTLVardef@176f86dorg.highwire.dtl.DTLVardef@1afed11org.highwire.dtl.DTLVardef@f53687_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa

Alfalfa biomass can be fractionated into leaf and stem components. Leaves comprise a protein-rich and highly digestible portion of biomass for ruminant animals, while stems constitute a high fiber and less digestible fraction, representing 50 to 70% of the biomass. However, little attention has focused on stem-related traits, which are a key aspect in improving the nutritional value and intake potential of alfalfa. This study aimed to identify molecular markers associated with four morphological traits in a panel of five populations of alfalfa generated over two cycles of divergent selection based on 16-h and 96-h in vitro neutral detergent fiber digestibility in stems. Phenotypic traits of stem color, presence of stem pith cells, winter standability, and winter injury were modeled using univariate and multivariate spatial mixed linear models (MLM), and the predicted values were used as response variables in genome-wide association studies (GWAS). The alfalfa panel was genotyped using a 3K DArTag SNP markers for the evaluation of the genetic structure and GWAS. Principal component and population structure analyses revealed differentiations between populations selected for high- and low-digestibility. Thirteen molecular markers were significantly associated with stem traits using either univariate or multivariate MLM. Additionally, support vector machine (SVM) and random forest (RF) algorithms were implemented to determine marker importance scores for stem traits and validate the GWAS results. The top-ranked markers from SVM and RF aligned with GWAS findings for solid stem pith, winter standability, and winter injury. Additionally, SVM identified additional markers with high variable importance for solid stem pith and winter injury. Most molecular markers were located in coding regions. These markers can facilitate marker-assisted selection to expedite breeding programs to increase winter hardiness or stem palatability. Author SummaryThe alfalfa stem constitutes a significant portion of forage yield, accounting for 50 to 70% of biomass yield, and influences various traits including plant height, standability, and digestibility. In our study, we identified thirteen molecular markers associated with stem color, presence of stem pith parenchyma, winter standability, and winter injury in a panel of five divergent stem digestibility populations. Multivariate trait modeling enhances the correlation among traits, thereby expanding the number of markers associated via GWAS. Similarly, machine learning algorithms increase the confidence of markers initially identified by GWAS and uncover new candidate regions that could serve as associated markers. Genes harboring markers associated to the four stem traits play roles in plant growth, response to plant injury, or tolerance to cold, underscoring their potential utility in enhancing traits such as cold tolerance and forage quality in alfalfa.

genomics↗

bioRxiv2024

Genome-Wide Transcriptome Dynamics in Auxin Homeostasis During Fruit Development in Strawberry (F. x ananassa)

The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle. Consistently, genes functionating in auxin biosynthesis and conjugation, such as TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAAs), YUCCA (YUCs), and GRETCHEN HAGEN 3 (GH3s) were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like PIN-FORMED (PINs), AUXIN/INDOLE-3-ACETIC ACID proteins (Aux/IAAs), TRANSPORT INHIBITOR RESPONSE 1 / AUXIN-SIGNALING F-BOX (TIR/AFBs) and AUXIN RESPONSE FACTOR (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), BASIC REGION/ LEUCINE ZIPPER motif (bZIP), and APETALA2/Ethylene Responsive Factor (AP2/ERF) groups. These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

developmental biology↗