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<title>bioRxiv Subject Collection: Genetics Plant Biology</title>
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This feed contains articles for bioRxiv Subject Collection "Genetics Plant Biology"
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739920v1?rss=1">
<title>
<![CDATA[
Characterization of NPR-14 in the Regulation of Sleep-Like Behaviour in Caenorhabditis elegans 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739920v1?rss=1
</link>
<description><![CDATA[
Sleep-like quiescence is an evolutionarily conserved state essential for physiological homeostasis; however, its dysregulation can lead to sleep disorders such as narcolepsy, which can be caused by abnormal neuropeptide signaling. In Caenorhabditis elegans, the G-protein-coupled receptor NPR-14 belongs to the orexin/allatotropin receptor family and has been proposed as a homolog of mammalian orexin receptors. Using npr-14 loss-of-function (lf) mutants, we demonstrate that NPR-14 promotes arousal and inhibits sleep-like quiescence. npr-14(lf) mutants exhibit prolonged quiescence, reduced locomotion, impaired sensory responses, and metabolic defects including elevated fat accumulation and decreased feeding and egg-laying. NPR-14 is expressed in ASH and ASI sensory neurons and in GABAergic DD, VD, and VC motor neurons, positioning it to modulate both sensory-motor integration and motor output directly. Genetic epistasis analysis revealed that NPR-14 functions upstream of EGL-4/protein kinase G (PKG): egl-4 loss-of-function suppressed the enhanced quiescence of npr-14 mutants, while egl-4 gain-of-function phenotypes were not enhanced by loss of npr-14. Caffeine treatment partially suppressed npr-14 mutant quiescence, suggesting convergence with adenosine-sensitive arousal pathways. These findings establish NPR-14 as a wake-promoting GPCR that inhibits EGL-4/PKG signalling to regulate quiescence and arousal. The NPR-14EGL-4 axis suggests functional parallels to arousal regulation in other systems.
]]></description>
<dc:creator><![CDATA[ Chin-Sang, I., Torki, F., Bendena, W. G. ]]></dc:creator>
<dc:date>2026-07-25</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739920</dc:identifier>
<dc:title><![CDATA[Characterization of NPR-14 in the Regulation of Sleep-Like Behaviour in Caenorhabditis elegans]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-25</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739894v1?rss=1">
<title>
<![CDATA[
Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739894v1?rss=1
</link>
<description><![CDATA[
Most genetic diversity stems from spontaneous mutations, that is, errors in DNA repair or replication. But for dozens of organisms across the tree of life, mutations at specific loci are not spontaneous but developmentally programmed: effectively, some organisms edit their own DNA sequences. This is perhaps most common among pathogens and parasites, many of which use editing to diversify genes that produce important antigens. Plant-parasitic potato cyst nematodes are damaging agricultural pests that establish a lifelong feeding site inside the root of their host plant. We previously observed extensive diversity of rare alleles at HYP1, the most highly expressed gene that encodes a protein secreted by potato cyst nematodes during parasitism. Importantly, HYP1 alleles differ from each other by complex, in-frame rearrangements of short repeated sequence motifs within a single exon. Combining several lines of evidence, we previously hypothesized that potato cyst nematodes use developmentally-programmed mutations, or editing, to diversify HYP1 alleles in the soma. In the current work, we now test this hypothesis. We employ highly accurate long-read DNA sequencing of a simplified genetic system to identify potential rare edited alleles, we use a transgenic yeast system to describe large de novo mutations at HYP1, and we interpret our findings in light of key population genetic parameters as well as the genetic diversity surrounding HYP1 and across the genome.
]]></description>
<dc:creator><![CDATA[ Hanlon, V., Sonawala, U., Raza, C. A. A., Kalkert, L., Harpum, G., Burkhardt, L. A., Helder, J., Eves-van den Akker, S. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739894</dc:identifier>
<dc:title><![CDATA[Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.24.740321v1?rss=1">
<title>
<![CDATA[
CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.24.740321v1?rss=1
</link>
<description><![CDATA[
Centromeres are essential for chromosome segregation and are epigenetically defined by CENH3/CENP-A nucleosomes. Centromere position along chromosomes varies within and between species, ranging from telocentric to metacentric architectures. Yet, how centromere position influences chromosome inheritance and karyotype evolution remains poorly understood. To reposition the centromere, we used CRISPR-Cas9 to break the centromeric satellite array of Arabidopsis thaliana chromosome 3. Fission chromosomes rapidly acquired telomeres, converting a metacentric into two stable telocentric neo-chromosomes. Neo-centromere formation involved genetic restructuring and de novo satellite higher-order repeat formation, together with epigenetic remodeling of CENH3 and DNA methylation. Crossing the six-chromosome fission line to five- chromosome wild type produced a meiosis-specific trivalent that mis-segregated and generated aneuploidy. Trivalent recombination doubled through two obligate crossovers, which were shifted towards the telomeres. Inheritance was strongly distorted in favor of the wild type centromere, as telocentrics segregated into inviable monosomic gametes. The reciprocal trisomic gametes were associated with centromere-proximal recombination, demonstrating that crossover position governs trivalent segregation. Distortion further increased when CENH3 was over-expressed, implicating centromere strength in the outcomes of trivalent meiosis. Our results reveal rapid centromere remodeling following karyotype change, and how trivalent centromere architecture distorts inheritance, with implications for hybrid incompatibility and synthetic chromosome design
]]></description>
<dc:creator><![CDATA[ Burns, R., Mandakova, T., Morgan, C., Topp, S., Gorringe, N., Li, T., Jenike, K. M., Wlodzimierz, P., Naish, M., Lysak, M. A., Henderson, I. R. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.24.740321</dc:identifier>
<dc:title><![CDATA[CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.24.740501v1?rss=1">
<title>
<![CDATA[
The receptor kinase NILR1 confers nematode resistance through developmental rather than canonical immune signaling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.24.740501v1?rss=1
</link>
<description><![CDATA[
NILR1 contributes to quantitative resistance against Heterodera schachtii and signals through a brassinosteroid-type kinase cascade, but whether its contribution engages canonical immune signaling or follows a distinct, developmentally biased logic has remained unclear. We profiled early transcriptional responses of wild-type and nilr1 roots to H. schachtii by RNA-seq at 30 min and 3 h post inoculation and analyzed them using a genotype x treatment interaction model, complemented by gene set enrichment and integration with cell-type-resolved, brassinosteroid-responsive regulatory networks. We found that canonical PTI marker transcription and flg22-induced ROS production were preserved or even elevated in nilr1, indicating that the tested PTI outputs are largely maintained despite increased susceptibility. Instead, genes whose nematode-induced responses showed NILR1-sensitive interaction effects were enriched for a HAT7/GTL1 centred cortex developmental module, and genetic disruption of GTL1/DF1 moderately altered H. schachtii parasitism, consistent with a role for this module in shaping host permissiveness. Our data support a model in which NILR1 contributes to nematode resistance primarily via developmental, brassinosteroid-type signaling rather than via the canonical PTI outputs assayed here, consistent with a co-option of BRI1 clade (LRR-RLK-Xb) architecture - a receptor family classically associated with development - into a pathway that modulates susceptibility to a plant-parasitic nematode.
]]></description>
<dc:creator><![CDATA[ Euler, M. F., Aslam, S., Neumann, S., Grundler, F. M. W. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.24.740501</dc:identifier>
<dc:title><![CDATA[The receptor kinase NILR1 confers nematode resistance through developmental rather than canonical immune signaling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.739694v1?rss=1">
<title>
<![CDATA[
Metabolome genome-wide association study reveals hierarchical and epistatic genetic control of flavonoid metabolism in soybean 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.739694v1?rss=1
</link>
<description><![CDATA[
Metabolic phenotypes are often governed by complex genetic architectures involving both additive and non-additive effects. However, the extent to which epistatic interactions contribute to the pathway-level regulation of plant metabolism remains unclear. In this study, we investigated the genetic architecture of flavonoid-related metabolites using metabolomic and genomic data from 200 soybean accessions cultivated under multiple environmental conditions. Broad-sense heritability estimates revealed that many metabolites were under strong genetic control, particularly flavonoid-related metabolites. Principal component analysis-based metabolome-wide genome-wide association studies identified four major loci associated with flavonoid metabolic variation, including a locus corresponding to flavonoid 3'-hydroxylase. Conditional analyses based on multilocus genetic backgrounds demonstrated that the effects of downstream loci were highly dependent on upstream genotypes. In particular, single-nucleotide polymorphism effects were frequently detectable only in specific allelic backgrounds defined by the major flavonoid 3'-hydroxylase locus, consistent with strong epistatic interactions among loci. Bayesian network analyses further supported a hierarchical genetic structure consistent with upstream regulation of downstream loci across the flavonoid biosynthetic pathway. These results demonstrate that highly heritable metabolic phenotypes can be controlled by a few loci exhibiting both additive and context-dependent non-additive effects. Our findings provide evidence that pathway-level metabolic diversity in soybean is generated through hierarchical and epistatic genetic control involving a limited set of key loci.
]]></description>
<dc:creator><![CDATA[ Hatta, T., Hamazaki, K., Fuji, Y., Toda, Y., Ichihashi, Y., Ohmori, Y., Yamasaki, Y., Takahashi, H., Takanashi, H., Tsuda, M., Tsujimoto, H., Kaga, A., Nakazono, M., Fujiwara, T., Hirai, M. Y., Iwata, H. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.739694</dc:identifier>
<dc:title><![CDATA[Metabolome genome-wide association study reveals hierarchical and epistatic genetic control of flavonoid metabolism in soybean]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.740370v1?rss=1">
<title>
<![CDATA[
Single-kernel near-infrared spectroscopy enables haploid kernel sorting in field and sweet corn using high-oil haploid inducers across diverse donor-inducer combinations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.740370v1?rss=1
</link>
<description><![CDATA[
Doubled haploid (DH) technology significantly shortens the breeding cycle for developing homozygous inbred lines in maize (Zea mays). Manual sorting of haploids from a larger bulk of hybrid kernels in an induction cross is a major bottleneck in DH development. Automated systems based on near-infrared (NIR) reflectance spectroscopy can be valuable tools for rapid haploid sorting, provided that sorting accuracy is sufficient for incorporation into the DH process. In this study, we evaluated the accuracy of a custom-built single-kernel NIR (skNIR) sorter for classifying haploid kernels from 12 high-oil haploid induction populations generated from two sweet corn and two field corn donors and four high-oil haploid inducers (HOHIs). We evaluated several general classification models that can be applied without population-specific recalibration or prior genotyping, including models that classified haploids based solely on predicted oil content, as well as multivariate methods that used all wavelengths of the NIR spectra. The highest classification accuracy was obtained using a general multivariate support vector machine (SVM) model. When combined with the two best-performing HOHIs, the general SVM model accurately sorted induction populations from two of the three donor backgrounds crossed with these inducers. Two oil-based methods showed less accurate classification than the multivariate SVM model, due to overlapping oil content distributions across the two kernel classes. Overall, this study demonstrates effective skNIR-based sorting of haploid kernels from diverse induction populations using a single general model. The practical deployment of this instrument in maize breeding programs is discussed.
]]></description>
<dc:creator><![CDATA[ Sharma, S., Gustin, J. L., Frei, U. K., Settles, A. M., Lübberstedt, T., Resende, M. F. R., Hershberger, J. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.740370</dc:identifier>
<dc:title><![CDATA[Single-kernel near-infrared spectroscopy enables haploid kernel sorting in field and sweet corn using high-oil haploid inducers across diverse donor-inducer combinations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.740211v1?rss=1">
<title>
<![CDATA[
Haplotype-based insights into the genetic architecture of net blotch resistance in barley 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.740211v1?rss=1
</link>
<description><![CDATA[
Net blotch, caused by Pyrenophora teres, is a major constraint to barley production worldwide and occurs as two epidemiologically distinct forms: net form net blotch (NFNB) and spot form net blotch (SFNB). Although numerous resistance loci have been reported in recent years, their genetic relationship remains poorly understood, and the effective deployment of resistance is constrained by the complex genetic architecture of net blotch resistance. In this study, we used a haplotype-based mapping approach to dissect the genetic basis of resistance to NFNB and SFNB in a diverse panel of 950 barley accessions from the Australian Grains Genebank (AGG). Disease responses were evaluated across 13 experiments, and a total of 40 quantitative trait loci (QTL) were identified, including 26 associated with NFNB, 29 with SFNB, and 15 common for both diseases. Most loci co-localized with previously reported QTL, while six putative novel haploblocks highlighted untapped genetic diversity within the AGG collection. Correlation analyses across phenotypic, genetic and haploblock levels revealed a partial but incomplete overlap in resistance mechanisms between NFNB and SFNB. Among the 4,497 haploblocks, approximately 60% of them showed positive local genetic correlations between the two diseases, suggesting shared genomic contributions to resistance. Haplotype composition analysis further identified a resistant haplotype group, mainly comprising accessions of Asian origin, that exhibited high levels of resistance to both forms of net blotch. Through in-silico haplotype stacking simulations, we demonstrated the cumulative genetic potential achievable by combining favourable haplotypes. When the breeding objective was to improve resistance to both NFNB and SFNB, dual-disease stacking strategies outperformed single-disease approaches, highlighting the value of prioritising haplotypes with positive pleiotropic effects. Overall, this study provides a comprehensive haplotype-level framework for understanding net blotch resistance and delivers practical insights for breeding barley cultivars with durable and broad-spectrum resistance to both NFNB and SFNB.
]]></description>
<dc:creator><![CDATA[ Liu, D., Zhang, X., Snyman, L., Garrard, T., Wallwork, H., Dadu, H., Maclean, M., Tong, J., Chen, C., Gamaralalage, D. J., Periyannan, S., Hickey, L., Hayes, B. J., Dinglasan, E. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.740211</dc:identifier>
<dc:title><![CDATA[Haplotype-based insights into the genetic architecture of net blotch resistance in barley]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.740281v1?rss=1">
<title>
<![CDATA[
Selective repurposing of the eukaryotic DNA replication machinery by a plant virus 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.740281v1?rss=1
</link>
<description><![CDATA[
Eukaryotic DNA viruses that replicate in the nucleus often exploit components of the host DNA replication machinery for genome replication. Geminiviruses, causal agents of devastating crop diseases worldwide, strictly depend on host factors to replicate their circular single-stranded (ss) DNA genomes, with only a single virus-encoded protein, Rep, required for this process. Rep recruits host replication proteins to the viral genome and catalyzes nicking and ligation at the initiation and termination sites of rolling-circle replication. Despite the reliance of geminiviral replication on plant proteins, the composition of the viral replisome remains largely unknown. Here, we use TurboID-based proximity labeling to identify plant proteins in the vicinity of the Rep proteins from the geminiviruses tomato yellow leaf curl virus (TYLCV) and abutilon mosaic virus (AbMV) during infection. Combining virus-induced gene silencing, infection assays, and chromatin immunoprecipitation, we identify host DNA replication-related factors required for viral genome replication and likely components of the viral replisome. Our results indicate that geminiviruses and related eukaryotic ssDNA viruses selectively repurpose components of the eukaryotic replication fork to support rolling-circle replication, and suggest that they follow a leading-strand replication mode while utilizing the lagging-strand DNA polymerase {delta}. These findings shed light on the molecular mechanism of geminiviral DNA replication and identify potential targets for engineering antiviral resistance in crops.
]]></description>
<dc:creator><![CDATA[ Shi, C., Medina-Puche, L., Pott, D. M., Wei, H., Acatay, S., Krenz, B., Hanley-Bowdoin, L., Lozano-Duran, R. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.740281</dc:identifier>
<dc:title><![CDATA[Selective repurposing of the eukaryotic DNA replication machinery by a plant virus]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.739952v1?rss=1">
<title>
<![CDATA[
Chloroplast expression of Chlamydomonas glycolate dehydrogenase en route to an improved photorespiratory bypass 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.739952v1?rss=1
</link>
<description><![CDATA[
Successes with photorespiratory bypass pathway engineering have relied on nuclear transformation, requiring subcellular targeting and protein localization in the target organelles for photorespiration. In the current study, mitochondrial Chlamydomonas glycolate dehydrogenase (CrGDH) was directly expressed in chloroplasts of Chlamydomonas and tobacco, as the first enzymatic step for a photorespiratory bypass. Proof-of-concept experiments in Chlamydomonas were followed by transgenic tobacco lines that confirmed the chloroplast accumulation of active CrGDH protein. Photosynthetic rates and biomass were comparable or less than those of wild type plants under the tested conditions, indicating that chloroplast expression of CrGDH alone is insufficient to improve plant performance. These results suggest that additional downstream enzymes within a complete photorespiratory bypass are required to metabolize glyoxylate derived from CrGDH activity and thereby benefit growth. One of the chloroplast transformed lines (APP2882) accumulated CrGDH while maintaining wild type levels of photosynthesis and biomass, providing a best candidate chassis for engineering full photorespiratory bypass pathways.
]]></description>
<dc:creator><![CDATA[ Jeong, J., Baek, K., Thomas, S., Stutz, S. S., Staub, J. M., Allen, D. K., Jin, Y.-S., Ort, D. R. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.739952</dc:identifier>
<dc:title><![CDATA[Chloroplast expression of Chlamydomonas glycolate dehydrogenase en route to an improved photorespiratory bypass]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.740329v1?rss=1">
<title>
<![CDATA[
Imprinted regulatory networks reveal the molecular cross-talk between paternal and maternal genomes in the endosperm of Arabidopsis arenosa 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.740329v1?rss=1
</link>
<description><![CDATA[
Imprinted genes do not act alone to shape seed development, but as a complex network - just like any other gene. Yet, the molecular context in which they are embedded, i.e. their gene network, remains largely understudied. To address this knowledge gap, we characterized the imprintome of Arabidopsis arenosa at the species-level and used gene regulatory network analyses. We show that genomic imprinting preferentially affects only a few pathways, offering candidates for dosage sensitive processes and the molecular arena of parental conflict. In these pathways, some imprinted genes act as hub genes, among which NRPE1, highlighting the importance of epigenetics in endosperm development. The interaction between parental genomes was rather one-sided: paternally expressed regulators preferentially targeted PEGs, while maternally expressed regulators targeted both PEGs and MEGs indiscriminately. This aligns with a self-promoting paternal influence and a maternal buffer under a parental conflict scenario. Shared paternal and maternal regulation of downstream targets was nevertheless common, and we reveal novel molecular interactions between imprinted regulators. Overall, our work shows how genomic imprinting may act as a molecular means for parental conflict, but also highlights the importance of parental molecular coordination in endosperm development.
]]></description>
<dc:creator><![CDATA[ Budinsky, T., Kovacik, M., Cermak, V., Pribylova, A., Salony, S., Iltas, O., Pecinka, A., Lafon Placette, C. ]]></dc:creator>
<dc:date>2026-07-24</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.740329</dc:identifier>
<dc:title><![CDATA[Imprinted regulatory networks reveal the molecular cross-talk between paternal and maternal genomes in the endosperm of Arabidopsis arenosa]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739621v1?rss=1">
<title>
<![CDATA[
Widely used GWAS methods can be poorly suited to SNP-level localization under diffuse polygenic architecture in livestock 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739621v1?rss=1
</link>
<description><![CDATA[
In livestock populations, genome-wide association studies (GWAS) can produce strong, apparently localized associations even when no truly discrete nearby causal effect exists. This occurs because small effective population sizes, strong family structure, long-range linkage disequilibrium (LD), and diffuse polygenic architecture can cause the effects of many variants to accumulate and be captured jointly across broad genomic intervals, making variant-level associations difficult to interpret biologically. Using real Duroc pig genotypes, we constructed a benchmark in which phenotypes were simulated under diffuse polygenic architecture across a genome partitioned into alternating effect and null windows, with central-null regions (at least 1 Mb away from effect-containing regions) positioned to detect long-range LD-driven signal propagation. We evaluated nine configurations of six GWAS methods (BOLT-LMM, REGENIE, fastGWA, FarmCPU, BLINK, and SLEMM) under this architecture. The central finding is that strong associations, of the kind normally read as evidence of nearby moderate- or large-effect variants, are produced by many of these methods even though the simulated signal is distributed across many tiny effects and cannot be localized to any single variant. The methods differed sharply in the extent of locus-level spillover: several produced large numbers of genome-wide significant loci within central-null regions, whereas the full-GRM mixed-model benchmark (SLEMM) suppressed this spillover almost entirely. These results show that, under a highly polygenic architecture with livestock-like LD, GWAS tool choice has major consequences for biological interpretation. When the goal is to localize biologically meaningful signals rather than to flag association peaks that may merely reflect tiny effects accumulated through LD across a broad block, methods that control long-range LD spillover should be prioritized.
]]></description>
<dc:creator><![CDATA[ Wang, X., Wang, J., Tiezzi, F., Huang, Y., Huang, W., Maltecca, C., Jiang, J. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739621</dc:identifier>
<dc:title><![CDATA[Widely used GWAS methods can be poorly suited to SNP-level localization under diffuse polygenic architecture in livestock]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.737205v1?rss=1">
<title>
<![CDATA[
Single anticodon-edited tRNA therapy targeting highly prevalent Arg>Ter premature termination codons causing inherited retinal diseases 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.737205v1?rss=1
</link>
<description><![CDATA[
Nonsense variants cause 18% of inherited retinal diseases (IRDs), yet current therapies require variant-specific development, leaving most patients untreated. Here, we combined a large-scale genetic analysis literature survey of >37,500 IRD patients with anticodon-edited (ACE)-tRNA engineering to create a single, gene-agnostic therapy targeting Arg>Ter nonsense variants which are the most prevalent subclass (35%) of premature stop codons (PTCs). We developed an optimized ACE-tRNA (V3) that achieved up to 86% readthrough across 13 clinically relevant variants, restored native PRCD localization in the arRP-causing p.R22* mutant, and demonstrated activity in photoreceptor-like cells. To enable translation, we established an AAV2/7m8 production platform and defined 1*10 GC/eye as the safe dose in mice. This patient genetics-guided strategy positions ACE-tRNA_V3 as a promising candidate for preclinical development, offering a precision medicine approach that targets the most common nonsense variant class with a single therapeutic molecule.
]]></description>
<dc:creator><![CDATA[ Sarma, A. S., Saleh, A., Eintracht, J., Kamal, H., Khetab, S., Salameh, M., Matsevich, C., Obolensky, A., Banin, E., Sharon, D. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.737205</dc:identifier>
<dc:title><![CDATA[Single anticodon-edited tRNA therapy targeting highly prevalent Arg>Ter premature termination codons causing inherited retinal diseases]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739560v1?rss=1">
<title>
<![CDATA[
Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739560v1?rss=1
</link>
<description><![CDATA[
Programmed chromosome elimination is a highly controlled developmental process in which specific chromosomes are selectively lost from defined cell types during development. Despite its broad occurrence across plants and animals, the molecular mechanisms driving the tissue-specific elimination of chromosomes remain largely unresolved. Here, we exploit the root-specific elimination of supernumerary B chromosomes in Aegilops speltoides as a tractable model to identify the genetic basis of programmed chromosome loss. A high-quality, chromosome-scale genome assembly was generated, assigning 398 Mb of sequence to the Ae. speltoides B chromosome. Transcriptome profiling across seven tissue types representing chromosome elimination-active, elimination-negative, and B chromosome nondisjunction conditions identified 3,262 genes consistently upregulated in elimination-associated tissues, including 1,035 B genes. Stepwise subtraction of genes expressed in post-elimination and B chromosome-retaining reference tissues, followed by intersection with genes expressed during B nondisjunction in anthers, identified a candidate gene set enriched for chromosome segregation functions. From this set, we prioritized SYN2-B, a B chromosome-encoded cohesin -kleisin subunit whose Arabidopsis thaliana ortholog AtSYN2 induces chromosome bridges and micronucleus formation when misregulated. CENH3-B, an -type centromeric histone variant identified through GO enrichment analysis of B genes expressed in elimination-associated tissues, was shown to be incorporated in centromeres of both A and B chromosomes by transient gene expression assays using protoplasts and 3D structured illumination microscopy. These findings support a model in which B chromosome-encoded perturbations of cohesin activity and centromere composition contribute to selective B chromosome nondisjunction and their elimination in root tissues. Moreover, the SYN2-B promoter is enriched for ethylene response factor-binding sites compared to its A-encoded paralog, suggesting that ethylene is implicated in the root identity pathway driving root-specific B chromosome elimination.
]]></description>
<dc:creator><![CDATA[ Kim, G., Thiel, J., Camara, A. S., Li, D., Bojdov, T., Fuchs, J., Cuacos, M., Kumlehn, J., Jhingan, S., Himmelbach, A., Potlapalli, B. P., Szymanski, J., Fiebig, A., Karafiatova, M., Hajirezaei, M.-R., Bartos, J., Houben, A. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739560</dc:identifier>
<dc:title><![CDATA[Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.23.740248v1?rss=1">
<title>
<![CDATA[
Genetic coupling of hydathode formation with leaf morphogenesis maintains water homeostasis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.23.740248v1?rss=1
</link>
<description><![CDATA[
Hydathodes are specialized leaf structures present across vascular plants that allow guttation by connecting the xylem to the external environment through epithem tissue and permanently open water pores. However, the genetic mechanisms controlling their formation and physiological roles remain poorly understood. Here, we identify a genetic regulatory network that controls hydathode formation and links this process to leaf morphogenesis. This network converges on auxin signaling to coordinate the formation of the three hydathode cell types. We further show that epithem development requires sustained cell proliferation with limited endoreduplication. Analysis of hydathode mutants demonstrates that hydathode size and number are required to prevent reversible leaf flooding. Together, these findings establish a genetic framework for hydathode morphogenesis and uncover a central role for hydathodes in maintaining leaf water homeostasis under fluctuating environmental conditions.
]]></description>
<dc:creator><![CDATA[ Savourat, P., Sarthou, A.-S., Papadopoulos, P., Vasselon, D., Olympio, A., Borrega, N., Pateyron, S., Paysant Le Roux, C., Quentin, C., Genty, B., NOEL, L. D., Routaboul, J.-M., Leonhardt, N., Laufs, P. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.23.740248</dc:identifier>
<dc:title><![CDATA[Genetic coupling of hydathode formation with leaf morphogenesis maintains water homeostasis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740203v1?rss=1">
<title>
<![CDATA[
Extreme cooling enables survival in extreme heat 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740203v1?rss=1
</link>
<description><![CDATA[
Complex, multicellular extremophiles face intense challenges in coordinating their cells, tissues, and organs to function in harsh environments. Tidestromia oblongifolia is a desert plant that thrives in Death Valley, where air temperatures exceed 50{degrees}C. Using natural collections of T. oblongifolia seed, we identified individuals that survive in daily air temperature regimens at the eukaryotic upper thermal limit of 60{degrees}C. Genome-wide association testing revealed genetic variation for survival in extreme heat, and transcriptomics identified pathways regulating physiological cooling. High-throughput infrared imaging showed that survival was enabled by extreme leaf cooling, a physiological mechanism not previously reported in a thermophilic organism. These discoveries provide insights into mechanisms of extreme heat adaptation in a complex organism that could be leveraged to engineer heat-resilient crops.
]]></description>
<dc:creator><![CDATA[ Feehan, J. M., Bitter, M. C., Lowry, D., Sharkey, T. D., Rhee, S. Y. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740203</dc:identifier>
<dc:title><![CDATA[Extreme cooling enables survival in extreme heat]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739231v1?rss=1">
<title>
<![CDATA[
eIF5A is an indispensable protein for eukaryotic cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739231v1?rss=1
</link>
<description><![CDATA[
eIF5A is an evolutionarily conserved protein found in all eukaryotes, and in Archaea and bacteria. It functions as a translation factor promoting ribosomal elongation, and it can also bind to genes in the nucleus and to mRNA. eIF5A is encoded by two paralogous genes in most eukaryotes, with one copy (TIF51A in yeast and EIF5A1 in humans) highly expressed and essential, and the other (TIF51B in yeast and EIF5A2 in humans) repressed in most cells and conditions. eIF5A is linked to viral infection, aging, diabetes and neurodevelopmental disorders. Whilst derepression of the duplicated silent gene EIF5A2 is associated with several cancers, promoting metastasis. To expand our knowledge of eIF5As function, we searched for suppressors of yeast temperature-sensitive mutants of TIF51A, which cannot grow at restrictive temperature. All suppressors contained mutations in the transcriptional repressors Rox1 and Mot3, resulting in the upregulation of the paralogous gene TIF51B. Next, we searched for suppressors of TIF51A temperature-sensitive mutants in yeast lacking the TIF51B gene. The frequency of suppression was 20-times lower and all suppressors were revertants or contained intragenic mutations in the Tif51A protein that conferred stability. Our results suggest that the duplicated eIF5A gene serves as a non-conventional backup system that rescues mutations in the first copy, but acting at the population level. Furthermore, our results expand our understanding of the repression mechanisms that keep the second eIF5A gene silent. Lastly, our results demonstrate that eIF5A is an indispensable protein in eukaryotic cells, whose function cannot be substituted by mutations in other proteins or pathways.
]]></description>
<dc:creator><![CDATA[ Alepuz, P., Prieto-Diez, S., Aguilar-Diez, A., Araque, L., Peris, D. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739231</dc:identifier>
<dc:title><![CDATA[eIF5A is an indispensable protein for eukaryotic cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740109v1?rss=1">
<title>
<![CDATA[
Elevated CO2 enhances tomato tolerance to Botrytis cinerea through transcriptional and metabolic defence reprogramming 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740109v1?rss=1
</link>
<description><![CDATA[
Atmospheric CO2; concentration is projected to rise substantially over the coming decades, yet its impact on the molecular mechanisms governing plant immunity remains poorly understood. Here, we investigated how elevated CO2; (eCO2; 650 ppm) combined with increased temperature (+5 C) influences tomato responses to Botrytis cinerea through integrated phenotypic, metabolomic, transcriptomic, and gene regulatory network (GRN) analyses across eight cultivars. Although cultivars displayed contrasting susceptibility under ambient conditions, eCO2 consistently enhanced tolerance across all genetic backgrounds. Multi-omics analyses revealed a partial uncoupling between transcriptional and metabolic responses during infection, with repression of photosynthesis- and carbon metabolism-related genes contrasting with the accumulation of carbon- and amino acid-derived metabolites. Under eCO2, this metabolic disruption was attenuated, preserving metabolic homeostasis during infection. GRN reconstruction identified a conserved WRKY-ERF regulatory module underlying the growth-defence trade-off, while functional perturbation demonstrated that its contribution to resistance depends on both genotype and environmental context, highlighting the importance of basal defence mechanisms. Targeted metabolomics further revealed that eCO2 promotes a metabolically primed state characterized by reinforcement of structural and chemical defence barriers rather than stronger activation of inducible immune responses. Together, our findings show that enhanced tolerance under eCO2 emerges from coordinated reorganization across regulatory and metabolic networks, providing a systems-level framework for understanding plant immunity and improving crop resilience under future climate scenarios.
]]></description>
<dc:creator><![CDATA[ Baistrocchi, F., Orero-Bayo, M., Yu, L., Sanchez-Lucas, R., Pastor, V., Garcia-Molina, A. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740109</dc:identifier>
<dc:title><![CDATA[Elevated CO2 enhances tomato tolerance to Botrytis cinerea through transcriptional and metabolic defence reprogramming]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740078v1?rss=1">
<title>
<![CDATA[
A continuum of CAM phenotypes in the carnivorous plant genus Pinguicula (Lentibulariaceae) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740078v1?rss=1
</link>
<description><![CDATA[
Premise Pinguicula are carnivorous plants occupying a wide range of habitats, from wetlands to barren rock cliffs, where CAM photosynthesis was recently discovered in several species. This ecological and physiological diversity makes the genus a promising system for exploring the environmental drivers and evolutionary transitions underlying variation in CAM. Here, we present a physiological survey of CAM with a particular focus on the Mexican Clade, which contains the recently identified CAM species. Methods We conducted a carbon isotope survey of live and herbarium specimens to identify candidate CAM species. We then measured diurnal gas-exchange patterns and changes in leaf titratable acidity to quantify CAM activity. Results Pinguicula species exhibited a variety of photosynthetic phenotypes. Pinguicula vulgaris showed no detectable evidence of CAM, whereas P. cyclosecta and P. moranensis demonstrated a C3-CAM physiology with most net assimilation via C3. Pinguicula martinezii also showed the same C3-CAM physiology under well-watered conditions but had strong facultative induction of CAM with drought. Pinguicula agnata displayed net assimilation via CAM. Titratable acidity had a positive correlation with {delta}13C within the species we sampled. Conclusions Our results support the existence of a CAM physiological continuum within Pinguicula. Notably, closely related species encompass physiologies that span the large variation of CAM. This diversity provides a rare opportunity for future studies to investigate the evolution of CAM in closely related species, including differences and similarities between differing states across the continuum.
]]></description>
<dc:creator><![CDATA[ Mok, D. W. L., VanBuren, R., Gilbert, K. J. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740078</dc:identifier>
<dc:title><![CDATA[A continuum of CAM phenotypes in the carnivorous plant genus Pinguicula (Lentibulariaceae)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740030v1?rss=1">
<title>
<![CDATA[
Organ identity shapes autophagy dynamics and selectivity in plants 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740030v1?rss=1
</link>
<description><![CDATA[
Plants, with their unique evolutionary trajectory and complex physiological adaptations, have developed organ-specific mechanisms to cope with various environmental stresses. Autophagy, an essential catabolic process, plays an important role in maintaining plant growth, immunity, and overall fitness. In this study, we reveal the spatio-temporal dynamics of autophagic responses in Arabidopsis thaliana roots and shoots under different stress conditions, including AZD8055 treatment and carbon and nitrogen depletion. Our findings demonstrate that roots exhibit stronger autophagic activity than shoots under all three conditions, highlighting the unique adaptations of these two organs. Furthermore, we dissect the selectivity of autophagy in targeting organelles, revealing immediate, delayed, and no uptake categories. Additionally, we observe organelles coexisting within autophagic bodies, shedding light on the complexity of cargo selection. This study enhances our understanding of plant specific autophagy dynamics, emphasizing its role in sustaining the source-sink functions and offering insights into plant adaptation to diverse stressors.
]]></description>
<dc:creator><![CDATA[ Dauphinee, A. N., Holla, S., Mazumdar, S., Ballhaus, F. I. M., Ohlsson, J. A., Impens, F., Maia, T., Timmerman, E., Dagdas, Y., Lofke, C., Dalman, K., Schumacher, K., Bozhkov, P. V., Minina, E. A. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740030</dc:identifier>
<dc:title><![CDATA[Organ identity shapes autophagy dynamics and selectivity in plants]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.739999v1?rss=1">
<title>
<![CDATA[
Postharvest tomato shelf life is genetically distinct from fruit firmness: evidence from two F2 populations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.739999v1?rss=1
</link>
<description><![CDATA[
Reducing postharvest fruit loss without compromising fruit quality is a major goal in tomato breeding. Fruit shelf life is a complex trait, influenced by postharvest changes in fruit firmness and weight, as well as by both genetic and environmental factors. A QTL mapping experiment was conducted to identify loci associated with fruit shelf life-related traits using two distinct F2 tomato populations. Fruit weight, firmness, shelf life (evaluated as both loss of fruit weight and loss of firmness over time), and colour space components were measured, and QTLs were mapped using a commercial low-density SNP genotyping panel and bulk segregant sequencing analysis experiments. We show that fruit firmness at harvest is only weakly predictive of postharvest firmness loss, indicating that shelf life should be treated as a dynamic trait rather than a static firmness phenotype. Across the two populations, 60 QTLs defining 26 genomic regions were identified, including both population-specific loci and shared regions on chromosomes 9 and 12. Several narrow intervals contained candidate genes related to ethylene signaling, cell-wall remodeling, calcium transport, aquaporin-mediated water balance and stress responses. The identified QTLs and candidate genes are directly relevant to breeding programmes seeking to improve postharvest performance without using major ripening mutants that compromise fruit quality.
]]></description>
<dc:creator><![CDATA[ Rosati, C., Tirado, F., Aprea, G., Bitton, F., Brault, M., duboscq, R., Ferrante, P., Pellegrino, K., Stamigna, C., Giuliano, G., Causse, M. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.739999</dc:identifier>
<dc:title><![CDATA[Postharvest tomato shelf life is genetically distinct from fruit firmness: evidence from two F2 populations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740042v1?rss=1">
<title>
<![CDATA[
RenSeq and whole genome sequencing uncover allelic diversity of clubroot resistance genes in commercial breeding canola lines 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740042v1?rss=1
</link>
<description><![CDATA[
Clubroot disease, caused by the obligate biotrophic pathogen Plasmodiophora brassicae, is a major threat to canola (Brassica napus) production worldwide. Clubroot-resistant (CR) cultivars remain the most effective disease-management strategy, but the genetic basis of resistance in commercial canola remains poorly understood because many resistance sources are proprietary and associated genotypic information is rarely accessible. Although nucleotide-binding leucine-rich repeat (NLR) immune receptors account for most cloned CR genes, no pan-NLRome has incorporated CR lines used in commercial canola breeding. Here, we combined whole-genome sequencing and resistance gene enrichment sequencing (RenSeq) to assemble and annotate the NLR repertoires of five homozygous CR inbred lines (IH1-IH5) used for commercial breeding and displaying contrasting resistance profiles against predominant Canadian P. brassicae pathotypes. We integrated these NLRomes with the susceptible cultivar Westar to construct a comparative pan-NLRome for canola. Across the five CR lines, total NLR content was highly conserved, ranging from 504 to 517 genes, with TIR-NLRs representing the predominant class. C-JID-containing TIR-NLRs accounted for more than 30% of each NLR repertoire, and integrated-domain analysis identified conserved and genotype-specific NLR-IDs, including previously unreported domains in IH4. Pan-NLRome analysis resolved 366 NLR orthogroups (OGs), 60.7% of which were core, and identified resistant-line-enriched OGs absent from Westar as candidate CR-associated loci. Unexpectedly, a homolog of the functionally characterized CR gene, CRa, was detected in five CR lines. Moreover, a homolog of another CR gene, Crr1a, was detected in both resistant and susceptible lines, indicating that the presence/absence of a gene alone does not predict resistance. Instead, structural variation affecting LRR and C-JID regions suggests that allele-level diversity within conserved NLR loci contributes to CR-associated variation, with implications for allele-specific marker development and durable CR deployment.
]]></description>
<dc:creator><![CDATA[ Wu, J., Mukhopadhyay, S., Javed, M. A., Asselin, Y., Fantino, E. I., Franke, C., Perez-Lopez, E. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740042</dc:identifier>
<dc:title><![CDATA[RenSeq and whole genome sequencing uncover allelic diversity of clubroot resistance genes in commercial breeding canola lines]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.739638v1?rss=1">
<title>
<![CDATA[
Water stress adaptive responses in plants require movement of ABA and AB-aldehyde from vascular to target tissues 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.739638v1?rss=1
</link>
<description><![CDATA[
Vascular plants rapidly coordinate root and shoot responses to water stress. Abscisic acid (ABA) mediates these adaptations; however, it remains unclear which cells produce ABA, whether ABA synthesis shifts during stress, and whether ABA movement is required for its adaptive functions. Here, we map ABA biosynthesis at cellular resolution in Arabidopsis and report that water-stress adaptive responses in roots and shoots require movement of ABA and its precursor AB-aldehyde from vascular tissues to target cells. We suggest that ABA accumulation arises from two parallel routes: (i) ABA synthesized in the vasculature via ABA2 and AAO3, then moving to guard cells, and (ii) phloem-derived AB-aldehyde being converted to ABA in the epidermis or bundle sheath by AAO1 and AAO2. Finally, we predict that tightly packed cells beneath leaf veins facilitate efficient ABA delivery to guard cells, an anatomical arrangement that has enabled angiosperms to evolve the use of ABA to rapidly close stomata.
]]></description>
<dc:creator><![CDATA[ Anfang, M., Kiradjiev, K. B., Ben Yaakov, S., Gothilf, D., Kanstrup, C., Bitman, B., Jepson, J. M., Fellus-Alyagor, L., Hirsch, D., Galperin, V. E., Watanabe, S., Okamoto, M., Kumar, R., Crocoll, C., Morghen, S., Hamann, T., Brotman, Y., Seo, M., Nour-Eldin, H. H., Sturrock, C. J., Mehra, P., Bennett, M. J., Rowe, J. H., Band, L. R., Shani, E. ]]></dc:creator>
<dc:date>2026-07-23</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.739638</dc:identifier>
<dc:title><![CDATA[Water stress adaptive responses in plants require movement of ABA and AB-aldehyde from vascular to target tissues]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.18.739365v1?rss=1">
<title>
<![CDATA[
Bidirectional hybridization between Ulva prolifera and U. linza (Ulvophyceae, Chlorophyta): Evidence for compatibility and paternal chloroplast inheritance 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.18.739365v1?rss=1
</link>
<description><![CDATA[
Ulva prolifera and U. linza are closely related species, with abundant adult thalli and reproductive cells co-occurring extensively in time and space during the Yellow Sea green tides. Elucidating their hybridization compatibility is crucial for species delimitation, assessing interspecific gene flow, and evaluating the ecological impacts of green tides. Previous studies suggested asymmetric gamete compatibility (only U. prolifera mt+ x U. linza mt-), but lacked sex-linked markers to reliably identify hybrid diploids and their reproductive modes, and did not examine chloroplast inheritance. Here, we performed bidirectional crosses using sexual strains of different geographic origins from both parents, with sex-linked markers to quantify progeny genotypes, examine fertility and reproduction pathway of F1 hybrids, and trace chloroplast inheritance using the species-specific petB marker. Our results showed that: (1) F1 hybrids were obtained in both cross directions, with significantly higher frequency in the direct cross (U. linza mt+ x U. prolifera mt-), indicating no complete reproductive isolation in either direction; the biased compatibility likely reflected genetic background differences among the limited strain combinations in a single study. (2) A considerable number of germinated progeny arose from parthenogenesis of parental gametes. (3) F1 hybrids from both crosses could undergo meiosis to form gametes and develop into gametophytes; additionally, F1 from the reciprocal cross produced diploid spores for asexual reproduction, suggesting meiotic disturbance. (4) Chloroplasts were maternally inherited in selfing of U. prolifera parent, but in all F1 hybrids they were paternally inherited, indicating a potential reversal of the inheritance pattern due to interspecific hybridization. These findings provided new insights into the potential for genetic exchange between U. prolifera and U. linza.
]]></description>
<dc:creator><![CDATA[ Xu, Z. Z., Zhao, J., Jiang, P. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.18.739365</dc:identifier>
<dc:title><![CDATA[Bidirectional hybridization between Ulva prolifera and U. linza (Ulvophyceae, Chlorophyta): Evidence for compatibility and paternal chloroplast inheritance]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.18.739356v1?rss=1">
<title>
<![CDATA[
Long-term realized genetic gain and population dynamics under genomic selection in Brazilian cassava germplasm 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.18.739356v1?rss=1
</link>
<description><![CDATA[
Genomic selection has become an important strategy in cassava breeding, enabling faster selection cycles and sustained genetic progress. Despite its widespread adoption, long-term evaluations integrating predictive performance, realized genetic gain, and genetic diversity remain scarce, particularly in clonally propagated crops. We present a comprehensive assessment of genomic selection outcomes in the Brazilian cassava breeding program across four recurrent selection cycles (C0 to C3) implemented between 2011 and 2024, using historical phenotypic and genomic data from 210 multi-environment trials. Predictive ability of genomic best linear unbiased prediction models ranged from low to moderate, depending on the traits genetic architecture and heritability. Prediction accuracies were highest in early cycles (C0 and C1) and showed modest declines in later cycles (C2 and C3). Root yield, shoot yield, plant height, starch content, and dry matter content exhibited stable predictive performance across cycles, with a gradual reduction in RMSE, indicating improved model calibration as training populations expanded. Regression analyses of genomic estimated breeding values revealed significant realized genetic gains for most yield-related traits. In contrast, dry matter content and starch content exhibited small, non-significant negative trends, consistent with known unfavorable genetic correlations with yield. Targeted reductions in plant architecture scores reflected deliberate selection for ideotypes suited to mechanized production systems. At the same time, analyses of genetic diversity revealed a slight decrease in observed heterozygosity, with higher values in the most advanced selection cycle. These results provide an integrated framework for monitoring predictive performance, realized genetic gain, and population genetic dynamics under long-term genomic selection. Collectively, they offer valuable insights into balancing short-term genetic improvement with long-term sustainability and support the development of strategies to optimize selection decisions, breeding planning, and population management in Brazilian cassava breeding programs.
]]></description>
<dc:creator><![CDATA[ de Freitas, G. M., Certuche, D. C. S., Jannink, J.-L., De Oliveira, E. J., Garcia, A. A. F. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.18.739356</dc:identifier>
<dc:title><![CDATA[Long-term realized genetic gain and population dynamics under genomic selection in Brazilian cassava germplasm]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739049v1?rss=1">
<title>
<![CDATA[
Generation of lachrymatory factor synthase-suppressed onion (Allium cepa L.) by Agrobacterium-mediated gene transfer for CRISPR/Cas9 genome editing 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739049v1?rss=1
</link>
<description><![CDATA[
Lachrymatory factor, an irritating volatile with tear-inducing property, is produced when onion bulbs are cut or chopped. We aimed to generate onion plants with reduced lachrymatory factor synthase (LFS) activity via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (CRISPR/Cas9) genome editing. Calli induced from primary roots were transformed with Agrobacterium tumefaciens carrying expression cassettes for CRISPR/Cas9, guide RNA, green fluorescent protein (GFP), and hygromycin resistance; callus lines that showed a high-frequency stable GFP expression were selected as "elite callus lines" that were suitable for transformation. Cleaved amplified polymorphic sequence (CAPS), heteroduplex mobility assay (HMA), and Sanger sequencing confirmed mutations introduced into the LFS gene, and plants were regenerated from the confirmed LFS-edited callus lines. The LFS enzyme activity in the leaves and bulbs of the LFS-edited plants was lower than that in control plants, while the LFS-edited plants exhibited severe growth abnormalities and failed to set seed, possibly due to long-term culture to maintain the elite callus line. The present study first demonstrated that onion genome editing, which modified a specific trait of onion, the reduction of LFS activity, was achieved. The results obtained opened the feasible way toward the final goal: the production of tear-free, higher health-functional onions.
]]></description>
<dc:creator><![CDATA[ Tamaru, S., Imai, S., Watanabe, S., Ikegai, T., Kondo, S., Igawa, T., Kamoi, T. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739049</dc:identifier>
<dc:title><![CDATA[Generation of lachrymatory factor synthase-suppressed onion (Allium cepa L.) by Agrobacterium-mediated gene transfer for CRISPR/Cas9 genome editing]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.22.740070v1?rss=1">
<title>
<![CDATA[
Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.22.740070v1?rss=1
</link>
<description><![CDATA[
How cis-regulatory sequences and their genetic variation govern chromatin accessibility, regulate gene expression, and the establishment of plant cell identities, making them fundamental to development, environmental responses, and phenotypic diversity. Here we present PEAgent, a framework for training, evaluating and interpreting deep-learning models that predict single-cell chromatin accessibility directly from DNA sequence, packaged in an interactive web portal and toolkit. Models were trained on single-cell chromatin-accessibility atlases of soybean, maize and rice, together spanning over 355,000 cells and 320 cell types and [~]150 million years of evolution. We unraveled a lexicon of 243 cell-type-resolved regulatory patterns, half of them composite, with TCP and bHLH showing the greatest influence and strongest conservation across species. Co-occurrence and in silico synergy analyses, explicitly modeling motif orientation and spacing, revealed two distinct cooperative modes acting at short and nucleosome-scale distances. We further showed that model predictions distinguish grass-conserved from rice-specific regulatory sequences far more accurately than sequence conservation scores alone, and validated the models predicted variant effects against cell-type-level chromatin accessible QTLs. PEAgent provides a foundational resource for decoding cell-type-specific plant cis-regulatory logic and interpreting noncoding variation in plants.

HighlightsO_LIPEAgent predicts single-cell chromatin accessibility directly from DNA sequence in soybean, rice and maize.
C_LIO_LINearly half of cell-type-resolved patterns are composite, with TCP and bHLH motifs most influential and conserved across species.
C_LIO_LICo-occurrence and synergy analysis reveals distinct cooperative grammar at short and nucleosome-scale distances.
C_LIO_LIPEAgent distinguishes grass-conserved from lineage-specific regulatory sequences better than sequence conservation scores alone.
C_LI
]]></description>
<dc:creator><![CDATA[ Yao, J., Li, J., Zhang, X., Li, X., Marand, A. P., Pickering, E., Schmitz, R. J. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.22.740070</dc:identifier>
<dc:title><![CDATA[Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739764v1?rss=1">
<title>
<![CDATA[
The systemically induced sugar transporter SWEET11 regulates growth-defense trade-offs during Serendipita indica symbiosis in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739764v1?rss=1
</link>
<description><![CDATA[
Sugar exchange at the root interface is a pivotal process governing the establishment and stability of plant-fungal symbioses. Precise regulation of sugar exchange determines the success of this ecologically significant interaction. Sugar Will Eventually be Exported proteins (SWEETs) constitute a family of regulatory, energy-independent bidirectional sugar transporters that influence plant development, stress resilience, and survival. However, how specific SWEET transporters coordinate systemic carbon allocation and immune regulation during beneficial plant-fungal interactions remains poorly understood. In this study, we examined the role of the systemically induced Arabidopsis sugar transporter SWEET11 during association with the beneficial endophytic fungus Serendipita indica and following treatment with its elicitor, cellotriose (CT). Expression profiling of SWEET family members revealed a rapid and preferential induction of SWEET11 in aerial tissues upon fungal colonization and CT treatment. Loss-of-function of SWEET11 compromises key mutualistic outcomes, including plant growth enhancement, fungal colonization efficiency, penetration ability, carbohydrate distribution, and the regulation of defense-related phytohormones such as jasmonic acid and abscisic acid. Global transcriptome analysis further demonstrated that SWEET11 regulates whole-plant responses by orchestrating genes involved in central metabolism, secondary metabolite production, sesquiterpenoid and triterpenoid pathways, as well as defense signaling and nutrient transport systems. We show that SWEET11 interacts with a stress associated SNF1-related protein kinase (SnRK2.8) and plays a crucial role in enabling fungal establishment while mitigating host defense responses, and supporting plant growth. Our data shows that SWEET11 functions as a shoot-derived sugar exporter that directs carbon toward roots, facilitating sugar unloading to S. indica. This controlled carbon supply allows the fungus to meet its metabolic demands without disrupting host sugar balance, thereby maintaining a stable and well-regulated symbiotic association under immune constraints.
]]></description>
<dc:creator><![CDATA[ Jogawat, A., Menon, S. H., Sanyasi, M., Goyal, D., Nair, A. M., Vadassery, J. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739764</dc:identifier>
<dc:title><![CDATA[The systemically induced sugar transporter SWEET11 regulates growth-defense trade-offs during Serendipita indica symbiosis in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739116v1?rss=1">
<title>
<![CDATA[
Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739116v1?rss=1
</link>
<description><![CDATA[
Theory predicts chromosomal rearrangements (CRs) to promote reproductive isolation and local adaptation by disrupting meiosis and altering recombination landscapes. These processes are especially important in holocentric organisms, whose diffuse centromeres facilitate CRs. Here, we investigated the genomic origins and evolutionary consequences of CRs in the holocentric sedge Carex laevigata, a species with extreme intraspecific chromosome-number variation (2n = 69-84). Establishing chromosome-scale genome assemblies, experimental crosses involving more than one thousand living plants throughout three generations and eight years, linkage mapping, and Quantitative Trait Loci (QTL) analyses, we identified extensive CRs among karyotypically distinct populations. Breakpoint regions of CRs were enriched in GC-rich and repetitive sequences, particularly LTR-Gypsy elements, suggesting recurrent genomic regions prone to structural instability. Inter-cytotype hybrids formed complex meiotic configurations and showed reduced germination success, consistent with hybrid dysfunction associated with increasing chromosomal divergence. Rearranged chromosomes exhibited strong recombination suppression and segregation distortion near breakpoint regions and within inverted segments. QTL analyses further identified fitness-related loci associated with both rearranged and collinear chromosomes. Together, our results corroborate theoretical predictions providing novel empirical evidence that CRs arise preferentially in structurally fragile genomic regions and contribute to genomic divergence through hybrid dysfunction and recombination suppression.
]]></description>
<dc:creator><![CDATA[ Villegas, R. S., V. Mohan, A., Gomez-Ramos, I., Luceno, M., Miguez, M., Maguilla, E., Corro, J. I. M., Herrero-Doblado, D., Sargheini, N., marques, A., Lucek, K., Escudero, M., Martin-Bravo, S. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739116</dc:identifier>
<dc:title><![CDATA[Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739607v1?rss=1">
<title>
<![CDATA[
A Modular, AI-assisted Digitization Toolkit for Resource-Constrained Herbaria: A Case Study from Zimbabwe 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739607v1?rss=1
</link>
<description><![CDATA[
Herbaria serve as invaluable spatio-temporal repositories of plant diversity information. Digitization of herbarium collections enhances the accessibility, discoverability, and long-term preservation of this important plant information, yet financial and infrastructural constraints often prevent herbaria in resource-constrained regions from digitizing their collections. Consequently, critical plant diversity data gaps remain due to underrepresentation of these collections in global biodiversity databases. Here, we describe an AI-assisted modular digitization toolkit specifically designed for herbaria operating under limited funding, developed and refined through our experience digitizing the crop wild relative (CWR) collection of the National Herbarium of Zimbabwe. The toolkit comprises three core components: (1) a portable, cost-effective photostation assembled from commodity parts, (2) a streamlined cascade workflow for systematic digital imaging, and (3) an AI-assisted data management pipeline for image quality control, label transcription, data analysis, and presentation. Compared to manual transcription and legacy optical character recognition approaches, AI-based transcription achieves lower time cost while maintaining high accuracy, and AI-driven data management delivers accessibility and reduced expenditure relative to conventional database infrastructure. The toolkit is designed to allow herbarium staff full autonomy over the digitization procedure, ensuring institutional ownership and the capacity for independent continuation beyond initial project support. By prioritizing affordability, modularity, and simplicity, this toolkit provides a replicable framework that may enable resource-constrained herbaria to locally generate high-quality scientific data for conservation and the sustainable utilization of plant genetic resources.
]]></description>
<dc:creator><![CDATA[ Gatula, L., Bezrukov, I., Atemia, J., Chapano, C., Gamundani, P. T., Zimudzi, C., Chatukuta, P. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739607</dc:identifier>
<dc:title><![CDATA[A Modular, AI-assisted Digitization Toolkit for Resource-Constrained Herbaria: A Case Study from Zimbabwe]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.21.739726v1?rss=1">
<title>
<![CDATA[
CRISPR-Cas9 Induced Knockout of BEL5 in Tetraploid Potato: Optimized Methodology via Repeated de novo Regeneration and Impact on Tuberization 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.21.739726v1?rss=1
</link>
<description><![CDATA[
CRISPR-Cas9 has emerged as a powerful tool for targeted genome editing in plants; however, its application in tetraploid potato (Solanum tuberosum ssp. tuberosum) remains challenging due to its vegetative propagation and complex highly heterozygous genome. Availability of whole-genome sequence data for the specific genotype is crucial to ensure complete knockout of all alleles of target genes while minimizing off-target mutations. In this study, using the tetraploid potato cultivar Desiree, we report, a complete CRISPR-Cas9-mediated knockout of the BEL5 gene, encoding a transcription factor, known as one of the key regulators driving tuber formation. We employed Agrobacterium-mediated transformation and demonstrated that repeated de novo regeneration could improve editing efficiency by promoting emergence of new mutations. BEL5 knockout plants exhibited a delayed onset of tuberization under inductive short-day conditions in hydroponics; however, their overall tuber yields were comparable to wild type plants. Based on our results, we propose a regulatory role of BEL5 in the timing of tuber onset but, unexpectedly, its dispensability for tuber development in modern cultivated potato. Besides providing functional insight into the BEL5 role in potato, this study includes a methodological approach for efficient CRISPR-Cas9 gene editing in this vegetatively propagated polyploid crop, along with strategies for detecting mutations in genes that lack clear phenotypic manifestation.
]]></description>
<dc:creator><![CDATA[ Zounkova, A., Chirivi, D., Pribylova, A., Martignago, D., Myslivcova, J., Masek, T., Fischer, L., Betti, C., Fornara, F., Maskova, P. ]]></dc:creator>
<dc:date>2026-07-22</dc:date>
<dc:identifier>doi:10.64898/2026.07.21.739726</dc:identifier>
<dc:title><![CDATA[CRISPR-Cas9 Induced Knockout of BEL5 in Tetraploid Potato: Optimized Methodology via Repeated de novo Regeneration and Impact on Tuberization]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-22</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
