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Summary Sweet sorghum accumulates large amounts of soluble sugar in its stem. However, a system‐based understanding of this carbohydrate allocation process is lacking. Here, we compared the dynamic transcriptome and metabolome between the conversion line R9188 and its two parents, sweet sorghum RIO and grain sorghum BTx406 that have contrasting sugar‐accumulating phenotypes. We identified two features of sucrose metabolism, stable concentrations of sugar phosphates in RIO and opposite trend of trehalose‐6‐phosphate (T6P) between RIO vs R9188/BTx406. Integration of transcriptome and metabolome revealed R9188 is partially active in starch metabolism together with medium sucrose level, whereas sweet sorghum had the highest sucrose concentration and remained highly active in sucrose, starch, and cell wall metabolism post‐anthesis. Similar expression pattern of genes involved in sucrose degradation decreased the pool of sugar phosphates for precursors of starch and cell wall synthesis in R9188 and BTx406. Differential T6P signal between RIO vs R9188/BTx406 is associated with introgression of T6P regulators from BTx406 into R9188, including C‐group bZIP and trehalose 6‐phosphate phosphatase (TPP). The inverted T6P signalling in R9188 appears to down‐regulate sucrose and starch metabolism partly through transcriptome reprogramming, whereas introgressed metabolic genes could be related to reduced cell wall metabolism. Our results show that coordinated primary metabolic pathways lead to high sucrose demand and accumulation in sweet sorghum, providing us with targets for genetic improvements of carbohydrate allocation in bioenergy crops.

Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species.

Duckweeds belong to the smallest flowering plants that undergo fast vegetative growth in an aquatic environment. They are commonly used in wastewater treatment and animal feed. Whereas duckweeds have been studied at the biochemical level, their reduced morphology and wide environmental adaption had not been subjected to molecular analysis until recently. Here, we review the progress that has been made in using a DNA barcode system and the sequences of chloroplast and mitochondrial genomes to identify duckweed species at the species or population level. We also review analysis of the nuclear genome sequence of Spirodela that provides new insights into fundamental biological questions. Indeed, reduced gene families and missing genes are consistent with its compact morphogenesis, aquatic floating and suppression of juvenile-to-adult transition. Furthermore, deep RNA sequencing of Spirodela at the onset of dormancy and Landoltia in exposure of nutrient deficiency illustrate the molecular network for environmental adaption and stress response, constituting major progress towards a post-genome sequencing phase, where further functional genomic details can be explored. Rapid advances in sequencing technologies could continue to promote a proliferation of genome sequences for additional ecotypes as well as for other duckweed species.

Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. Creeping bentgrass is a highly outcrossing allotetraploid, making genetic marker development difficult. Genetic markers anchored to miniature inverted-repeat transposable elements (MITEs) were developed in Agrostis that could be used in genetic linkage mapping, quantitative trait loci studies, or diversity analyses. The FindMITE software program identified 495 candidate M ITEs from 16,122 Agrostis DNA sequences. There was evidence of transposition in 79 of the candidate MITEs based on MITE insertional polymorphisms. Genetic markers were developed by MITE-display, a modified amplified fragment length polymorphism technique that anchors amplified fragments to MITEs. Four MITE-display primer combinations were tested on a creeping bentgrass experimental mapping population and 139 polymorphic markers were developed with a polymorphic information content of 0.33. Twenty-eight of the polymorphic genetic markers segregated normally. MITE-display genetic markers are a new class of genetic markers for studies of the Agrostis genome. These genetic markers target transposable elements and provide an easy method of identifying allelic variation between Agrostis accessions that may be used for diversity studies or genetic linkage map development.

Summary The amino acid methionine is a common protein building block that is also important in other cellular processes. Plants, unlike animals, synthesize methionine de novo and are thus a dietary source of this nutrient. A new approach for using maize as a source of nutrient methionine is described. Maize seeds, a major component of animal feeds, have variable levels of protein-bound methionine. This variability is a result of post-transcriptional regulation of the Dzs10 gene, which encodes a seed-specific high-methionine storage protein. Here we eliminate methionine variability by identifying and replacing the cis-acting site for Dzs10 regulation using transgenic seeds. Interestingly, two different mechanisms affect mRNA accumulation, one dependent on and the other independent of the untranslated regions (UTRs) of Dzs10 RNA. Accumulation of chimeric Dzs10 mRNA was not reduced in hybrid crosses and was uncoupled from genomic imprinting by Dzr1, a regulator of Dzs10. Uniform high levels of Dzs10 protein were maintained over five backcross generations of the transgene. The increased level of methionine in these transgenic seeds allowed the formulation of a useful animal feed ration without the addition of synthetic methionine.

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines. Office of Science (BER), US Department of Energy, USDA NIFA; USDA CRISUnited States Department of Agriculture (USDA) [5325-21000-017-00]; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [0922457] Funding Source: National Science Foundation We thank Uffe Hellsten for help with population genetics. Genomic DNA sequencing was performed at the US Department of Energy Joint Genome Institute through the Community Sequencing Program. Deep sequencing of the Bd1-1 transcriptome was performed at the Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR. This work was supported by the Office of Science (BER), US Department of Energy, USDA NIFA, and by the USDA CRIS project 5325-21000-017-00.

A map has been developed of nuclease-hypersensitive sites of P-rr, the standard allele of the P-locus of Zea mays L. Using a traditional DNase I assay, eight such sites have been found that are specific for the expressing tissue and span a region of more than 25 kb of the P-locus, making it one of the largest plant genes yet described. The maps of the standard allele have also been compared with the recently described moderately stable P-pr allele, which arose from epimutation. Six of the eight sites exhibit the same tissue-specificity in P-pr plants, while two stay repressed as in non-expressing tissues of plants with the standard allele. Interestingly, the two repressed sites coincide with two hypermethylated restriction sites that have previously been correlated with the expression potential of the P-pr allele. On the other hand, four of the DNase I sites, coinciding with CpG islands that were not hypermethylated by the epimutation, also showed no differences in their sensitivity to DNase I between the standard allele and the P-pr allele. This suggests that the epimutation affects both site-specific methylation changes and a specific local chromatin structure of the P gene involved in its regulation.

Summary The methionine content in maize kernels is largely determined by the level of a methionine-rich 10 kDa protein, encoded by the gene Zps10/(22). In the maize inbred BSSS53 this gene is over-expressed compared with its normal expression in inbred lines like W64A and W22. This is in part due to the trans-acting factor Zpr10/(22). However, compared with the normal level of expression, this gene is under-expressed in the inbred Mo17 and the high-methionine zein accumulates to very low levels. Therefore, differential expression of this gene between BSSS53 and Mo17 is even larger than in other inbred lines of maize. Repression of 10 kDa zein expression in Mo17 is not due to the translatability of 10 kDa zein mRNA or a cis-acting mutation in the mRNA and neither is it due to a change in the transcription rate per se. However, steady state levels of mRNA appear to be controlled in trans by narrowing the developmental time frame of mRNA accumulation.

During the replication of the minicircular DNA of Escherichia coli 15 an open circular form II has been identified as a precursor of superhelical form I. Pulse-labeled form II DNA contains a newly synthesized linear strand which is non-covalently associated with a circular template strand. Equilibrium centrifugation of isolated linear strands in alkaline CsCI shows that the incorporation of label occurs with equal frequency in either of the complementary strands indicating a symmetrical mechanism of replication. Labeling of replicative intermediates is observed in short pulses at 25 °C. Upon alkali denaturation these molecules yield small labeled DNA fragments (4–6 S) suggesting a discontinuous mode of strand synthesis.

The nucleotide sequence of two zein cDNAs in hybrid plasmids A20 and B49 have been determined. The insert in A20 is 921 bp long including a 5' non-coding region of 60 nucleotides, preceded by what is believed to be an artifactual sequence of 41 nucleotides, and a 3' non-coding region of 87 nucleotides. The B49 insert is 467 bp long and includes approximately one-half the protein coding sequence as well as a 3' non-coding region of 97 nucleotides. These sequences have been compared with the previously published sequence of another zein clone, A30 . A20 and A30 , both encoding 19 000 mol. wt. zeins , have approximately 85% homology at the nucleotide level. The B49 sequence, corresponding to a 22 000 mol. wt. zein, has approximately 65% homology to either A20 or A30 . All three zeins share common features including nearly identical amino acid compositions. In addition, the tandem repeats of 20 amino acids first seen in A30 are also present in A20 and B49 .

The DNA · protein complex (form I*) of minicircular DNA of Escherichia coli has associated with it an endonucleolytic activity which converts the supercoiled form I into an open circular form II by introducing one single-stranded break per molecule. This nick can occur with similar frequency in either strand. Prolonged incubation results in the formation of linear duplex molecules (form III). The endonuclease requires a divalent cation (Mg2+ or Mn2+) and is inhibited by high salt concentration and transfer RNA. It might provide a swivel mechanism during the replication of minicircular DNA.