The co-occurrence of germline and somatic oncogenic alterations is frequently observed in breast cancer, yet their combined influence on tumour evolution and therapy resistance remains poorly defined. Through an integrated clinicogenomic analysis of more than 5,800 patients, we show that germline (g) pathogenic variants dictate the evolutionary trajectory of acquired resistance. We specifically find that gBRCA2-associated tumours are uniquely predisposed to develop acquired RB1 loss-of-function alterations, resulting in poor outcomes on standard-of-care frontline CDK4/6 inhibitor (CDK4/6i) combinations. This vulnerability is driven by a dual mechanism: baseline RB1 hemizygosity (heterozygous loss resulting in a single functional RB1 allele), which lowers the evolutionary barrier to biallelic inactivation, and ongoing homologous recombination deficiency, which promotes acquisition of RB1 loss-of-function alterations under the selective pressure of CDK4/6i. Preclinical models from gBRCA2 carriers showed near-uniform resistance to CDK4/6i, with consistent post-treatment Rb loss. Across multiple independent models and in our clinical data, PARP inhibition consistently outperformed CDK4/6i. Our findings suggest that prioritizing PARP inhibition in gBRCA2 carriers may intercept RB1-loss trajectories and delay resistance. More broadly, we establish a predictive framework for forecasting drug-resistant trajectories based on pre-treatment allelic configuration and mutational signatures.

Plant-parasitic nematodes are economically important threats to global crop production. The beet cyst nematode (Heterodera schachtii) is a crucial pest in sugar beet (Beta vulgaris ssp. vulgaris). While all species of the genus Beta are highly susceptible, the three species of the beet wild relative genus Patellifolia are entirely resistant. Recently, we cloned the Hs4 gene from P. procumbens, which confers complete resistance. In this study, we aimed to determine whether putative Hs4 orthologs exist in Beta and Patellifolia species. The Hs4 gene consisted of 4999 bp, with six exons and five introns. Patellifolia species contain highly similar Hs4 homologs. Single nucleotide polymorphisms and insertions/deletions between accessions and species could be detected. We found an exonic integration of three bases, resulting in the addition of one amino acid. Interestingly, this variant was present in single accessions of all three Patellifolia species. Beta vulgaris ssp. vulgaris contains an Hs4 homolog (BvHs4) with 60 % protein identity to Hs4. BvHs4 homologs were present in all Beta species analyzed. Further, we examined the expression patterns of Hs4 and BvHs4 homologs. While Hs4 homologs from Patellifolia species are strongly expressed in roots, BvHs4 homologs are expressed mainly in leaves. When the spatio-temporal expression of Hs4 was examined, no response to nematode inoculation was observed. These results are highly relevant for searching for functional Hs4 alleles and breeding nematode-resistant varieties.

Durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.] is a staple crop for the pasta and semolina industries, particularly in Mediterranean and semi-arid regions where climate variability poses major challenges to yield stability. This study evaluates the performance of single-environment (SE), multi-trait (MT), multi-environment (ME), and multi-trait–multi-environment (MTME) genomic prediction models across seven key traits, such as grain number per spike, grain weight per spike, number of spikelets per spike, spike length, spike weight, heading date, and plant height. Using genomic (G) and target gene-based (G2) relationship matrices with two cross-validation scenarios (CV1 and CV2), MTME models achieved the highest prediction accuracies, particularly under CV2 and sowing-by-season grouping. Modeling G2 information improved predictions for morpho-phenological traits (i.e. heading date and plant height), confirming the utility of functional allele data for capturing gene effects. MTME models effectively leveraged inter-trait and inter-environment covariance, providing biologically realistic predictions of genotype performance across simulated Mediterranean environments. These findings establish MTME genomic prediction as a powerful and scalable framework for climate-resilient durum wheat improvement, supporting predictive and data-driven breeding pipelines aimed at enhancing genetic gain and stability across years and environments.

The increasing challenges posed by climate change, resource degradation, and the demand for sustainable agriculture necessitate advanced yet accessible tools for crop improvement. TILLING and its variant, Eco-TILLING, are non-transgenic reverse genetics approaches that enable the identification of induced and naturally occurring genetic variation across diverse crop species. TILLING combines chemical mutagenesis with high-throughput mutation detection to identify functional alleles in specific genes, while Eco-TILLING facilitates the discovery of natural polymorphisms in germplasm collections and wild relatives. These techniques effectively bridge functional genomics and applied plant breeding, particularly in polyploid, orphan, and vegetatively propagated crops. However, limitations include the low frequency of true knockout mutations, the predominance of silent or weak-effect alleles, the need for extensive population screening, and the chimeric nature of M1 plants that complicates early-generation selection. Despite these constraints, TILLING-based approaches remain valuable tools for modern breeding programs, with strong regulatory acceptance and adaptability across agro-ecological conditions.

Phenol color reaction has been used to distinguish between two subspecies of Asian rice (Oryza sativa), indica and japonica. The trait is controlled by one single Phr1 gene, which encodes a PPO enzyme that catalyzes the oxidation of phenolic compounds into brown or black pigments upon contact to phenol solution. In O. sativa, ssp. indica responds to phenol chemical assay by altering the rice hull color to black, whereas ssp. japonica remains unaffected due to mutations that render the gene non-functional. Although the different characteristics between subspecies in Asian rice is well known, there is no information about the variation of this trait in African rice, Oryza glaberrima, which was originated and domesticated independently of Asian rice. In this study, we found both phenol negative and positive lines in O. glaberrima and its wild ancestor O. barthii and detected the responsible non-functional mutation (1-bp deletion) in the exon 1 of the Phr1 gene. Geographical distribution of its haplotype suggested that this mutation originated in O. barthii in Mali and was later inherited by O. glaberrima. The predominance of the non-functional Phr1 alleles in O. glaberrima lines and the occurrence of the identical haplotypes in negative group of both O. barthii and O. glaberrima suggest that the negative phenol reaction was favored during domestication and breeding selection. The presence of a selection event is also supported by low nucleotide diversity of Phr1 locus. However, genetic diversity of Phr1 persists in African rice germplasm, as the functional alleles are still present in O. glaberrima. We also compared the nucleotide diversity of Phr1 in African rice with that in Asian rice and found that their origins of the phenol responsive phenotype are independent. These findings expand the current understanding of African rice domestication and offer the valuable molecular marker for improved rice breeding.

IntroductionSorghum is a vital crop for food and nutritional security in drought-prone regions. However, the genetic potential of Sudanese Feterita landraces for stay-green (Stg) traits remains largely unexplored. MethodsThis study evaluated 133 Feterita genotypes using an integrated approach combining field phenotyping with KASP genotyping targeting the Stg3A and Stg3B QTLs. The genotypes were assessed during the 2022 season at the Gezira Research Station using an augmented design, and 14 morphological and agronomic traits were recorded for each genotype. Results and DiscussionSubstantial phenotypic variation was observed, with particularly high coefficients of variation for flowering stalks per plant (81.25%), senescence (49.09%), and grain number per panicle (43.33%). Genetic diversity analysis revealed moderate marker informativeness (GD = 0.407, I = 0.293, and PIC = 0.592). The AMOVA indicated weak population differentiation (Fst = 0.014), with 94% of the variation occurring within populations and substantial gene flow (Nm = 6.117). Pairwise Fst identified West Darfur and Blue Nile as genetically distinct, whereas Kordofan, White Nile, and Al-Gezira formed a cohesive cluster. Significant marker-trait associations were detected, including snpSB0054 (SGR1) with plant height and flowering time, snpSB0072 with panicle length, and snpSB0101 (SGR3) with grain number and seed yield. These findings highlight Feterita as a valuable reservoir of functional Stg alleles that influence senescence dynamics and drought-related yield traits. This study provides the first targeted characterization of stay-green alleles in Sudanese Feterita and lays the foundation for exploiting this germplasm in marker-assisted breeding to develop climate-resilient sorghum varieties in the future.

Flowering time is crucial for plant adaptation to regional climate conditions and for reproduction in agricultural production. Turnip (Brassica rapa ssp. rapa) is a traditional adaptive vegetable cultivated on the Qinghai-Xizang Plateau. However, little is known about the potential molecular mechanisms underlying the adaptive evolution of flowering time in turnip in different regions, especially on the Qinghai-Xizang Plateau. In this study, the key adaptive trait of flowering time, which is positively correlated with altitude, was analyzed in 104 turnip accessions grown worldwide. Whole-genome resequencing and Sanger sequencing discovered that the FRIa gene, a key regulator of flowering time in turnip, had sequence variations, with five distinct alleles and eight genotypes being defined. By combining the association analyses of FRIa genotypes and flowering time as well as genetic validation, FRIa1 was identified as a highly functional allele that contributes to delayed flowering of turnip for adaptation to the Qinghai-Xizang Plateau. Four specific SNP variations were determined to be critical for the strong function of FRIa in turnip. Our results provide new insights into the adaptation of flowering time in turnip along altitudinal gradients and shed light on the adaptive evolution of FRIa in turnip on the Qinghai-Xizang Plateau.

BackgroundPolyfunctional thiols are essential contributors to the aromatic profile of varietal white wines like Sauvignon Blanc. These compounds are released during fermentation by Saccharomyces cerevisiae cells from grape-derived precursors, with the carbon-sulfur β-lyase encoded by the IRC7 gene playing a crucial role. However, most oenological yeast strains lack the fully functional IRC7 allele, limiting their thiol-releasing ability.ResultsIn this study, we used CRISPR/Cas9-based cisgenesis to replace the native allele with the fully active IRC7L, A553 variant into four oenological S. cerevisiae strains, commonly used to produce different white and red wines. Interestingly, all cisgenic strains showed enhanced thiols release, confirming the direct role of IRC7 in their biosynthesis. Fermentation performance, including the production of ethanol and multiple metabolites, remained however unchanged. GC-MS analyses then confirmed that strain-specific profiles of aromatic molecules were also preserved, indicating that genome editing did not affect other relevant oenological traits. Importantly, the cisgenic strains released thiols even when fermenting musts with low precursors content, without the need for additional supplements.ConclusionsThis work demonstrates that targeted IRC7 gene editing via CRISPR/Cas9 is a precise and efficient strategy to enhance thiol production in oenological yeasts, without compromising fermentative behavior or aromatic identity. Importantly, although the strains are formally GMOs, the modification mimics natural allelic variation. Our findings provide a foundation for developing next-generation wine yeasts optimized for high-aroma varietal wines and support the broader application of genome editing in fermentation biotechnology.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13036-025-00613-w.

Polycythemia vera (PV) and essential thrombocythemia (ET) are chronic myeloproliferative neoplasms (MPNs), often associated with mutations in JAK2, CALR, and MPL. Differentiating PV from ET can be challenging in borderline cases, particularly when hemoglobin (Hb), hematocrit (Hct) and erythropoietin (EPO) values are inconclusive. Functional iron parameters and JAK2 variant allele frequency (VAF) may provide additional discriminatory value. To assess the diagnostic utility of transferrin saturation index (TSI), serum ferritin, EPO, and JAK2 VAF in distinguishing PV from ET, and to evaluate their association with mutational profiles. We conducted a retrospective, single-center study including 260 adult patients diagnosed with PV or ET between 2009 and 2024. Demographic, clinical, molecular, and laboratory parameters—including ferritin, TSI, EPO, Hb, Hct, and JAK2 VAF—were analyzed. Comparative and correlation analyses were performed using appropriate statistical tests. Compared to ET, patients with PV had significantly lower ferritin (median: 35.65 vs. 95.05 ng/mL), TSI (12.9% vs. 21.64%), and EPO (2.23 vs. 6.11 mIU/mL), but higher Hb (17.7 vs. 14.3 g/dL) and Hct (54.6% vs. 43.0%) (all p < 0.001). TSI discriminated PV from ET better than ferritin (p < 0.001 vs. p = 0.128). Among JAK2-mutated cases, VAF was higher in PV than ET (median: 48% vs. 21%, p = 0.003). VAF correlated inversely with ferritin, TSI, and EPO, and positively with Hct. TSI and JAK2 VAF outperform ferritin as diagnostic markers to differentiate PV from ET. Integrating functional iron parameters with molecular data improves diagnostic accuracy, particularly in clinically ambiguous cases, and supports their inclusion in MPN diagnostic algorithms.

The objective of this study was to provide the first genomic diagnosis of chronic granulomatous disease (CGD) in a referral hospital in Southern Brazil, a rare and underdiagnosed disease with limited data in the country. Six male patients (P1-P6) were clinically and genetically analyzed, through medical reports review and massively parallel sequencing by a panel for the CYBB, CYBA, NCF1, NCF2, and NCF4 genes and whole genome sequencing. The gene-scan technique was used to detect the Tyr26HisfsTer variant (ΔGT) in NCF1 and to distinguish it of its pseudogenes (ΨNCF1), which naturally have ΔGT. Variants were classified according to the American College of Medical Genetics and Genomics guidelines. Structural modelling was performed for missense variants using PyMOL and I-TASSER to verify their potential impact on the NADPH oxidase complex, which is defective in CGD. Among the clinical manifestations, the most commonly affected organs were the lungs, skin, and lymph nodes, with all patients presenting with recurrent infections and pneumonia. Adverse reactions to BCG vaccination were observed in two patients. Four patients carried variants in CYBB: (P1) p.Cys257Ser, a novel variant, and (P2) p.Cys257Arg, both classified as likely pathogenic and predicted to significantly affect the structure of NADPH oxidase, with Gibbs free energy values of 6.66 and 6.23 kcal/mol, respectively (reference value: &amp;gt;1.6 kcal/mol); p.Arg157Ter (P3), and p.Trp483Ter (P4), both classified as pathogenic and predicted to undergo nonsense-mediated mRNA decay. Gene-scan analysis revealed the ΔGT in two siblings: P5 (homozygous) and P6 (heterozygous). It was hypothesized that P6 may have an NCF1-related pseudogene lacking the ΔGT originated by unequal recombination with NCF1, resulting in the absence of functional alleles in P6. This study underscores the importance of genetic characterization for accurate diagnosis, reducing diagnosis odysseys and supporting the indication of bone marrow transplantation to prevent fatal outcomes, and reinforcing the contraindication of Bacillus Calmette–Guérin vaccination in patients with CGD.

Young-onset dementia, although rare, has a profound impact on patients and their families. One significant form, Autosomal Dominant Alzheimer's Disease (ADAD) is caused by dominantly inherited mutations in the PSEN1, PSEN2, or APP genes. Mutations of the presenilin gene cause a shift to longer Aβ peptides which aggregate faster. Importantly, there is a linear correlation between age of onset of dementia and how the mutations affect the short over long ratio of Aβ peptides. Current therapies offer only symptomatic relief and fail to address the genetic basis of the disease. Our goal is to develop a highly precise and safe genetic therapy for these patients that addresses the root cause. We have obtained iPSCs from heterozygous PSEN1 A431E carriers and developed a novel Psen1 A431E mouse model that develops Aβ plaques. We aim to design highly selective antisense oligonucleotides (ASOs) targeting a single nucleotide change in the allele carrying the PSEN1 A431E mutation, while sparing the normal PSEN allele's function. Preventing disease progression will be validated in vivo in our mouse models. Neurons derived from two PSEN1 A431E lines were used to screen several ASOs targeting the mutation. Mutant mRNA levels were significantly knocked-down, while sparing the WT allele expression, showing high selectivity with a single nucleotide difference can be reached. Two WT isogenic lines were generated as controls to assess the therapeutic effect of the treatment on the short over long Ab ratio. Upon ASO treatment, a significant decrease of long Aβ42 and Aβ43 species along with a significant increase of short Aβ37 and Aβ38 species resulted in a shift in Aβ ratio towards WT control Aβ profile. In vivo treatment with Psen1 A431E targeting ASOs in mice similarly showed high selectivity and significant target knock-down and shift in the Aβ profile by decreasing long Aβ species. We provide proof of concept that it is possible to generate active ASOs selectively targeting mutant PSEN1, addressing the genetic root cause of ADAD. Such gene therapy approach could be applied to all ADAD causing mutations and potentially addressing the disease before symptoms appear, delaying or even preventing the progression of pathology.

The objective of the study is to conduct a molecular genetic screening of garden strawberry samples for the presence of target functional alleles of genes involved in the formation of the strawberry fruit aroma complex (the FaOMT gene, which controls mesifuran production and is responsible for the fruity-caramel aroma, and the FaFAD1 gene, which is associated with the synthesis of γ-decalactone). The study was conducted using the scientific collection of living plants at the Sverdlovsk Horticultural Breeding Station in 2024–2025. The objects of the study were 40 varieties and 60 hybrids created by intervarietal hybridization within the Fragaria × ananassa species. Genotype diversity for the studied genes was assessed using PCR and electrophoretic separation of amplification products in agarose gel. To identify valuable genotypes – sources of the monogenic trait of the presence of mesifuran in fruits, the codominant molecular marker FaOMT-SI/NO was used, and to identify donors of the monogenic trait of the presence of γ-decalactone in fruits, the marker FaFAD1 was used. The Polka and Festivalnaya varieties served as positive controls for the FaOMT gene, while Aprica and Pandora served as negative controls. Salsa served as a positive control for the FaFAD1 gene, while Karmen and Polka served as negative controls. The study revealed the homozygous functional FaOMT allele in the following varieties: Akvarel, Darenka, Desna, Duet, Geyser, Italmas, Yaroslavna, Asia, Cardinal, Elsanta, Honeoye, Salsa, Sonsation, and Totem, as well as in 28 selected hybrids. Heterozygous combinations of FaOMT alleles were detected in 45 cultivars. Varieties lacking the functional FaOMT allele were also identified: Assol, Alfa, Darunok Vchitelyu, Aprica, Dukat, and Pandora. The functional state of the FaFAD1 gene allele was identified in 14 cultivar samples, including the following varieties: Aquarelle, Borovitskaya, Darenka, Darunok vchitelyu, Olvia, Cardinal, Elsanta, Florence, Florida 90, Isaura, Salsa, Pandora.

In Plasmodium vivax malaria, the Duffy Binding Protein (DBP), a key erythrocyte binding-like (EBL) protein, enables invasion of DARC (Duffy Antigen/Receptor for Chemokines) positive reticulocytes. Another EBL member, the erythrocyte binding protein 2 (EBP2, also known as EBP/ DBP2), shares structural features with DBP, suggesting a role in erythrocyte invasion. P. vivax genomes may harbour multiple ebl gene copies, though their functional role is unclear. Considering DBP and EBP2 as key vaccine candidates, this study investigates copy number variation (CNV) in these two ebl genes across Amazonian populations. Furthermore, the relationship between CNV and host DARC genotypes was investigated, as DARC is the best-characterized host receptor associated with susceptibility or resistance to P. vivax. A total of 191 P. vivax isolates from three malaria-endemic sites of the Amazon region (eastern, western, and southwestern) were analysed. DARC polymorphisms associated with functional (FY*A, FY*B) and non-functional (FY*BES) alleles were genotyped by real-time PCR with allele-specific oligonucleotides. CNV at dbp and ebp2 loci was estimated by quantitative PCR (qPCR), using the β-tubulin gene as an internal reference. Gene copy numbers were stratified by geographical origin and host DARC genotype. Amplification of dbp and ebp2 genes varied across Amazon regions. In the western region, 25% of P. vivax isolates showed dbp gene amplification (up to 8 copies), compared to 2-9% in the southwestern and eastern regions (2-3 copies). Overall, ebp2 amplification was less frequent, detected in 15% of P. vivax isolates from the western and in 1-4% from other regions. In the study areas, all individuals were DARC positives, and no association was observed between gene CNVs and DARC genotypes. This study identifies dbp and ebp2 gene amplifications in P. vivax isolates from the Amazon rainforest, with regional CNV variation but no association with any DARC-positive genotype. These findings support further investigation into gene amplifications to elucidate their biological and immunological significance in DARC-positive populations.

BackgroundRecent animal studies have revealed STING (Stimulator of interferon genes) as a potential key player in Alzheimer's disease (AD). The actual impact of human STING on AD, however, is unknown. Mouse STING studies were done in WT/WT. However, TMEM173, the human gene encodes STING, has 5 common, distinct, sometimes opposite functional alleles that result in 25 TMEM173 genotypes. Only ∼50% of whites, 36% of African Americans (AA), 22% of East Asians are WT/WT. Past STING cancer immunotherapy clinic trials, which did not consider human TMEM173 heterogeneity, all failed.Objective(1) Discover new protective and risk AD genetic factors across populations or AA-specific. (2) Establish the physiological significance of common human TMEM173 genotypes and human diseases.MethodsWe conduct a large-scale (∼15,000 individuals) case-control analysis between TMEM173 genotypes and AD using data from The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site. The data include late-onset AD (LOAD) non-Hispanic White (NHW), early-onset AD (EOAD) NHW, and AA.ResultsA common H232/HAQ TMEM173 genotype is associated with AD protection across the populations. An AA-specific TMEM173 genotype H232/Q293 increases the risk for AA males (OR = 17.7148), especially in the APOE ε3/ε3 population.ConclusionsThe findings discovered the first AA-specific high AD risk factor and established an association between human TMEM173 and AD, paving the way for STING-targeting effective AD healthcare.

Ethyl methanesulfonate (EMS) mutagenesis is widely used to generate genetic diversity in crops, but its efficiency is strongly genotype‐dependent, and which underlying mechanisms remain poorly understood. Here, a large‐scale phenotypic analysis of 420 diverse accessions of rice (Oryza sativa L.) is performed, revealing extensive variation in EMS tolerance (survival rate) and mutagenesis efficiency (mutation frequency). The Aus subpopulation consistently outperformed others for both traits. A genome‐wide association study (GWAS) identified a major locus, SRD7, linked to reduced survival rate under EMS stress. Within this locus, the Rc gene, a key regulator of proanthocyanidins biosynthesis, is identified as the candidate causal factor. Haplotype analysis showed that functional Rc alleles confer high EMS tolerance, a conclusion further validated using transgenic knockout lines. Using near‐isogenic lines (NILs), it is confirmed that Rc not only improves seed survival after EMS treatment, but also unexpectedly increases genome‐wide mutation frequency. Mechanistic studies demonstrated that Rc enhances the antioxidant capacity of seeds by elevating CAT, SOD, and POD activities, while reducing H2O2 accumulation, thereby alleviating EMS‐induced oxidative damage. The findings establish Rc as a pleiotropic regulator that enhances EMS mutagenesis efficiency, providing a feasible strategy for accelerating the development of improved rice germplasm.

Genetic variations in vernalization (Vrn), photoperiod (Ppd), and reduced plant height (Rht) genes significantly influence durum wheat adaptability. However, the systematic integration of these functional alleles into genomic prediction (GP) models has been limited. This study identified genetic markers associated with heading date (HD), flowering time (FT), and plant height (PH) via genome‐wide association study (GWAS) in 186 durum wheat [Triticum turgidum ssp. durum (Desf.) Husn.] genotypes, including landraces, old cultivars, and modern cultivars, grown in eight sowing × season environments. GWAS confirmed major loci at Rht‐B1 (Q.PH.cer‐4B), Ppd‐A1 (Q.HD.cer‐2A), Ppd‐B1 (Q.FT.cer‐2B.1), and Vrn‐A1 (Q.HD.cer‐5A), underpinning trait variation. Nineteen distinct allelic combinations (ACs) derived from Vrn‐A1, Ppd‐A1, Ppd‐B1, and Rht‐B1 showed strong selection for specific alleles (e.g., Vrn‐A1c, Ppd‐A1a, and Rht‐B1b) in modern cultivars. GP models evaluated prediction accuracy (PA) by incorporating ACs, GWAS‐derived markers (M), or both (AC‐M) as fixed effects using 4399 SNPs under single (SE) and multi‐environment (ME) scenarios. High prediction accuracies were achieved, notably in ME models (PA up to 0.93 for all analyzed traits). Incorporating functional ACs along with markers (AC‐M) yielded consistent PA improvements. These results affirm the importance of Vrn, Ppd, and Rht genes and suggest that targeted integration of functional alleles can moderately enhance GP accuracy, potentially improving durum wheat breeding efficiency under varying environmental conditions.

Reduced seed shattering is a key yield-improving trait selected during the domestication of the Asian rice, Oryza sativa, from its wild ancestor, O. rufipogon. Three quantitative trait loci, qSH1, sh4, and qSH3, are reported to be involved in the reduced seed-shattering behaviour of cultivated rice. Genotyping surveys of these loci have shown that the sh4 mutation is conserved in all cultivars, whereas the qSH1 mutation is only observed in some japonica cultivars. Furthermore, the qSH3 mutation is observed in indica and japonica cultivars; however, aus cultivars carry a functional allele of wild rice at qSH3, indicating there may be distinct genetic mechanisms in aus for its reduced seed-shattering behaviour independently of qSH1 and qSH3. Through genetic analysis of the segregating populations between an aus cultivar, Kasalath, and wild rice introgression lines carrying the domesticated allele at sh4, we detected three loci associated with the reduced seed-shattering behaviour of Kasalath. Subsequent progeny tests validated their effects on this trait. These findings indicate that there are common and distinct genetic loci governing seed-shattering reduction in rice cultivars, providing novel insights into the complex process of rice domestication. This knowledge may help improve breeding strategies to optimise yield through targeted genetic selection.

Cadmium (Cd) contamination in agricultural soils poses a significant threat to the safety of pepper (Capsicum annuum L.) products. The development of low-Cd-accumulating pepper varieties is a promising strategy to ensure food safety. To identify potential genetic targets involved in regulating Cd accumulation in pepper fruits, we conducted a genome-wide selective sweep analysis in high- and low-Cd-accumulating pepper materials. By integrating genome-wide selective sweep analysis with gene expression profiling, we identified CaDTX12 (Capana11g002353), a gene encoding a detoxification efflux carrier (DTX). Heterologous expression of CaDTX12 significantly enhanced Cd accumulation in both yeast and Arabidopsis. Silencing of CaDTX12 via VIGS resulted in a 27.8% reduction in Cd content in pepper fruits. Two genotypic variants of CaDTX12 were identified (X15-CaDTX12 and X55-CaDTX12). Among these, X15-CaDTX12 represents the functional allele, exhibiting significantly higher Cd accumulation capacity compared with X55-CaDTX12. The CaDTX12 protein is localized to the tonoplast membrane. Furthermore, CaDTX12 exhibited a consistent expression pattern with that of CaDTX1, CaHMA1, CaHMA3, CaNRAMP3, CaZIP11, and CaSOD-Fe, and the silencing of CaDTX12 led to the downregulation of these associated genes. In conclusion, our findings suggest that CaDTX12 functions in Cd transport on the vacuolar membrane, and together with proteins including CaDTX1, CaHMA1, CaHMA3, CaNRAMP3, CaZIP11, and CaSOD-Fe, it collectively promotes Cd accumulation in pepper fruits and enhances Cd tolerance. These findings provide novel insights into the molecular mechanisms underlying Cd accumulation in pepper fruits and offer potential genetic targets for developing low-Cd-accumulating pepper varieties through breeding programs.

Introduction/Background: Cardiovascular disease (CVD) is the leading cause of death for American adults and has a multifactorial onset including genetic factors. However, there is poor uptake of guideline-directed genetic testing, and the clinical utility of more routine genetic testing in the setting of CVD is uncertain. Research Questions/Hypothesis: Determine the diagnostic yield and clinical impact of a comprehensive clinical genome sequencing (cGS) test applied in a broad sample of typical CVD patients. Methods: A prospective, open-label, single arm, single-center clinical trial was conducted. Inclusion required a diagnosis of at least one among: cardiomyopathy/heart failure, aortopathy, arrhythmia, coronary or peripheral artery disease, or dyslipidemia. Participants (n=1000) received a CLIA/CAP certified genetic sequencing test that included: pathogenic and likely pathogenic variants from 215 CVD-associated genes, 4 common risk alleles for CVD, and 35 non-CVD ACMG secondary finding genes, as well as 65 functional pharmacogenetic alleles from 10 genes. The rate of new genetic diagnoses and changes in clinical management (medication changes, diagnostic tests, or new specialty consultation) occurring within 6 months of genetic test results were collected. Results: Of the 1000 participants, 50% were female, 39% self-identified as Black, and average age was 68 years (Table). A total of 167 participants received a monogenic or risk-allele finding (16.7%). Among these, 74 had CVD gene findings, roughly half of which were within three genes: TTR (n = 16), TTN (n = 14), and LDLR (n = 8). Non-CVD ACMG secondary findings occurred in 14 patients. Risk allele findings were reported in 100 participants. Among those with vs. without (n=833) a monogenic or risk allele finding, a change in management occurred in 27 (16.2%) compared to 16 (1.9%, p&lt;0.0001). The most common changes made were: a radiologic test (n=16), a referral a specialist (n=13), a new genetic diagnosis (n=11), a medication change (n=8), or a lab test (n=4)[DL1] [K2] . Pharmacogenetic findings were present in &gt;99% of patients and led to medication change recommendations in 30 patients. Conclusion(s): In this study utilization of routine genetic testing in CVD patients found functional genetic variants in ~1 in 6 patients, among whom a new genetic diagnosis or a change in management occurred in 16.2% within 6 months. Longer follow up is needed to capture the full potential impact of genetic testing.

Background: Hereditary hemorrhagic telangiectasia (HHT) and hereditary pulmonary arterial hypertension (HPAH) are genetic diseases that affect the pulmonary vasculature. HHT and HPAH are due to a haploinsufficiency in components of the bone morphogenetic protein receptor type 2 (BMPR2) pathway. Despite shared genetics, HHT and HPAH cause different pulmonary vascular lesions. In HHT, pulmonary arteriovenous malformations (pAVMs) can occur. These are abnormal shunts between arteries and veins that can lead to stroke. HPAH is characterized by extensive remodeling of the lung including the formation of plexiform lesions, convolutes of vascular channels that were described as a pathological hallmark of PAH. The pathobiology of pAVMs and plexiform lesions is incompletely understood. Recent studies suggest that a local bi-allelic loss of HHT causing genes in clonally expanding endothelial cells (ECs) might be required for AVMs to form in patients with HHT. In plexiform lesions, clonal EC expansion was also described. Hypothesis: We hypothesized that local somatic mutations in ECs might be involved in the pathogenesis of pulmonary vascular lesions in HHT and HPAH. Aims: We here aimed at detecting somatic mutations in pulmonary vascular lesions of a patient with HHT and end-stage PAH caused by a mutation in ENG . Methods: Targeted deep sequencing of 3 HHT causing genes and 11 vascular malformation associated genes was performed on 4 pAVMs and 14 plexiform lesions of the patient. Results: The disease-causing germline mutation in ENG was detected in every sample. No somatic mutation in the functional allele of ENG was detected in the pulmonary vascular lesions. However, we identified a somatic mutation in the gene encoding for Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Alpha ( PIK3CA) in one of the plexiform lesions. This mutation is a confirmed activating somatic mutation in the Catalogue Of Somatic Mutations In Cancer that was previously functionally confirmed as a moderately potent oncogenic mutation. Conclusion and Outlook: We here describe a rare case of an ENG mutation carrier with HHT and HPAH. We identified a somatic activating mutation in PIK3CA in one of her plexiform lesions. To explore if the mutation contributes to the overgrowth of ECs in a plexiform lesion on a background of a haploinsufficiency in ENG , we are performing functional studies on iPSC-derived ECs from this patient after introduction of the mutation in PIK3CA by Crispr/Cas9.