Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most problematic diseases for rice production, threatening global food security. Genetic resistance to some M. oryzae races can be achieved using major resistance genes that recognize their corresponding fungal avirulence genes. Weedy rice, a close relative of cultivated rice that competes with the crop, has evolved unique genetic mechanisms to resist M. oryzae infections; thus, weedy rice can serve as an excellent resource for blast control. In this study, we assessed disease scores of 183 F5 and F6 recombinant inbred lines (RILs) derived from a weedy rice × crop biparental mapping population and their parental lines, a Black Hull Awn weedy rice strain (PI 653413, RR14) and the aus-196 rice variety, using four distinct common U.S. blast races (IB33, IG1, IE1K, and IC17) under greenhouse conditions. All the parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance. Genotyping-by-sequencing of the RIL population and parents generated 1,498 single-nucleotide polymorphisms, which were used to construct a linkage map, and quantitative trait locus (QTL) mapping of blast resistance was performed using r/qtl. A single major blast resistance QTL on chromosome 12 was mapped to the Pi-ta/Pi39(t)/Ptr locus. Identification of Pi-ta/Pi-39(t)/Ptr as the key contributor to blast resistance in weedy rice provides insight into the evolution and adaptation of weedy rice and can aid in the development of blast-resistant rice varieties through marker-assisted selection.

Castor (Ricinus communis L.) in Euphorbiaceae family is an important tropical crop cultivated for seeds containing industrially valuable oil. With economic development, demand for castor beans and oil is rapidly increasing, yet production is severely affected by fungal diseases, particularly Fusarium and Macrophomina, due to limited advanced breeding methods. F. oxysporum f. sp. ricini -induced wilt in castor is a major pathogenic factor responsible for severe yield losses. Wilt resistance, a complex trait controlled by quantitative trait loci (QTLs), was investigated in this study by developing a linkage map and identifying novel QTLs in castor using F2:3 population. The was developed from the cross between two castor inbred lines, 48 - 1 (Jwala) and the wilt-susceptible genotype JI-35, and screened under pot conditions. Linkage map was developed using 71 SSR markers. A genetic map comprising 13 linkage groups, spanning a total of 1,028.7cM centimorgans (cM). Analysis of genotypic and phenotypic data from the mapping population, evaluated for wilt in pots, identified two QTLs on LG1 and 6 explaining 12.44-16.58% of phenotypic variation. PCR amplification using linked markers on LG 1 in resistant and susceptible F₄ families of the mapping population demonstrated that these markers effectively distinguish plants resistant or susceptible to wilt disease. These markers can be utilized for developing resistant varieties via backcross breeding and for screening germplasm at the seedling stage.

ABSTRACTIn legumes, flowering time is regulated by genes responsive to temperature and photoperiod, presenting challenges for high‐latitude lentil producers who must adapt cultivars to short growing seasons and extended daylight hours. Therefore, prolonged vegetative periods are favored in those areas. To address this, we studied a recombinant inbred line (RIL) population, derived from a cross between the adapted cultivar CDC‐Milestone and the non‐adapted line ILL8006, to investigate phenology‐related traits under long‐day conditions in western Canada. Significant variation in days to emergence (DTE), days to flowering (DTF), and days to pod maturity (DTM) enabled analysis of the vegetative (VegP) and reproductive (RepP) periods within the population. We constructed a high‐density genetic linkage map using molecular markers linked to genes in the Lcu.2RBY reference genome, identifying quantitative trait loci (QTLs) for those traits across four site‐years in Saskatchewan. Differential expression analysis of known flowering time genes enhanced interpretation of the QTL results for flowering time. Three major DTE QTLs (qDTE2/3.II, qDTE2/3.III, and qDTE2/3.IV) on chromosome 2 explained 16%–28% phenotypic variability, depending on the environment, with in silico analysis identifying six curated genes as putative candidates within that region. A key DTF QTL (qDTF6.I) on chromosome 6 accounted for 23%–56% of phenotypic variability, harboring a homolog of the FLOWERING LOCUS T gene, whose role was explored alongside other candidate genes. Dissecting the vegetative period into DTE and DTF revealed distinct genetic controls for each trait, enabling breeders to combine early or late emergence and flowering to optimize adaptation and yield in diverse agroclimatic conditions.

Herbivory is destructive for crop production in many regions worldwide. The induced plant response to herbivores promotes resistance; therefore, characterizing the mechanisms underlying natural host resistance is highly important. However, the genetic components of resistance to herbivores in the staple food crop soybean remain elusive. Here, a key defense gene, GmMYC3, was identified via joint linkage and association mapping in soybean. GmMYC3 encodes an MYC2 transcription factor that is rapidly activated after jasmonic acid treatment or herbivore attack and confers resistance to a major pest, the common cutworm (CCW), in soybean. GmMYC3 positively regulates multiple biotic stress-related genes, among which GmMYC3 triggers high expression of Kunitz-type trypsin inhibitors alongside its homolog GmMYC1 and downstream GmWRKY56. GmMYC3 overexpression results in massive accumulation of trypsin inhibitors in soybean leaves, interferes with the protein digestion and absorption function in larvae that are fed these leaves, and retards larval and pupal development of the CCW. The results of the field tests of the transgenic plants corroborate the defense role of GmMYC3. Evolutionary and population genetic analyses suggest that the elite haplotype of GmMYC3 contributes to resistance against the CCW without significant reduction in seed yield and quality. Notably, this haplotype appears at a low frequency in domesticated germplasms. This study sheds light on the molecular mechanism underlying plant resistance to the CCW and provides potentially valuable resources for breeding soybean plants with elevated resistance against this pest.

BackgroundTetrad sterility-type cytoplasmic male sterility (T-CMS) is characterized by sterile pollen grains that stick together to form a tetrad-like structure (tetrad pollen). T-CMS has been observed in interspecific hybrids with the cytoplasm of Solanum verrucosum (2n = 2x = 24) and in potato cultivars with the cytoplasm of S. stoloniferum (2n = 4x = 48).ResultsIn this study, we developed a BC1 population from a T-CMS-type F1 hybrid (S. verrucosum PI 498061 × 2x breeding clone) backcrossed with S. verrucosum PI 498061. We then generated two sib-mated and two self-mated populations from the BC1 plants. Among the 361 plants across these five populations, we identified plants with varying degrees of fertility restoration. Their pollen phenotypes included normal fertile pollen, tetrad pollen with acetocarmine-stainable grains, tetrad pollen containing only premature pollen, and solitary sterile pollen. Pollen tube germination was confirmed for some stained tetrad pollen grains. We measured the frequencies of normal pollen, stained pollen, and tetrad pollen in all plants. The frequencies of normal and stained pollen were strongly correlated, but both were weakly correlated with tetrad pollen frequency. A linkage map with 648 SNP loci was constructed, and QTL analysis was performed for these three frequencies. Five QTLs (QTL1, QTL3, QTL5, QTL11a, and QTL11b on chromosomes 1, 3, 5, and 11, respectively) were identified. Among these, QTL5 and QTL11a showed strong associations with the normal and stained pollen frequencies (R2 = 39%), while QTL1 and QTL3 were strongly linked to the tetrad pollen frequency (R2 = 84%). In QTL1 and QTL11a, S. verrucosum-type homozygotes improved pollen normality, whereas in QTL3 and QTL5, S. verrucosum-type homozygotes reduced pollen quality, resulting in tetrad pollen.ConclusionsAt least two genetic effects involving five QTLs are necessary to restore fertility in the T-CMS lines: one affecting maturation and stainability, and the other for separating tetrad pollen into individual pollen grains.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07657-6.

BackgroundEnterococcus faecalis is one of the leading causes of bacterial infectious diseases. Describing this infection-inducing pathogen can facilitate evidence-based infection prevention and control. Yet clinical isolates of E. faecalis are difficult to structurally distinguish from non-clinical isolates, so a more precise and comprehensive typing assay is needed to equip us for this challenge. With its high accuracy and completeness, Whole-genome sequencing (WGS) has initiated a technological revolution in exploring the genetic variation of microbes. We aimed to investigate the use of WGS in characterizing the phylogenetic and pathogenic features of E. faecalis clinical isolates in the northern Chinese city of Tianjin. We analyzed these isolates’ sequence types (STs), their phylogenetic relationship to their global counterparts, their possible domestic spread events, their genetic linkage and the possible within-hospital transmission. We also screened their profiles of antibiotic resistance genes (ARGs), virulence genes, pathogenicity islands (PAIs), and chromosome-encoded type IV secretion system (CE-T4SS). Furthermore, we verified the ARG profiles with the antimicrobial susceptibility results.ResultsAmong the 53 clinical E. faecalis isolates, we identified 15 known STs and reported 2 novel STs (ST1970 and ST1971). Three dominant STs exhibited different clustering patterns: ST16 isolates grouped with other Chinese isolates, ST745 isolates formed a separate cluster, and ST179 isolates overlapped with other global isolates. Isolates within some STs exhibited closer pairwise single nucleotide polymorphism (SNP) distances, but direct transmission was unlikely due to the lack of coincidence between the phylogenetically close isolates. Although local isolates generally carried a small number of ARGs and multiple virulence genes, isolates assigned to distinct STs varied in the distributions of ARGs, virulence genes, PAIs, and CE-T4SS. Also, the ARG profiles correlated well with their antibiotic-resistant phenotypes.We demonstrated for the first time the phylogenetic and pathogenic characterization of E. faecalis clinical isolates in the Tianjin area. Additionally, we revealed a robust correlation between these features and the STs of the isolates, indicating clinical isolates belonging to different STs might vary in pathogenic ability.ConclusionsWGS exhibited excellent capabilities in characterizing local clinical E. faecalis, making it a potential tool for epidemiological studies and infection management. In the meantime, fully exploiting the use of genomic data from local clinical strains can enhance antimicrobial resistance surveillance and provide insights into potential pathogenicity, aiding the development of more effective treatment strategies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04487-2.

Net-form net blotch (NFNB) is a devastating fungal disease for barley. Three potentially novel QTL for resistance and identified SNP markers can contribute to the global control efforts of NFNB. Pyrenophora teres f. teres, the fungus responsible for the barley disease, net-form net blotch (NFNB), leads to considerable yield and quality reductions. This research involved collecting phenotypic and genotypic data from a barley doubled haploid (DH) mapping population consisting of 277 lines, which were exposed to the highly virulent Ptt isolate GPS18. The DH lines were derived via anther culture from second-generation hybrids of a cross between the disease-resistant barley cultivar Avcı 2002 ("A") and the susceptible cultivar Bülbül 89 ("B"). Anther pretreatment with 1.0M mannitol resulted in a statistically superior response compared to 0.7M mannitol in the F2 progeny of the A × B cross. The highest callus induction rate was 37.6% in the "Br_Ind" medium, and the highest green plant formation rate was 24.7% in the "PD_Reg" medium. The use of sequencing-based diversity array technology (DArT-seq) identified 9170 SNP markers, which facilitated the creation of a linkage map spanning 1682.97cM, with an average density of 1.49 markers/cM. Quantitative trait loci (QTL) analysis identified three QTL associated with Ptt resistance located on chromosomes 3H, 4H, and 6H. All three can be considered novel with the 3H QTL mapping in between Rpt1 and QRptta3, the 4H QTL maps to a distinct region of Rpt7, and the 6H QTL maps in between the Qns-6H.3 and SFNB-6H-33.74 loci. The SNPs associated with disease resistance identified within these QTL offer a foundation for developing DNA-based tests for resistance.

Leaf rust (LR) is one the most widely distributed and serious pathogen hampering the wheat production globally. To combat the continuous evolution of pathogens and breakdown of resistance, matching resistance genes must be discovered at the same pace from the diverse sources. In this study, we identified the US genome species Aegilops kotschyi acc pau 396, which is resistant to the Indian Puccinia triticina pathotypes 109R31-1 (77 − 5), 21R55 (104-2), and 121R60-1 (77 − 9). An LR resistance introgression line, ILkots was developed from this accession of Aegilops kotschyi in the background of Triticum aestivum cultivar PBW343. To examine the genetics of transferred resistance, a mapping population of 222 F3:4 plants was generated by crossing ILkots with the LR-susceptible cultivar WL711NN. Field experiments were conducted using a randomized complete block design (RCBD). Genetic analysis revealed that resistance was conferred by a single, dominant gene temporarily designated as Lrkots. Bulked segregant analysis (BSA) in combination with AFFYMETRIX 35 K Wheat Breeders’ AXIOM array mapped Lrkots on chromosome 3DL. A partial genetic linkage map of the genomic region carrying Lrkots included five Kompetitive allele-specific PCR (KASP) markers and two simple sequence repeat (SSR) markers spanning 8.2 cM. Lrkots was flanked by the KASP marker AX-94,443,154 (0.32 cM) on the proximal end and the SSR marker Xbarc71 (7.9 cM) on the distal end, defining a 3 Mb region in the RefSeq v1.0 genome assembly. This interval contains eight candidate genes encoding protein domains involved in disease resistance responses.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-99077-7.

Stem strength is a key factor influencing lodging resistance in soybeans and other crops. To identify quantitative trait loci (QTLs) associated with stem strength in soybean, we assessed the peak forces required to break a 20 cm stem base segment for each individual within a collection of 2138 plants from eight F2 and F3 segregating populations in 2023 and 2024. These populations were derived from four crosses between soybean varieties with contrasting stem strength. Most populations exhibited an approximately normal distribution of stem strength. Using BSA-seq, we identified 17 QTLs associated with stem strength from four populations. Among these, one QTL overlapped with a previously reported locus, while the remaining 16 represented novel loci. Notably, nine loci overlapped with known lodging QTLs, suggesting a genetic relationship between stem strength and lodging. Three QTLs were repeatedly detected in multiple populations, indicating their stability. Further linkage mapping with molecular markers confirmed these three stable QTLs. Among them, qSS10 and qSS19-2 were identified as major QTLs, refined to 1.06 Mb and 1.54 Mb intervals, with phenotypic variation explained (PVE) 23.31–25.15% and 14.21–19.93%, respectively. Within these stable QTL regions, we identified 13 candidate genes and analyzed their sequence variation and expression profiles. Collectively, our findings provide a valuable foundation for future research on stem strength in soybeans and reveal novel genetic loci and candidate genes that may be utilized for the genetic improvement of soybean lodging resistance and yield stability.

Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on C. sativa cultivation and research throughout most of the 20th century has delayed crop improvement using modern breeding approaches. As a result, genetic loci contributing to key agronomic traits, including with respect to maximizing yield as a seed crop, remain largely unknown. In this study, a feminized segregating F2 mapping population, derived from a tall parent with spacious inflorescences and large seeds and a short-stature parent with compact inflorescences and small seeds, was phenotyped for key seed and agronomic traits related to yield. A mid-density Single Nucleotide Polymorphism (SNP) genotyping panel was used to generate a genetic linkage map of 291.5 cM with 455 SNPs. Quantitative Trait Locus (QTL) mapping identified major loci for hundred-seed weight—qHSW3, 26.59 percent variance explained (PVE), seed volume—qSV1, 33.24 PVE, and plant height—qPH9, 46.99 PVE. Our results provide novel target regions, associated molecular markers, and candidate genes for future breeding efforts to improve C. sativa.

Genome‑wide association studies, linkage mapping and transcriptomic analysis reveal TraesCS1B02G308200 as a candidate gene associated with nitrogen use efficiency in wheat. Enhancing nitrogen use efficiency (NUE) in wheat production can substantially increase crop productivity while minimizing nitrogen application. In this study, QTLs for NUE-related agronomic traits were detected in two populations: (1) a natural population of 243 wheat accessions from the Yellow and Huai River Valleys in China (CH population) and (2) a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero (AC population). Nine agronomic traits were evaluated under two nitrogen regimes, namely, normal and low-nitrogen stress, at two experimental sites during two growing seasons. A total of 836 and 154 QTLs were identified through association and linkage analyses, respectively, based on the low-nitrogen tolerance index of the nine traits across all environments. By further transcriptome analysis of Chilero at the jointing, anthesis and grain-filling stages, a total of 48 differentially expressed genes were identified within the colocalization interval of the two populations. A stable QTL, QYSI1B.2 (chr1B: 501.04-508.02Mb), was successfully validated in both populations. By examining local linkage disequilibrium, QYSI1B.2 was refined to a smaller physical region spanning 506.02-507.19Mb. A possible candidate gene, TraesCS1B02G308200, which encodes a WRKY transcription factor, was identified through evaluation of its expression levels. These findings provide a foundation for exploring the molecular targets underlying wheat NUE.

IntroductionLodging is a significant challenge in rice production, particularly for high-yielding cultivars. Previous research has shown that stem characteristics, such as internode length and diameter, are key determinants of lodging resistance. However, the genetic mechanisms controlling these traits remain poorly understood.MethodsTo investigate the genetic basis of lodging-related stem traits, a recombinant inbred line (RIL) population was developed from a cross between Zhenshan 97 and C309, two rice varieties with contrasting stem architectures. A high-density genetic linkage map was constructed using 3,307 bin markers generated by next-generation sequencing. Comprehensive phenotypic analysis was conducted for heading date, internode length, and diameter.ResultsA total of 54 quantitative trait loci (QTLs) were identified across the genome. Importantly, 15 pleiotropic QTLs were detected, each affecting multiple internode-related traits. These pleiotropic loci include well-known functional genes such as SCM2 and Gn1a, as well as several novel loci potentially involved in regulating stem strength and lodging resistance. Additionally, RNA-Seq analysis was performed to identify candidate genes associated with these traits. Among the 1,263 expressed genes within the 15 pleiotropic QTL regions, 183 differentially expressed genes were identified. LOC_Os06g11130 was highlighted as a key gene for further investigation. Haplotype analysis and linkage disequilibrium analysis revealed significant haplotype variation in LOC_Os06g11130, further confirming its potential role in lodging resistance.DiscusssionThis study enhances our understanding of the genetic architecture of internode traits associated with lodging resistance in rice. The identification of pleiotropic and major-effect QTLs provides valuable genetic resources for marker-assisted selection and genomic breeding, with the potential to improve lodging resistance in high-yielding rice cultivars. These findings contribute to the development of rice varieties that balance high yield potential with enhanced lodging resistance.

Helianthus annuus L. is one of the major oilseed crops worldwide, and its production is seriously affected by a highly destructive necrotrophic pathogen, Sclerotinia sclerotiorum (S. sclerotiorum). The use of resistant cultivars is the best control measure via molecular breeding; however, the gene action underlying resistance to this stress is not well-established. Here, we conducted QTL analysis for S. sclerotiorum resistance in a recombinant inbred line (RIL) population that were developed from parents with resistant (C6) and susceptible (B728) to the disease. A high-density genetic linkage map with 6059 single nucleotide polymorphism (SNP) markers and a total length of 2763 cM was developed. The lesion length (LL) and the lesion area (LA) in the field, under climate chamber conditions or greenhouse conditions, were assessed following standardized inoculation protocols. A total of 16 major QTL for LL and 12 for LA were detected across three experimental environments, explaining 1.58–32.86% of the phenotypic variation. Of these, a major-effect QTL, qSCL2.4 on chromosome 2, could explain 30.22% of phenotypic variance with alleles from parent C6 which had more increased resistance to S. sclerotiorum. Fine-mapping in the BC1F3 population narrowed the locus to a 226.7 kb interval. HaWRKY48, which encodes a WRKY transcription factor located in this region, was prioritized as the prime candidate gene. Polymorphism analysis of HaWRKY48 in 138 sunflower accessions revealed eight SNPs defining six haplotypes. Resistance was associated with Hap3 and susceptibility to Hap1/Hap6. These findings advance our understanding of the genetic mechanisms governing sunflower resistance to S. sclerotiorum and provide valuable genetic markers for molecular breeding of resistant cultivars.

Somatic mutations in long-lived conifers are rarely characterized yet offer a unique window into the spontaneous genetic forces that shape variation in plants. In Pinus taeda, dwarf phenotypes originate from abnormal branches, colloquially known as "witches' brooms", where progeny derived from the affected branch segregate for dwarfism in an apparent Mendelian 1:1 ratio. In this study, we genotyped six unrelated wind-pollinated families segregating for dwarfism using single-nucleotide polymorphism markers that had been previously positioned on a linkage map. Trait-loci association analyses identified a genomic region on linkage group eight (spanning 98-155 cM) that was strongly associated with dwarfism across unrelated families. This finding suggests that independent, de novo somatic mutations within a common genomic region are the basis for stable dwarf phenotypes in P. taeda. The implicated region is quite large and it remains to be determined if the same growth regulation gene or genes are responsible, but the shared region is evidence for disruption of a common pathway. To more formally describe the witches' broom phenomenon and distinguish mutants from pathogen-induced brooms, we propose the Latin name Ramus nanus mutatus. We discuss the contribution of somatic mutations to variation in forest trees, the potential utility of the dwarfing mutation for rootstocks in forestry seed orchards, and the next steps toward characterizing the pathways underlying dwarfism and their homology in other conifer species.

Safflower (Carthamus tinctorius L.) is a drought-resilient oilseed crop. Besides producing edible oil rich in oleic and linoleic acid, it is also used in biofuels, cosmetics, colouring dyes, pharmaceuticals and nutraceuticals. Despite its significant economic uses, availability of genetic and genomic resources in safflower are limited. We report an improved de novo genome assembly of safflower (Safflower_A2). A chromosome-level assembly of 1.15 Gb with telomeres and centromeric repeats, was constructed using PacBio HiFi reads, optical maps, Illumina short reads, and Hi-C sequencing. Safflower_A2 shows better contiguity, completeness, and high-quality annotation than previous assemblies. The assembly was further validated with the help of a single nucleotide polymorphism (SNP)-based linkage map. A genome-wide survey identified genes for comprehensive exploration of disease resistance in the safflower. Employing the de novo genome assembly as a reference, we used resequencing data of a global core-collection of 123 accessions to carry out a SNP-based genome-wide association study, which identified significant associations for several traits, their haplotypes of agronomic value, including seed oil content. Resequencing data was also applied for a pan-genome analysis which provided critical insights into genome diversity identifying an additional ∼11000 genes and their functional enrichment that will be useful for region-specific breeding lines. Our study provides insights into the genomic architecture of safflower by leveraging an improved genome assembly and annotation. Additionally, resources including high-density linkage map, marker-trait associations, and pan-genome developed in this study provide valuable resources for use in breeding and crop improvement programs by the global research community.

Ear diameter (ED) is a key agronomic trait that significantly influences maize yield and is regulated by both genetic and environmental factors. We systematically dissected the genetic basis of ED using a diverse multi-parent population of 858 recombinant inbred lines (RILs). Through an integrated approach combining quantitative trait locus (QTL) mapping and genome-wide association study (GWAS), we identified multiple stable loci associated with ED. Notably, we pinpointed two novel and significant loci on chromosomes 5 and 7, which harbor key candidate genes: Zm00001d020000, encoding a phosphatidate cytidylyltransferase involved in membrane biosynthesis, and Zm00001d016356, a putative Kinesin-like protein potentially regulating cell division. Functional annotation, haplotype, and protein structural analyses support their roles in regulating ear development. A comprehensive comparison of 13 genomic selection (GS) models, which demonstrated that the non-linear support vector regression (SVR) model achieved superior predictive accuracy. This highlights the substantial contribution of non-additive genetic effects, such as epistasis, to ED. Furthermore, we identified 45 elite RILs with stable performance across environments, providing valuable breeding materials. Our study unveils novel SNPs and candidate genes, elucidated the complex genetic architecture underlying maize ear diameter. We demonstrate that integrating GWAS and linkage mapping with advanced GS models provides a powerful strategy to dissect complex traits and deliver practical resources for accelerating yield improvement in maize breeding programs. The candidate genes identified represent promising targets for future functional validation.

Grape cluster compactness is a key trait that influences fruit quality, yield, and disease susceptibility. Understanding the genetic basis of this trait is essential for optimizing vineyard management and improving grapevine cultivars. In this study, we performed quantitative trait locus (QTL) mapping to identify genomic regions associated with cluster architecture and yield components in a bi-parental population derived from Vitis vinifera cv. Riesling × Cabernet Sauvignon. A total of 138 full-sibling progeny were evaluated over two growing seasons at Oakville, Napa Valley, California. Traditional yield-related traits were measured, including cluster number, total cluster weight, and average cluster weight. Additionally, an image-based phenotyping pipeline leveraging the foundation model Segment Anything Model (SAM) was employed to segment individual berries, measure their size and shape, and compute cluster compactness with minimal manual intervention. Trait correlations revealed that compact clusters tended to have a higher berry count but smaller berry size, highlighting the role of compactness in modulating cluster structure. Heritability estimates varied across traits, with berry dimensions and compactness displaying moderate to high heritability, indicating strong genetic control. Two parental linkage maps were constructed using a pseudo-test cross strategy. QTL mapping identified multiple loci associated with cluster architecture and yield components, with several stable QTLs detected across both years, with marker effects ranging from 7.6% to 22.1%. Notably, a QTL for cluster compactness was found in both seasons on chromosome 1 in Cabernet Sauvignon. Other stable QTLs were associated with berry size (chromosomes 6 and 17) and berry count (chromosome 5 in Cabernet Sauvignon and chromosome 7 in Riesling). Additional QTLs were detected in a single year, reflecting the influence of environmental variation. Our findings provide valuable insights into the application of foundation models requiring no prior training and minimal intervention for high-quality segmentation and enhance our understanding of the genetic architecture of cluster compactness and yield traits. The genomic regions identified in this study offer promising targets for breeding programs aimed at improving grape quality and disease resistance.

A genetic linkage map of Grifola albicans f. huishuhua (Maitake) is an important resource for chromosome analysis and the genetic basis of phenotypic variation determination. A total of 92 monokaryotic isolates were selected from the F1 generation of Q3-8 × Y1-18 in this study. Restriction site-associated DNA sequencing, as well as identification of single nucleotide polymorphisms (SNPs), was performed, aiming to illustrate a high-density genetic linkage map. A total of 1122 high-quality SNP markers were located on a map with a length of 1473.60 centimorgan (cM) by screening 589534 SNPs. This map covers 12 linkage groups (LGs) with an average genetic distance of 122.80 cM. Three quantitative trait loci (QTLs) related to the growth rate of G. albicans f. huishuhua strains were identified using the composite interval mapping method. These QTLs were mapped to linkage groups (LGs) as follows: LG3 (qmgv), LG4 (qmb), LG5 (qmd), LG8 (qrdm1, qrdm2), and LG10 (qmgrc1, qmgrc2, qmgrc3). The genes associated with mycelial growth rate and biomass production of these strains were identified. This information could be used for molecular marker-assisted selective breeding in G. albicans f. huishuhua.

BackgroundAlcohol-associated liver disease (ALD) constitutes a global health crisis, yet the molecular mechanisms driving its pathogenesis remain unresolved, critically impeding the development of effective therapeutics. A fundamental challenge is the differentiation of correlational biomarkers from the causal drivers of disease. Here, we perform a systematic characterization of the ALD causal proteome to uncover novel pathogenic mediators and prioritize therapeutic targets.MethodsWe implemented a multi-stage pipeline integrating human genetics with multi-level experimental validation. A two-sample Mendelian randomization (MR) framework, leveraging large-scale plasma proteomics and ALD GWAS data, was employed to nominate proteins causally linked to ALD. These candidates underwent functional enrichment analysis to delineate their biological roles. To rigorously control for confounding by genetic linkage, findings were validated using SMR. We then employed single-cell RNA sequencing from a murine ALD model to determine the hepatic cellular origins of the validated targets. Finally, their functional relevance was established in vivo using a chronic-plus-binge ethanol feeding mouse model.ResultsOur MR analysis identified 17 proteins with a putative causal association with ALD. Functional enrichment analysis implicated these candidates in inflammatory and immune response pathways. After stringent SMR validation, we identified four high-confidence causal proteins: TREML2 (Triggering Receptor Expressed on Myeloid cells-like 2) and MMP12 (Matrix Metallopeptidase 12) as risk factors, and PLA2R1 (Phospholipase A2 Receptor 1) and MAX (MYC Associated Factor X) as protective factors. Single-cell transcriptomics resolved the cellular sources of these proteins within the liver, identifying hepatic myeloid cells (macrophages and monocytes) as the primary source of the risk-promoting TREML2 and MMP12. In contrast, the protective protein PLA2R1 was predominantly expressed in hepatocytes, while MAX exhibited broad expression. These genetic predictions were phenocopied in our ALD mouse model; hepatic expression of Treml2 and Mmp12 was significantly upregulated, whereas Pla2r1 and Max were downregulated, corroborating their respective roles in disease pathogenesis.ConclusionBy systematically integrating genetic causal inference with multi-level functional genomics, we identify and validate four causal protein drivers of ALD. Our findings unveil a novel pathogenic axis where ALD risk is governed by a balance between pro-inflammatory, matrix-remodeling myeloid cells (driven by TREML2/MMP12) and homeostatic hepatocyte functions (mediated by PLA2R1/MAX). These genetically validated targets provide critical insights into ALD pathophysiology and represent promising, mechanistically-defined avenues for therapeutic intervention.

Cross-breeding of ornamental broodstock with close genetic relatives is one of the causes of the reduction of variations in the colour and body shape of fish offspring. The aim of this study is to analyse polymorphism in hybrid fish from butterfly female or male koi (bFK, bMK) and female or male comet (FC, MC) and other sources (osFC) and the genetic relationships between the offspring and the two parental lines based on Random Amplified Polymorphic DNA. The broodstock bFK, bMK, FC and MC was obtained from the experimental pond Ciparanje and the other comets from Parung. Hybrid fish (FC ꓫ MC, FC ꓫ bMK and OSC ꓫ BMK) were obtained from spawning process. RAPD results showed that the hybrid fish osFCbMK had a higher genetic variation by OPA-02 than by OPA-13. However, OPA-13 primer was able to detect bFKMC and FCbMK polymorphisms in the hybrid fish compared to OPA-02 primer. The OPA-13 phenogram is more suitable for detecting genetic linkage between the hybrid osFCbMK and comet parental (osFC and MC) or koi parental (bFK or bMK) by 40% and bFKMC and offspring (bFK or bMK) by 30%, compared to the OPA-02 phenogram (11% and 24% respectively. The genetic closeness between the FCbMK hybrid and the FC parental is 19% (OPA-13 phenogram) and 2% (OPA-02 phenogram). OPA-13 primer is able to detect hybrid polymorphism of butterfly koi fish and comet goldfish and genetic relationship of koi with comet.