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Article
Open AccessPhytochromes transmit photoperiod information via the evening complex in Brachypodium
Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been...
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Wireless Fixed Camera Network for Greenhouse-Based Plant Phenoty**
An indoor wireless fixed camera network was developed for an efficient, cost-effective method of extracting informative plant phenotypes in a controlled greenhouse environment. Deployed at the Donald Danforth ...
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Article
Comparative evolutionary genetics of deleterious load in sorghum and maize
Sorghum and maize share a close evolutionary history that can be explored through comparative genomics1,2. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 m...
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Article
Open AccessChlorophyll fluorescence imaging captures photochemical efficiency of grain sorghum (Sorghum bicolor) in a field setting
Photosynthesis is one of the most important biological reactions and forms the basis of crop productivity and yield on which a growing global population relies. However, to develop improved plant cultivars tha...
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Article
Open AccessExceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetra...
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Article
Characterization of aphid resistance loci in black raspberry (Rubus occidentalis L.)
Viruses vectored by the aphid Amphorophora agathonica cause decline in black raspberry plant health resulting in a shortened life and poor fruit quality of the infected plantings. New aphid resistant cultivars co...
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Article
Open AccessExtreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla
Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmos...
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Chapter
Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome
The US Pacific Northwest is the primary production region of black raspberry, and this high-value specialty crop has been underutilized for several decades. Black raspberries contain high levels of anthocyanin...
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Article
Open AccessPrecise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based pl...
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Article
Open AccessA glimpse into the future of genome-enabled plant biology from the shores of Cold Spring Harbor
A report on the 10th plant genome meeting entitled ‘Plant genomes and biotechnology: from genes to networks’, held at Cold Spring Harbor Laboratory, 2–5 December, 2015.
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Chapter
The Brachypodium distachyon Reference Genome
Grasses provide the bulk of human calories but improvement in grass yields is hindered by the characteristically large and complex genomes of these species; the genomes of wheat, maize, and sugar cane are 17,0...
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Article
Open AccessHighly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis
The optical signature of leaves is an important monitoring and predictive parameter for a variety of biotic and abiotic stresses, including drought. Such signatures derived from spectroscopic measurements prov...
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Article
Open AccessSingle-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
Oropetium thomaeum is a resurrection plant that can survive extreme water stress through desiccation to complete dryness, providing a model for drought tolerance; here, whole-genome sequencing and assembly of the...
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Article
Open AccessA genetic linkage map of black raspberry (Rubus occidentalis) and the map** of Ag 4 conferring resistance to the aphid Amphorophora agathonica
We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance.
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Article
Comparative analyses of C4 and C3 photosynthesis in develo** leaves of maize and rice
Efforts to improve the efficiency of photosynthesis in crop plants will benefit from a resource of transcriptomic and metabolomic data on maize and rice.
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Article
Open AccessA new alternative in plant retrograde signaling
The reduced or oxidized state of plastoquinone in chloroplasts regulates splicing in the nucleus to control nuclear gene expression in response to changing environmental conditions.
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Article
Open AccessParallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon
The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has...
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Article
Open AccessFunctional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon
Lignin is a significant barrier in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monom...
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Article
Open AccessMethylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variatio...
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Article
Open AccessGenome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It ...
