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PremiseThere is considerable variation in leaf lobing and leaf size, including among grapevines, some of the most well-studied leaves. We examined the relationship between leaf lobing and leaf size across grapevine populations which varied in extent of leaf lobing.MethodsWe used homologous landmarking techniques to measure 2,632 leaves across two years in 476 unique, genetically distinct grapevines from 5 biparental crosses which vary primarily in the extent of lobing. We determined to what extent leaf area could explain variation in lobing, vein length, and vein to blade ratio.ResultsAlthough lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and decreases as a function of vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing.ConclusionsFor a given leaf area, more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.

Suppose a legal rule makes it negligent to have a loaded gun out in the open in a place of business. Should a defendant who violated this rule by using a loaded gun as a paperweight be liable for his client’s broken toes when the gun falls onto her foot? Problems manifesting this basic structure have occupied scholars and Restatement reporters for decades. In this essay, I reframe untaken precautions as a bundle of risk control services, each of which counteracts a particular risky element, like “shooting capacity” or “heaviness” in the case of the gun. Tort law ought to induce actors to produce all, and only, the risk control services that are worth the cost of providing. Cashing out that prescription is tricky because precautions often jointly provide multiple risk mitigation services, and more than one precaution may meet the legal standard. Nonetheless, the task becomes tractable if we examine the cost structure of precautions — and, analogizing to break-even analysis for products, identify which risk control services contribute to rather than detract from a precaution’s bottom line. The risk services framework partially redeems but also revises harm-within-the-risk and negligence per se doctrines that limit negligence liability based on the type of danger or category of victim involved in a given accident. By enabling us to assess which ostensible risk control services are really societal disservices, this approach provides a firmer basis for calibrating the scope of liability.

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motifs plays a fundamental role in researching transcriptional regulatory mechanisms in cells and in helping construct regulatory networks. Current algorithms developed for motif searching focus on the analysis of ChIP-enriched peaks but are not able to integrate the ChIP signal in nucleotide resolution. We present a weighted two-stage alignment tool (TESA). Our framework implements an analysis workflow from experimental datasets to TFBS prediction results. It employs a binomial distribution model and graph searching model with ChIP-exonuclease (ChIP-exo) reads depth and sequence data. TESA can effectively measure the possibility for each position to be an actual TFBS in a given promoter sequence and predict statistically significant TFBS sequence segments. The algorithm substantially improves prediction accuracy and extends the scope of applicability of existing approaches. We apply the framework to a collection of 20 ChIP-exo datasets of E. coli from proChIPdb and evaluate the prediction performance through comparison with three existing programs. The performance evaluation against the compared programs indicates that TESA is more accurate for identifying regulatory motifs in prokaryotic genomes.

Context Conversion of grasslands to croplands can usually result in the degradation of soils and increased greenhouse gas (GHG) emissions such as carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4). However, little is known about the impacts of grassland conversion to recently tilled croplands on soils and GHG fluxes. Aims A field experiment was established in 2016 to evaluate the impacts of grassland conversion to tilled cropland under different landscape positions (upslope, backslope, and footslope) on select soil properties and soil GHG fluxes. Key results The findings showed that the grassland conversion significantly increased soil bulk density and electrical conductivity but reduced pH and total nitrogen (TN). The conversion impacted soil biome community grassland and tilled croplands. The landscape position significantly impacted soil pH (footslope upslope). The grassland conversion significantly decreased soil CO2 fluxes, but increased soil CH4 and N2O fluxes. The landscape position significantly impacted soil CO2 (footslope > upslope and backslope) and CH4 (upslope > footslope and backslope) fluxes for some periods. Soil CO2 and N2O fluxes generally followed upward and downward trends over time, respectively. Conclusions These results indicate that grassland conversion was able to lose soil N, increase soil compaction, acidity, salts, and soil N2O and CH4 fluxes, and decrease the diversity of abundant genera and CO2 fluxes. Footslope increased TN, soil acidity, CO2, and CH4 fluxes, compared with upslope and backslope. CO2 fluxes under grassland and tilled cropland significantly increased over time, whereas N2O fluxes under grassland significantly reduced. Implications Conversion of grassland to tilled cropland significantly impacted on sol quality. It caused a loss in soil N and increased soil compaction, acidity and salts. Grassland conversion also decreased the abundance and diversity soil microbiome.

Background‘Chambourcin’ is a French-American interspecific hybrid grape variety grown in the eastern and midwestern United States and used for making wine. Currently, there are few genomic resources available for hybrid grapevines like ‘Chambourcin’.ResultsWe assembled the genome of ‘Chambourcin’ using PacBio HiFi long-read sequencing, Bionano optical map sequencing and Illumina short read sequencing. We produced an assembly for ‘Chambourcin’ with 26 scaffolds with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. 33,791 gene models were predicted, of which 81% (27,075) were functionally annotated using Gene Ontology and KEGG pathway analysis. We identified 16,056 common orthologs between ‘Chambourcin’ gene models,V. vinifera‘PN40024’ 12X.v2, VCOST.v3, Shine Muscat (Vitis labruscana x V. vinifera) andV. ripariaGloire. A total of 1,606 plant transcription factors representing 58 different gene families were identified in ‘Chambourcin’. Finally, we identified 304,571 simple sequence repeats (SSRs), repeating units of 1-6 base pairs in length in the ‘Chambourcin’ genome assembly.ConclusionsWe present the genome assembly, genome annotation, protein sequences and coding sequences reported for ‘Chambourcin’. The ‘Chambourcin’ genome assembly provides a valuable resource for genome comparisons, functional genomic analysis and genome-assisted breeding research.

PremiseGrapevine leaves have diverse shapes and sizes. Their shape and size is known to be influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. In order to determine the importance of grapevine leaf shape and size to canopy temperature, we examined the relationship in five seedling populations grown in a vineyard in California, USA.MethodsAll of the populations had one parent with compound leaves of the Vitis piasezkii type and each population had a different second parent with non-compound leaves. In previous work, we measured leaf shape and size using 21 homologous landmarks. Here, we paired these morphology data with measurements taken using an infrared thermometer to measure the temperature of the canopy. By recording time of sampling and canopy temperature, we were able to determine which vines were cooler or hotter than expected, using a linear model.ResultsWe established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. In contrast, leaf shape was not strongly correlated with variation in temperature.ConclusionsUltimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall vine canopy temperature, but further work is needed to determine if this is due to variation in leaf size, differences in the openness of the canopy, or other related traits.

Categories intentionally create discontinuities. By breaking the world up into cognizable chunks, they simplify the information environment. But the signals they provide may be inaccurate or scrambled by strategic behavior. This Article considers how law might approach the problem of optimal categorization, given the role of categories in managing and transmitting information. It proceeds from the observation that high categorization costs can be addressed through two opposite strategies—making classifications more fine-grained (splitting), and making classifications more encompassing (lumping). Although continuizing and other forms of splitting offer intuitive answers to inaccurate classification and gaming along category lines, lumping is sometimes a better solution. If category membership carries multiple and offsetting implications, the incentive to manipulate the classification system is dampened. To take a simple example, insurance that covers only one risk is more vulnerable to adverse selection than is an insurance arrangement that covers two inversely correlated risks. Making categories larger, more durable, and more heterogeneous can produce such offsets. These and other forms of bundling can arrest damaging instabilities in categorization.

The viticulture industry needs advanced grape cultivars with genes that enhance disease resistance and environmental stress tolerance to meet the challenges of a changing climate. To discover beneficial allelic variants of grape genes, we established an F1 mapping population from a cross between two North American grapevines, Vitis rupestris Scheele and Vitis riparia Michx. We generated genotyping-by-sequencing (GBS) markers and constructed parental linkage maps consisting of 1177 and 1115 GBS markers, respectively (LOD threshold ≥ 14), which were validated by mapping the sex-determining locus to chromosome 2. Taking advantage of loci heterozygous in both parents, we also constructed an integrated map containing 2583 markers. We mapped a major quantitative trait locus (QTL) for downy mildew (Plasmopara viticola) resistance to chromosome 10 of V. rupestris using both greenhouse- and in vitro-generated leaf resistance data. This QTL explains 66.5% of the phenotypic variance under greenhouse conditions, and its 2-LOD confidence interval corresponds to region 2,470,297 to 3,024,940 bp on chromosome 10 in the Vitis vinifera L. PN40024 reference genome sequence (assembly 12X.v2). We provide PN40024-projected positions of the GBS markers, which can be used as anchors to develop additional markers for the introgression of this V. rupestris haplotype into cultivated grape varieties.

Grapevine sustainability is impacted by the timing of dormancy initiation and freezing tolerance in fall and winter and chilling fulfillment and bud break in the spring. These traits have genetic and local temperature contributing factors, therefore, this study was undertaken to develop an understanding of these characteristics in four recently developed cold climate cultivars. The cold hardiness and chilling fulfillment profiles were monitored in Brianna, Frontenac gris, La Crescent and Marquette using differential thermal analyses and bud break assays. Bud cold hardiness of all cultivars increased with the declining temperatures from November through February, after which the buds began to lose freezing tolerance. There were significant differences in cold hardiness and chilling fulfillment between cultivars during the endodormant and ecodormant period of winter. Marquette had the greatest freezing tolerance from early November through midwinter suggesting it has potential as a sentinel cultivar for comparisons of new cold climate selections. Brianna was slower to acclimate and deacclimated more rapidly than the other cultivars. Chilling fulfillment under natural field or constant 4 &deg, C conditions showed no main effect differences for chilling accumulation condition, however, there were significant cultivar, condition, and time point interactions, indicating the cultivars differed in chilling fulfillment responses.

Background Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown. Results Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season. Conclusions These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine ‘Chambourcin’ (Vitis L.) as a model to explore the rootstock–scion relationship. We examined leaf shape, ion concentrations, and gene expression in ‘Chambourcin’ grown ungrafted as well as grafted to three different rootstocks (‘SO4’, ‘1103P’ and ‘3309C’) across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on ‘Chambourcin’ leaf morphology, ionomics, and gene expression., Horticulture: dissecting the effects of grafting Researchers in the US have uncovered how rootstocks affect scions following grafting, which will help to develop more resilient crops. A team led by Allison Miller of Saint Louis University grafted the ‘Chambourcin’ grape variety onto three different rootstocks and investigated the effect on leaf shape, ion concentration, and gene expression in the scion. They discovered that the rootstock influenced how leaf shape changed in response to different irrigation conditions. A similar irrigation-dependent effect of rootstock was found for the ion composition in the shoot. The team also identified roughly 100 genes with altered expression in each of the grafted vines, including five genes which were altered by all three graft combinations. These findings are a first step toward understanding the relationship between rootstocks and scions and modulating it to produce crops better adapted to challenging environments.

Significance We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes (H1 and H2) among the cultivated grapevines, both chimeras of male (M) and female (f) haplotypes. The two independent recombinations carry different genetic signatures which long predate the domestication of grapevine, suggesting independent evolutions of this trait in wild European grapevine gene pools prior to human domestication., Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.

Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD buds. Gene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.

Projects like highways, bridges, pipelines, and wildlife corridors exhibit indivisibilities — we need the whole thing to have anything of value. Many environmental and social goals have a similar all-or-nothing character: staying above or below a certain critical threshold can make all the difference. This essay focuses on the role of visibility in addressing resource dilemmas that have this structure. I examine how two kinds of visibility can help avoid catastrophic consequences and advance desirable ones. The first involves recognizing when an indivisibility is present — that is, appreciating the vulnerability of resources to thresholds and cliff effects before it is too late. The second involves seeing how individual decisions about resources stack together to generate outcomes. When a resource problem suffers from poor visibility along these dimensions, finding ways to clear the view can improve the prospects for cooperative solutions.

Resources often produce more value in combination than they do separately: think of segments of a highway or parts of a machine. I argue that property’s defining purpose is to group together complements, and that property law and theory should focus on identifying and realizing valuable bundles of resources. While some complementarities align with traditional asset boundaries and can be protected by exclusion rights, realizing others requires crossing or eschewing boundaries to recombine resources in ways that further larger social, economic, or ecological objectives. The gains associated with the entrenching and excluding functions of property thus vie with the gains that come from breaking through those entrenchments to reconfigure resources and rights. Conceptualizing property as complementarity – a kind of bundling machine – allows both sorts of projects to be accommodated within a common analytic structure. A law-of-complements view thus offers a new way to understand, in functional terms, what is distinctive about property. Taking complementarity seriously also has dramatic distributive implications, given that some of the most valuable complementarities exist between human capital and property.

SummaryIn many perennial crops, grafting the root system of one individual to the shoot system of another individual has become an integral part of propagation performed at industrial scales to enhance pest, disease, and stress tolerance and to regulate yield and vigor. Grafted plants offer important experimental systems for understanding the extent and seasonality of root system effects on shoot system biology.Using an experimental vineyard where a common scion ‘Chambourcin’ is growing ungrafted and grafted to three different rootstocks, we explore associations between root system genotype and leaf phenotypes in grafted grapevines across a growing season. We quantified five high-dimensional leaf phenotyping modalities: ionomics, metabolomics, transcriptomics, morphometrics, and physiology and show that rootstock influence is subtle but ubiquitous across modalities.We find strong signatures of rootstock influence on the leaf ionome, with unique signatures detected at each phenological stage. Moreover, all phenotypes and patterns of phenotypic covariation were highly dynamic across the season.These findings expand upon previously identified patterns to suggest that the influence of root system on shoot system phenotypes is complex and broad understanding necessitates volumes of high-dimensional, multi-scale data previously unmet.

Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research.

This chapter examines whether and how malign motives can convert the otherwise innocent exercise of a property right into a civil wrong. As a doctrinal matter, courts have been willing to grant that motives do indeed matter in certain cases. Tracking a distinction drawn within the theory of rights proper between specificationism and generalism, this chapter imagines two ways of making sense of this phenomenon: one might liken property rights to a lattice wherein they are defined permanently at the outset to exclude badly motivated conduct, or one might instead analogize them to a blanket in which holes can be cut around badly motivated acts piecemeal. The chapter opts for the second conceptualization because it meshes better with property’s in rem aspect—they “cover” all cases, one might say—and the organic way property rights evolve. Motives rarely alter property rights, but by factoring in the owner’s incivility as well as victims’ interests and broader social interests, exceptional cases come into focus that illuminate the structure of property rights.

Background De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). Results The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families. Conclusions The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data. Electronic supplementary material The online version of this article (10.1186/s12864-018-4434-2) contains supplementary material, which is available to authorized users.

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent., Trait introgression requires universal markers, but cross-species transferability of current SNP markers can be as low as 2%. Here, the authors use an AmpSeq haplotype strategy targeting the collinear core genome for marker development and show transferability increases to 91.4% in the Vitis genus.