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Plant genome size influences the functional relationships between cellular and whole‐plant physiology, but we know little about its importance to plant tolerance of environmental stressors and how it contributes to range limits and invasion success. We used native and invasive lineages of a wetland plant to provide the first experimental test of the Large Genome Constraint Hypothesis (LGCH)—that plants with large genomes are less tolerant of environmental stress and less plastic under stress gradients than plants with small genomes. We predicted that populations with larger genomes would have a lower tolerance and less plasticity to a stress gradient than populations with smaller genomes. In replicated experiments in northern and southern climates in the United States, we subjected plants from 35 populations varying in genome size and lineage to two salinity treatments. We measured traits associated with growth, physiology, nutrition, defense, and plasticity. Using AICc model selection, we found all plant traits, except stomatal conductance, were influenced by environmental stressors and genome size. Increasing salinity was stressful to plants and affected most plant traits. Notably, biomass in the high‐salinity treatment was 3.0 and 4.9 times lower for the invasive and native lineages, respectively. Plants in the warmer southern greenhouse had higher biomass, stomate density, stomatal conductance, leaf toughness, and lower aboveground percentage of N and total phenolics than in the northern greenhouse. Moreover, responses to the salinity gradient were generally much stronger in the southern than northern greenhouse. Aboveground biomass increased significantly with genome size for the invasive lineage (43% across genome sizes) but not for the native. For 8 of 20 lineage trait comparisons, greenhouse location × genome size interaction was also significant. Interestingly, the slope of the relationship between genome size and trait means was in the opposite direction for some traits between the gardens providing mixed support for LGCH. Finally, for 30% of the comparisons, plasticity was significantly related to genome size—for some plant traits, the relationship was positive, and in others, it was negative. Overall, we found mixed support for LGCH and for the first time found that genome size is associated with plasticity, a trait widely regarded as important to invasion success. [ABSTRACT FROM AUTHOR]

White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash. [ABSTRACT FROM AUTHOR]

Polyploidy is conspicuous in the genus Phlox, and some species exhibit variation in ploidy levels, or cytotypic variation. Diploid, tetraploid and hexaploid populations of P. nana occur across parts of the species distribution in the southwestern United States and northern Mexico. A recent study highlighted two areas for which ploidy level inferences were challenging: a population on the Pecos Plains of New Mexico ("Caprock") and the Davis Mountains region of West Texas. Plants in these areas were sampled and chromosome counts and flow cytometry methods were used to assess ploidy levels and genome sizes. Homoploid variation in genome size was unambiguously documented: the genome size of tetraploid plants from the Davis Mountains was significantly larger than that of plants from Caprock. The general condition of larger genome sizes for plants in the Davis Mountains explains previous difficulty in determining ploidy levels within the region. Most plants at the Caprock population appeared to be tetraploid (2n=28), but chromosome counts revealed variants, including some putative pentaploids. Within the Davis Mountains region, both diploid (2n=14) and tetraploid (2n=28) cytotypes were documented, with a parapatric distribution. Overall, this study clarifies patterns of cytotypic diversity in P. nana, highlights an example of infraspecific, homoploid genome size variation, and contributes to a framework for ongoing evolutionary investigation in this study system. [ABSTRACT FROM AUTHOR]

Annual ryegrass (Lolium multiflorum Lamarck) is planted annually on more than 1 million ha of pastures in the southeastern United States. The exact ploidy level and genome size of the annual ryegrass germplasm collection (USDA- ARS, Germplasm Resources Information Network, GRIN) are unknown and the future use of this germplasm relies on their determination. The study was conducted to (i) estimate the ploidy level and determine the DNA content of 139 accessions from the GRIN collection, 15 experimental lines, and 13 commercial cultivars through flow cytometry; and (ii) identify morphological and agronomic characteristics that could be used to differentiate diploid from tetraploid annual ryegrass. A total of 140 diploid and 27 tetraploid lines were successfully identified through flow cytometry. The average 2C DNA content was 6.13 ± 0.36 pg for the diploid lines and 12.30 ± 0.83 pg for the tetraploids. Diploid and tetraploid annual ryegrass showed significant differences for morphological and agronomic variables such as seed size, leaf width and length, guard cell size, plant height, tiller size, plant biomass, and seed head length, and all variables were significantly correlated with DNA content. The use of morphological and agronomic variables may guide the determination of ploidy when flow cytometry is not available. Ploidy level and genome size information will benefit those that request accessions from the GRIN system for specific studies at the diploid or tetraploid level in the species. [ABSTRACT FROM AUTHOR]

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species. [ABSTRACT FROM AUTHOR]

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species. [ABSTRACT FROM AUTHOR]

Background and Aims The amount of DNA in an unreplicated haploid nuclear genome (C-value) ranges over several orders of magnitude among plant species and represents a key metric for comparing plant genomes. To extend previously published datasets on plant nuclear content and to characterize the DNA content of many species present in one region of North America, flow cytometry was used to estimate C-values of woody and herbaceous species collected in Wisconsin and the Upper Peninsula of Michigan, USA. Methods A total of 674 samples and vouchers were collected from locations across Wisconsin and Michigan, USA. From these, C-value estimates were obtained for 514 species, subspecies and varieties of vascular plants. Nuclei were extracted from samples of these species in one of two buffers, stained with the fluorochrome propidium iodide, and an Accuri C-6 flow cytometer was used to measure fluorescence peaks relative to those of an internal standard. Replicate extractions, coefficients of variation and comparisons to published C-values in the same and related species were used to confirm the accuracy and reliability of our results. Key Results and Conclusions Prime C-values for 407 taxa are provided for which no published data exist, including 390 angiosperms, two gymnosperms, ten monilophytes and five lycophytes. Non-prime reports for 107 additional taxa are also provided. The prime values represent new reports for 129 genera and five families (of 303 genera and 97 families sampled). New family C-value maxima or minima are reported for Betulaceae, Ericaceae, Ranunculaceae and Sapindaceae. These data provide the basis for phylogenetic analyses of C-value variation and future analyses of how C-values covary with other functional traits. [ABSTRACT FROM AUTHOR]

The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5× genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/ gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein ( RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein ( LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database () will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community. [ABSTRACT FROM AUTHOR]

A partnership between scientists, high school teachers, and their students provides authentic research experiences to help students understand the nature and processes of science. The Partnership for Research and Education in Plants (PREP) engages students in a large-scale genomics research project using classroom-tested protocols that can help to find the function of a disabled gene in the widely studied plant Arabidopsis thaliana. Here, we describe the framework of PREP in the classroom within the context of the National Science Education Standards. [ABSTRACT FROM AUTHOR]

Carbohydrate-active enzyme glycosyltransferase family 8 (GT8) includes the plant galacturonosyltransferase1-related gene family of proven and putative α-galacturonosyltransferase (GAUT) and GAUT-like (GATL) genes. We computationally identified and investigated this family in 15 fully sequenced plant and green algal genomes and in the National Center for Biotechnology Information nonredundant protein database to determine the phylogenetic relatedness of the GAUTs and GATLs to other GT8 family members. The GT8 proteins fall into three well-delineated major classes. In addition to GAUTs and GATLs, known or predicted to be involved in plant cell wall biosynthesis, class I also includes a lower plant-specific GAUT and GATL-related (GATR) subfamily, two metazoan subfamilies, and proteins from other eukaryotes and cyanobacteria. Class II includes galactinol synthases and plant glycogenin-like starch initiation proteins that are not known to be directly involved in cell wall synthesis, as well as proteins from fungi, metazoans, viruses, and bacteria. Class III consists almost entirely of bacterial proteins that are lipooligo/polysaccharide α-galactosyltransferases and α-glucosyltransferases. Sequence motifs conserved across all GT8 subfamilies and those specific to plant cell wall-related GT8 subfamilies were identified and mapped onto a predicted GAUT1 protein structure. The tertiary structure prediction identified sequence motifs likely to represent key amino acids involved in catalysis, substrate binding, protein-protein interactions, and structural elements required for GAUT1 function. The results show that the GAUTs, GATLs, and GATRs have a different evolutionary origin than other plant GT8 genes, were likely acquired from an ancient cyanobacterium (Synechococcus) progenitor, and separate into unique subclades that may indicate functional specialization. [ABSTRACT FROM AUTHOR]

The article presents the 2008 yearly reports of the Crop Science Society of America (CSSA) in the U.S. It includes lists of presidents of CSSA from 1956 to 2008, the report of the editor-in-chief, the managing editor of the journal "Crop Science," which include the overall size of the journal and the number and types of papers published. The report also contains updates on the "Journal of Plant Registration," "The Plant Genome" and the "Journal of Environmental Quality." The editorial policy ad the editorial board update of the different journals are also mentioned.

The article offers an analysis on the sequence-driven grass model system of foxtail millet, also known as the Setaria Italica. It states that foxtail millet is a diploid C4 panicoid crop, whose genome is being arranged by the Joint Genome Institute (JGI) of the U.S. Department of Energy. It mentions that it will be used in the investigation of plant architecture, genome evolution, and physiology in the bioenergy grasses. Discussions of the origin of foxtail millet are presented.

The comovirus Bean pod mottle virus (BPMV) is widespread in the soybean-growing regions in the United States. It has a bipartite genome consisting of RNA1 and RNA2, which are encapsidated separately. We previously have reported the occurrence in nature of two distinct subgroups of BPMV strains (subgroups I and II), as well as reassortants between the two subgroups. Here, we report the isolation and molecular characterization of naturally occurring partial diploid reassortant strains, which are diploid for RNA1 and haploid for RNA2. Whereas the RNA1s of the partial diploids are derived from two distinct strain subgroups (I and II), the RNA2 is derived from either subgroup I or II. The partial diploid strains induced strikingly severe symptoms on soybean, which could be explained based on the presence of two distinct RNA1s in the same plant. This conclusion was supported by the finding that pseudo-recombinants constructed with two diverse RNA1s induced very severe symptoms on soybean that mimicked those produced by the naturally occurring partial diploids. No enhancement of symptom severity was observed with pseudo-recombinants constructed with closely related RNA Is. Likewise, no enhancement of symptom severity was noted with pseudo-recombinants that are diploid for RNA2 and haploid for RNA1. The potential role of genetic reassortment in the epidemiology and pathogenesis of BPMV is discussed. [ABSTRACT FROM AUTHOR]

To solve the chronic problem of maize (Zea mays L.) kernel infection by Aspergillus flavus in the southeastern USA, genetic resistance to A. flavus is needed. A 2-yr study of a diallel cross of five parents containing the leafy gene (Lfy) was conducted to evaluate the inhertance of resistance to A. flavus during 2003 and 2004. The maize percent kernel infection (PKI) rates were determined via the media-free and kernel-isolated incubation method. Highly significant general combining ability (GCA), specific combining ability (SCA), and reciprocal effects were found. Parents 914 and A619 had desirable (negative) GCA effects to enhance the average performance of A. flavus resistance in hybrid progeny. The crosses 914 x A632, 914 x Wf9, and Hy x Wf9 had consistently negative SCA effects across years. The reciprocal effects were detected, indicating the presence of maternal effects in the maize kernel and the importance of direction of a cross. For example, A632 x Hy had the largest positive significant reciprocal effect; the reversal of this cross, i.e., Hy x A632, should impart resistance to progeny. ANorth Carolina Design-II analysis of four female lines (914, A632, HY, and Wf9) crossed with three male lines (A619, B73, and Mo17), was used to estimate additive and dominance genetic variances. Narrow-sense heritability for PKI was 37.6% and broad-sense heritability estimate was 89.1%. Breeding procedures to handle both additive and dominance variances would need to be used to improve resistance to PKI. [ABSTRACT FROM PUBLISHER]

The relative susceptibility of 44 genotypes of wild Fragaria L. and commercial cultivars of strawberry Fragaria xananassa Duch to Meloidogyne hapla Chitwood and Pratylenchus penetrans (Cobb) Filipjev & Shuurmans Stekhoven was evaluated in the greenhouse. Eleven genotypes were highly resistant to populations of M. hapla from Washington State and Oregon, with Rf values (initial nematode density/final population density) less than 0.5. However, root growth of most genotypes, including resistant genotypes, was reduced by M. hapla. Thirteen genotypes were ranked more resistant to P. penetrans than F. xananassa 'Totem', a susceptible cultivar. Root growth of most genotypes was not affected by P. penetrans under these experimental conditions. We conclude that commercial cultivars and wild Fragaria genotypes can provide a readily exploitable source of resistance to M. hapla. Conversely, sources of resistance to P. penetrans were uncommon in the germplasm evaluated. The F. xananassa cultivars, which already have commercially important characteristics, appear to be a better source of resistance for both nematode species than the wild, unimproved germplasm. [ABSTRACT FROM AUTHOR]

Presents a list of events significant in the field of plant molecular biology. International Conference on Plant Diseases in France in December 2003; Agricultural Microbes Genome II Conference in California in January 2004; Maize Genetics Conference in Mexico in March 2004; Plant Senescence in Massachusetts in June 2004.

Background: Hard red winter wheat (HRWW; Triticum aestivm L.) plants from genotypes selected in the Northern Great Plains of the U.S. have less tissue water after exposure to cool autumn temperatures than plants from the Southern Great Plains. It is generally assumed that the reduced tissue water content of northern compared to southern cultivars is due to an impedance to water uptake by northern plants as a result of the low autumn temperatures. We hypothesize that if low temperature impedes water uptake then less soil water would be removed by northern than by southern-selected cultivars. This hypothesis was tested by comparing plant water uptake of a northern (FR) and a southern (FS) cultivar in relation to their foliage water content at 2°C. Results: At 2°C foliage water content of FR plants decreased more rapidly than that of FS plants, similar to field results in the fall. During 6 wk, foliage water content of FR plants decreased 20 to 25% of the pre-treatment value, compared to only 5 to 10% by FS plants. Plant water uptake was about 60 g H2O·g FDW-1 by FS plants, while FR plants maintained plant water uptake in excess of 100 g H2O·g FDW-1 during the 6 wk period at 2°C. When four other northern genotypes of equal freeze resistance were studied, foliage water content and plant water uptake change were similar to FR plants. Conclusion: In these northern-selected HRWW cultivars foliage water content reduction resulting from cold acclimation is not due to impedance to plant water uptake. [ABSTRACT FROM AUTHOR]

The article discusses the developments in plant genomics. It cites the move by the U.S. Department of Agriculture (USDA) to inform crop trait firms that regulatory oversight is not required for plants developed through certain novel approaches to genetic modification. Among the companies that were informed are Indianapolis-based Dow AgroSciences and Maryland-based Cibus Genetics.

The article discusses the contribution of Carole Meredith to the success in grape genome efforts in the U.S. Meridith had spent over 30 years studying grape genetics and had helped start the grape genome initiatives that bore fruit last 2007. Before shifting her career to winemaking, she had earned fame for using genetic fingerprinting to resolve the origins of some of the world's great wines including Chardonnay and Cabernet Sauvignon. She shares that their effort in tracing the roots of the iconic American wine grape Zinfandel to an ancient Croatian grape, Crljenak kastelanski, has attracted press and wine-geek consumers. She believes that there are biases in U.S. when it comes to funding of grape research.

The article presents a study which explores how geographic selection mosaics are influenced by resource variability, feeding specialization, and vagility of interacting taxa. Here, researchers examine interactions among ponderosa pine, also called Pinus ponderosa, two allopatric species of tree squirrel, also known as Sciurus, and one type of red crossbill, also known as Loxia curvirosta in the western U.S. Details on the geographical variation in community composition and species interactions are also discussed.

This article discusses a study on secrets about bread-quality genes--and other genes--from the genetic makeup of wheat. Conducted by scientists from the U.S. Agricultural Research Service (ARS), the study found that unraveling the makeup of wheat's gene pool poses a formidable challenge. Olin D. Anderson, a plant geneticist at the ARS, explained that wheat is a complex union of three ancestral grass genomes that together make the wheat genome 10 times the size of the human genome. The scientists are comparing and contrasting genetic material of Chinese Spring wheat with that of several other wheat plants.

The article focuses on the release of several indica rice genetic stocks, by the U.S. Department of Agriculture. These include the Early Plant Death, Narrow Leaf, Extreme Dwarf, and Gold Leaf stocks. They are expected to be useful to scientists conducting studies in germplasm and to breeders for determining lines in breeding programs. Mutant of these genetic stocks is being observed in a single M2 row. Progeny testing of the Early Plant Death produces three segregating rows. Seeds of Narrow Leaf plants are composited to form a genetic stock that is true breeding.

The article discusses the accomplishments of the public policy efforts and initiatives of the American Association of Family and Consumer Sciences in the U.S. It refers to the bill House of Representatives 4635 which was signed by U.S. President Bill Clinton on October 27, 2000. Prior to the signing of Clinton, AAFCS has already persuaded its members through its Public Policy Alert to support the bill because it has included committee language for the National Science Foundation funding for plant genome research and research programs for children. It has reached a final agreement with the members of the Congress, Senate and the Administration which contain funding for many programs of its members including the 21st century community learning centers.

The article provides information on the Plant Genetic Resources, Genomics, and Genetic Improvement national program of the U.S. Department of Agriculture's Agricultural Research Service (ARS). Crop genetic improvement, crop genetic and genomic resources and information management, and crop biological and molecular processes are the three components of the program. It relates how ARS researchers responded to the Ug99 stem rust disease in wheat and barley crops.

The article reports on the increase in the amount of grants supporting plant genome research in the U.S. with funding from the National Science Foundation (NSF) valued at nearly 102 million U.S. dollars. The stated objective of the funding is to increase understanding of plant gene function and plant genome-environment interaction. Thirty-two projects focused on economically important crop plants were chosen by the NSF, including the switchgrass research project at the University of Texas in Austin.

The article reports that the U.S. National Science Foundation has announced that it will award almost $60 million to 20 projects concerned with plant genome research. In addition to this, the U.S. Department of Agriculture awards approximately $13 million in grants via its plant genome program. The U.S. Department of Energy has also awarded similar grants. Purdue University plant genetics researcher Clifford Weil provides quotes.

The article reports that the U.S. National Science Foundation (NSF) has awarded nearly $60 million in grants for plant-genome science in October 2008, with the bulk of the funding allocated to research in crop species. The NSF provided $3.2 million for research on how genetic and biochemical pathways help Medicago truncatula and $4.8 million to Pennsylvania State University for research on corn genetics.

The article reports that plant breeders and scientists are expanding plant genomics research and field studies to figure out the species with the best biofuel potential in the U.S. Many researchers are seeking at well-known species whose genomes have already been sequenced for clues to making other plants better energy crops such as Arabidopsis, rice, poplar and corn. Other researchers plan to take on sequencing projects for species few had cared about. These include perennials such as switchgrass and Miscanthus.

The article discusses the significance of the Plant Genome Initiative to corn growers in the U.S. It is considered as the long-awaited dream of corn farmers because it is geared toward improving crop output and harness corn's potential as a biofuel. The program was just in time for the 50th annual Maize Genetics meeting in Washington, D.C. on February 27 to March 2, 2008. It revealed that Richard Wilson of Washington University and his colleagues pieced together a rough draft of corn's 2.3 billion bases, almost a year ahead of schedule. The initiative was assisted by Senator Christopher Bond, who formerly chaired the panel that oversees National Science Foundation (NSF).

The article reports that it is crunch time for the U.S. National Science Foundation (NSF). It delivered bleak news to backers of a proposed high-energy physics experiment at Brookhaven National Laboratory in Upton, New York. And, in a last-minute reversal, the panel restricted the agency's ability to strike the best deal on the icebreaking services needed to ferry scientists into the Polar Regions. The Senate panel did single out a few programs for special attention, including adding 6 million dollar to the 94 million dollar plant genome program and a similar amount for the Experimental Program to Stimulate Competitive Research to bolster 25 research-poor states. The Senate panel took a whack at the Rare Symmetry Violating Processes project, a high-energy physics experiment at Brookhaven National Laboratory that would look for effects beyond the Standard Model. Finally, the senators sided with the U.S. Coast Guard in ongoing negotiations over who should crunch the pack ice blocking entry to NSF's logistics headquarters in Antarctica, saying NSF "shall procure icebreaking services from the Coast Guard."