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Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation. [ABSTRACT FROM AUTHOR]

Chloroplast DNA (cpDNA) is most often maternally inherited and highly conserved leading to previous observation of little to no sequence variation. Comparing cpDNA haplotypes have provided valuable insight into the establishment and migration of polyploid populations. However, to use chloroplast haplotypes to their full potential intrapopulational variation needs to be addressed. In this study, cpDNA haplotype variation was surveyed within 16 natural populations of prairie cordgrass ( Spartina pectinata Link) located east of the 100th west meridian and north of the 35th north parallel in the U.S.A. using two non-coding, polymorphic chloroplast regions. Two main clades were defined with subclades as follows: haplotype 1 and haplotype 2A and 2B. It was discovered that seven populations showed intrapopulational chloroplast genome variation. Of the total amount of variation, 95.5% occurred within the octoploid populations and 4.5% occurred within the tetraploid populations. Both variant haplotypes, 2A and 2B, were found in a larger sampling of one of the natural populations, but no variation was found in a mixed ploidy population. The intrapopulational cpDNA variation we found in this study cannot directly be related to mechanisms of introduction of the non-native populations into native populations. Therefore, this cpDNA variation could be novel natural variation that has been fixed as the octoploid populations were established and moved northwest. This analysis provides insight into determining the usefulness of indels and single nucleotide polymorphisms for population identification and may provide information in regards to the origin of chloroplast variation and its subsequent fixation and establishment in natural prairie cordgrass populations. [ABSTRACT FROM AUTHOR]

Information on genome size, ploidy level, and genomic polymorphisms among accessions of the genus Miscanthus can assist in taxonomic studies, help understand the evolution of the genus, and provide valuable information to biomass crop improvement programs. Taxonomic investigation combining variation in plant morphology, genome size, chromosome numbers, and simple sequence repeat ( SSR) marker polymorphisms were applied to characterize 101 Miscanthus accessions. A total of 258 amplicons generated from 17 informative SSR primer pairs was subjected to cluster and principal coordinate analysis and used to characterize genetic variation and relationships among 31 Miscanthus accessions, including four interspecific Miscanthus hybrids created from controlled pollinations, and four Saccharum, six Erianthus, and one Sorghum bicolor accessions. Miscanthus accessions were distinct from accessions in the genera Erianthus and Saccharum. Miscanthus accessions fell into five taxonomic groups, including the existing taxonomic section Miscanthus, diploid and tetraploid Miscanthus sacchariflorus, and a fourth ( M. × giganteus) and fifth group ( Miscanthus 'purpurascens'); the last two being intermediate forms. In contrast to previous work, our findings suggest diploid and tetraploid M. sacchariflorus are taxonomically different, the latter more closely related to M. sacchariflorus var lutarioriparius. We also suggest that Miscanthus 'purpurascens' accessions are interspecific hybrids between Miscanthus sinensis and diploid M. sacchariflorus based on DNA content and SSR polymorphisms. The evolution of Miscanthus and related genera is discussed based on combined analysis and geographical origin. [ABSTRACT FROM AUTHOR]

• Premise of the study: Looming petroleum shortages and projected negative impacts of human-induced climate change may be partly alleviated by the development and use of bioenergy feedstock crops. Miscanthus xgiganteus, a highly productive sterile triploid hybrid grass that was discovered in Japan several decades ago, has considerable potential as an alternative source of energy. Given the risks, however, involved in the reliance upon production of one clone of this hybrid, which is a natural cross between Miscanthus sacchariflorus and Miscanthus sinensis, for lignocellulosic bioenergy production, natural occurrences of triploidy were investigated in sympatric populations of tetraploid M. sacchariflorus and diploid M. sinensis in Japan. • Methods: Seeds were counted and DNA content was estimated by flow cytometry for plants of M. sacchariflorus and M. sinensis in several sympatric populations throughout Japan. Chromosomes were also counted for select plants. • Key results: Based on seed-set data, M. sacchariflorus has significantly lower seed set than M. sinensis in Japan. Putative triploid seeds were found on M. sacchariflorus plants in southern Japan. • Conclusions: This is the first report of the natural occurrence of Miscanthus triploid plants in several decades. If found to be sterile and similar in productivity to the commonly cultivated clone of M. xgiganteus, these triploid plants might serve as additional sources of genetic variation for bioenergy production. Seed set data also indicates that other triploid plants might be found in more northern regions of Japan. [ABSTRACT FROM AUTHOR]

• Amaranthus tuberculatus represents one of the most dramatic cases of weed invasion documented in the midwestern USA. The species is infamous for evolving resistance to multiple herbicides, and predicting whether these resistances may be transferred to widespread weeds of the Amaranthus hybridus aggregate is a matter of epidemiological concern. Here, we explore the patterns of genetic exchange between Amaranthus tuberculatus and A. hybridus in an effort to understand whether allele introgression occurs throughout the genome and if fecundity penalties are associated with genetic exchange. • We evaluated 192 homoploid BC1s at 197 amplified fragment length polymorphism (AFLP) loci, as well as two loci associated with herbicide resistance: ALS and PPO. We also assessed the fecundity of each genotype by evaluation of seed production or pollen development. • It was discovered that genetic exchange between the species is unidirectional. Whereas A. hybridus alleles transfer with little or no penalty to A. tuberculatus, the reciprocal exchange is significantly distorted and potentially of limited evolutionary consequence. • Our previous hypothesis suggesting unidirectional introgression at ALS owing to circumstantial linkage is now modified to account for the more generalized distortion of genetic exchange observed in this study. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In maize, the st1 mulant has been observed to result in chromosomes that stick together during both mitotic and meiotic anaphase. These sticky chromosomes result in abnormal chromosome separation at anaphase. Although the mechanism producing the st1 mutant phenotype is unknown, delayed replication of knob heterochromatin has been implicated in similar phenomena that result in sticky chromosomes. Primed in situ labeling (PRINS) was used to locate the 180-bp knob DNA sequences on mitotic metaphase chromosomes of several maize lines. The chromosomal regions labeled by PRINS corresponded to the reported C bands found in these lines. Additionally, PRINS was used to identify knob-bearing regions in anaphase spreads of a line carrying the st1 mutant and a nonmutant line having a similar number of chromosome knobs. The increase in abnormal anaphasc figures in the st1 mutant was not accompanied by an increase in association of knob DNA with abnormal anaphases. Thus, the increase in chromosomal stickiness appears to be due to an increase in stickiness of knob and nonknob chromosomal regions. The mechanism responsible for the st1 mutant, therefore, is hypothesized to be different from that implicated in the other previously described sticky chromosomes situations. [ABSTRACT FROM AUTHOR]

Concerns have arisen about the possible effects of herbicide contamination in aquatic ecosystems. Crop herbicides are introduced into the aquatic environment both inadvertently through runoff events and intentionally through the use of those registered for use in waterways. Acetochlor and atrazine are two agricultural crop herbicides that have often been reported to contaminate waters. Diquat and fluridone are both registered aquatic management herbicides. In this study, a mammalian in vitro cell cytotoxicity assay was used to evaluate the cytotoxicity of these four commonly used herbicides. The ranked order of the cytotoxicity was: diquat (C1/2 = 0.036 mM ± 0.011) > acetochlor (C1/2 = 0.060 mM ± 0.010) > fluridone (C1/2 = 0.172 mM ± 0.029) atrazine (C1/2 = 0.581 mM ± 0.050). In addition, flow cytometric analysis was conducted on CHO cells to investigate the potential impact of these four herbicides on the cell cycle. Acetochlor and diquat had the greatest impact on the cell cycle. Acetochor exposure resulted in a decreased number of cells in the G1 phase of the cell cycle, whereas diquat exposure resulted in a decreased number of cells in both the G1 and G2 phases. Both atrazine and fluridone resulted in a decrease in cells in the G2 phase. The agricultural crop herbicides and aquatic management herbicides gave similar results in cytotoxicity and in the cell-cycle assay at the end points tested. [ABSTRACT FROM AUTHOR]

Weedy Amaranthus species pose a serious threat to agriculture. One of the areas that causes the greatest concern is development of herbicide resistance and subsequent transfer of herbicide resistance genes among the species. To determine the potential impact of interspecific hybridization, one must first be able to detect such hybrids. To determine if genome size could be useful in the detection of inter-specific hybrids among the weedy Amaranthus species, the genome sizes of the weedy Amaranthus species sympatric in Illinois were analyzed. In a series of experiments, the genome sizes of these species were determined by flow cytometric analysis. A significant variation was observed with respect to nuclear DNA content in the eight species examined. The genome sizes ranged from ≈0.95 pg in A. palmeri to ≈1.4 pg in A. tuberculatus. Overlap of genome sizes among the species does exist; however, due to the reproductive biology of the species, this overlap does not preclude the detection of interspecific hybrids. Any dioecious weedy Amaranthus plant in Illinois that has a genome size between 1.3 pg and 1.1 pg is probably a hybrid. Thus, the potential for genome size determination to reveal interspecific hybrids among weedy Amaranthus species has been demonstrated. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Amphibian metamorphosis is a complex process that has been speculated to involve DNA amplification and chromatin rearrangement. While recent studies have concentrated on chromatin rearrangement, only a few studies have dealt with variation in the amount of DNA during amphibian metamorphosis. In this study, nuclei were isolated from Xenopus laevis at various developmental stages. The nuclei were examined in both an unfixed state and a fixed state. The nuclei were stained with propidium iodide and analyzed by flow cytometry to determine their fluorescence intensity. The unfixed nuclei had higher fluorescence variation compared with the fixed nuclei. This increase in variation appeared due to the presence of nuclei of variable fluorescence intensity within the unfixed nuclei. Upon optimum fixation, which has been speculated to result in more homogeneous chromatin conformation and to reduce staining artifacts, the nuclei were observed to have less fluorescence intensity variation. The differential fluorescence observed in this study is consistent with the hypothesis that large-scale intra- individual DNA variation is not associated with amphibian metamorphosis. [ABSTRACT FROM AUTHOR]

Determining the ploidy of plant germplasm is a necessary step in breeding or genetic studies in species. The purpose of this research was to determine the presence of ploidy level differentiation of hairy vetch (Vicia villosa) germplasm. Flow cytometry and root tip chromosome squashing methods were employed to assess 45 accessions labeled V. villosa available through the USDA germplasm collection. Flow cytometry determined that 43 of the accessions were 2C, one accession was 4C, and one accession was 6C. Analysis of accessions by root tip chromosome counts indicated that all accessions were diploid. The 2C accession contains 14 chromosomes and their chromosomes were approximately one-half and one-third in size as compared to the chromosomes of the 4C and 6C accessions, respectively. The 4C accession was observed to have 16 chromosomes and the 6C accession was observed to have 14 chromosomes. The large-scale differences in DNA amounts were due to chromosomal size variability as opposed to ploidy differences. This revealed the incidence of species misidentification of these two V. villosa accessions to be Vicia pannonica. All the V. villosa accessions were observed to be diploid and have similar DNA amounts. Flow cytometry proved to be useful in the efficient assessment of these accessions. [ABSTRACT FROM AUTHOR]

Reports of genome size variation in soybean [Glycine max (L.) Merr.] have ranged from 40 to 0%. This wide range has resulted in doubts of the existence of intraspecific DNA variation in soybean. Eighteen soybean lines were analyzed by flow cytometry to determine their genome size. The lines were selected on the basis of diversity of origin. Intraspecific genome size variation was observed at approximately 4%. To ensure that the variation observed was reproducible and not due to technique error, the two highest and lowest genomes size accessions were reanalyzed. The order and variation observed between the high and low genome size accessions were maintained. To ensure further that the differences were reproducible, seeds from the two highest and lowest genome size accessions were planted in different locations in the USA, grown to maturity, harvested, and the seeds returned to Illinois. The harvested seed was analyzed and again the order and variation in genome size between the high and low genome size accessions were similar to the previous two analyses even though more than 1 yr had passed between the analysis. In addition, two experiments using Amaranthus palmeri S. Wats as an internal standard were conducted. In both of these experiments, the observed variation between the previously reported high and low genome size soybean lines was approximately 1 to 2%. The variation between the high and low genome size soybean lines is reproducible. The variation reported here indicates that the DNA amount variation is between 1 and 4%, lower than was originally reported. [ABSTRACT FROM AUTHOR]

For improvement of hairy vetch (Vicia villosa Roth) as a winter cover crop, it is necessary to gain insight into the magnitude of variability present in the species. This study was conducted to assess the sources of genetic and phenotypic variability of V. villosa accessions. Thirteen morphological and agronomic traits were measured on 42 populations of V. villosa and two populations of V. pannonica Crantz in field studies at Urbana, IL, for 2 yr. These measurements include initial seed weight, germination, stem length, stem width, leaf length, and leaf width in the fall and spring, winter survival, biomass, and a ratio of organic C to total N (C:N ratio) of the plants. The multivariate data set was analyzed by canonical discriminant analysis (CDA) in combination with a clustering procedure. In this analysis, the first two canonical variates were significant and accounted for 94% of the among-accession variability. The canonical variates indicated that fall and spring measurements of the leaf and stem, and C:N ratio are the most differentiating traits among the accessions. The canonical variates were used to cluster the accessions into four subgroups on the basis of the differentiating traits. Canonical discriminant analysis was useful in identifying the genetic variation and the traits that better describe the variation among hairy vetch populations. Cluster analysis was successful in differentiating the accessions into similar subgroups on the basis of the measured traits. Plant breeders can use the information on variation among Vicia accessions and focus on traits of particular significance. [ABSTRACT FROM AUTHOR]

Flow cytometry was used to characterize isolates of Phialophora gregata, the causal organism of brown stem rot (BSR) in soybean, using the fluorescence intensity of YOYO-1 stained conidia. The conidia were derived from isolates of P. gregata isolated from fieldgrown soybean vascular tissue from two locations in Wisconsin. At each location, four soybean cultivars were grown. Two cultivars were susceptible to BSR and two cultivars were resistant to BSR. Ninety-six isolates, one per plant, were characterized for DNA content. The stained conidia were analyzed with an EPICS XL (Coulter Corporation, Hialeah, Florida, USA) flow cytometer cell sorter with CICERO software (San Rafael, CA, USA). The isolates differed in their mean DNA content, ranging from 78.0 to 116.8 arbitrary units. Statistical analysis showed a significant difference in the DNA content variability of the isolates between the two locations. A notable difference in DNA content variability was observed between the isolates collected from the resistant cultivars between the two locations. However, no significant variation occurred in the DNA content of the isolates collected from susceptible cultivars within or between locations. The observed variation among the isolates is hypothesized to be due to the occurrence of separate populations of P. gregata and selection for mean DNA content that could colonize specific plant genotypes. [ABSTRACT FROM AUTHOR]

Several studies have indicated a possible link between genome size and earliness in maize. In this study, an original maize population, South African photo-period insensitive maize composite II (C[SUB0]) and several selected generations were analyzed for days to flowering, plant height, ear height, and yield. The selection criterion was earliness. Over six cycles of selection a 14-day decrease in days to flowering was obtained with no significant reduction in grain yield. In the initial population (C[SUB0]) and the most advanced selection (C[SUB6]) 101 plants were analyzed for nuclear DNA content. A significant decrease in the mean nuclear DNA content of the C[SUB6] population (102 AU) was observed with respect to the C[SUB0] population (105 AU). This reduction was the result of a decrease in frequency of plants in the C[SUB6] population with large genome sizes. Therefore it was concluded that selection for earliness resulted in selection against plants with large genome sizes. Hence, the nucleotype of a maize plant can be modified by selection such as early flowering time. [ABSTRACT FROM AUTHOR]

Previous studies have indicated a relationship between genome size and cold tolerance in plants. Many species adapted to growth in cool environments have large genome sizes. These studies are based on interspecific DNA content variation. In this study, the nuclear DNA content of eight maize populations was determined. These populations were obtained from the University of Nebraska and represent populations selected for cold tolerance and their respective unselected original populations. Intraspecific DNA content variation was observed between the selected and unselected populations. Upon assessing the data based solely on cold tolerance, no clear relationship between genome size and cold tolerance was apparent. When both freeze tolerance and cold tolerance were considered, populations which were cold tolerant and exhibited a certain degree of freeze tolerance were observed to have significantly larger genomes relative to the unselected populations. Thus, it appears that the relationship between intraspecific genome size variation and cold tolerance is similar to the relationship between interspecific genome size variation and growth at cooler temperatures in plants. [ABSTRACT FROM AUTHOR]

Nuclei were isolated from stems, mesocotyls, nodal roots and root tips of two maize hybrids. The fluorochrome, propidium iodide (PI), was used to stain the nuclei that were passed through a flow cytometer-cell sorter. Significant differences in fluorescence intensities were observed among the diploid nuclei from the different plant organs. These observations, in conjunction with previously reported DAPI fluorescence data, reflect the state of chromatin condensation in diploid nuclei isolated from meristematic and differentiating tissues. Nuclei from root meristematic tissues showed no or very little chromatin condensation. Mesocotyls and nodal roots, 1-wk-old, appeared to contain chromatin in a more diffuse state owing to completed differentiation which allows more DNA to be accessible to PI. Mesocotyls, 2-wk-old owing to senescence, contained degraded chromatin in which DNA was more accessible to PI because it lacked associated proteins. The diploid nuclei from stems had the highest amount of chromatin condensation. The results show the usefulness of flow cytometry for analyzing chromatin condensation in plant nuclei. The study also shows the importance of selecting a particular type of fluorochrome in the analysis of nuclear chromatin. [ABSTRACT FROM AUTHOR]

With 1 figure and 2 tables Abstract In vivo doubled haploid (DH) technology provides a means of creating new maize inbred lines relatively quickly; however, productivity is limited by false-positive (FP) plants for haploidy and for dihaploidy, which consume resources of space and labour until detected. This work examines the potential for using stomata guard cell length measurement as a means for early detection of FP plants. We found that the true haploid and DH plants could be differentiated from FP and untreated diploid controls as early as Leaf 2 stage by stomata guard cell length measurement. Furthermore, DH plants were distinguishable from haploid and other diploid plants by the Leaf 7 growth stage. Results suggest that, when used together with screening through the anthocyanin colour marker system and flower fertility, stomata guard cell measurement is an easy, non-destructive, early screening method that may lead to a greater efficiency in DH production systems and optimization of resource allocation for space and labour. [ABSTRACT FROM AUTHOR]

Date palm is an important fruit crop and member of palm family, reported with varied ploidy levels, i.e., 14 (2n = 28) to 18 (2n = 36) pairs of chromosomes and genomic size due to the limited work done on its cytological aspect. The amount of nuclear DNA content is extremely important to understand the hereditary constituent of any species. Hence, the present study was conducted with the aim to estimate the ploidy level and especially the genomic size (C value) of date palm by studying fifty date palm cultivars with flow cytometry using propidium iodide (PI) as the fluorescent dye. The maize genome size (5.14 pg) was used as the internal reference. The results obtained regarding genomic size of date palm cultivars significantly varied and ranged from 1.59 to 1.84 pg 2C−1 or 780.11 to 903.06 Mbp when converted into base pairs of DNA. The average genome size of studied cultivars was observed to be 1.726 2C−1, while, that of nuclei significantly varied from cultivar to cultivar and appeared independent to the genomic size of the studied cultivars. Intraspecific variations were not detected among five exotic cultivars (Amber, Sugae, Medjool, Safawi and Ajwa) grown in Pakistan in relation to their place of origin. The cluster analysis exhibited two main groups of cultivars, the first group comprised 65.3% (33 cultivars) and the second group contained 35.7% (17 cultivars). In addition, no ploidy was observed among all the studied cultivars. The findings regarding the estimated genomic sizes of studied cultivars may be helpful in understanding date palm genetics, breeding and genome sequencing programs further. [ABSTRACT FROM AUTHOR]

Atrazine is one of the major surface water contaminants in the midwestern United States. Speculations have arisen on the potential effects of atrazine contamination to anuran larvae developing in these surface waters. In this study, Xenopus laevis tadpoles were exposed to environmentally relevant concentrations of atrazine. Nuclear and morphological endpoints were used to assess the effects of atrazine on developing X. laevis. Atrazine significantly affected metamorphing X. laevis after three-weeks exposure compared to controls as revealed by flow cytometric nuclear DNA analysis. The flow cytometric analysis was reflective of developmental effects. The number of nuclei per organism also was analyzed. Nuclei number was found to be associated with X. laevis development. Nuclei counting showed significant effects of atrazine after five-weeks exposure. A third endpoint, Nieuwkoop and Faber (NF) morphological staging, also demonstrated that atrazine significantly affected development after four weeks. Atrazine was found to alter the timing of metamorphosis of X. laevis using both nuclear analysis and gross morphology. The NF staging was found to be a sensitive assay to measure effects of development, whereas flow cytometry provided an impartial quantitative measure [ABSTRACT FROM AUTHOR]

Pesticide contamination of drinking water supplies has increased over the past decade. A major concern is how exposure to combinations oflow levels of pesticides, especially herbicides, could affect publichealth. Flow cytometric analysis was performed to determine the clastogenic potential of herbicide interaction on Chinese hamster ovary (CHO) cells. The cells were exposed to atrazine, simazine, cyanazine, and all possible combinations of these chemicals for 48 hr. Two concentrations were used for each sample: the U.S. EPA maximum contamination level (MCL) and the highest contamination level found in Illinois water supplies. Nuclei were isolated from the cells and analyzed by flow cytometry. The effects of clastogenicity were measured by the coefficient of variation (CV) of the G1 peak of whole cells and the change in CV of the largest chromosome in the flow karyotype. At both levels tested, atrazine caused chromosomal damage to the CHO cells. Simazine was observed to induce whole-cell clastogenicity but not flow karyotype damage. Cyanazine did not induce any measurable chromosomal damage in either analysis. Each of the herbicides, although all three were triazines, had different effects with respect to chromosome damage as measured by flow cytometry. CHO cells treated with a combination of atrazine and simazine, or atrazine and cyanazine, were observed to have whole-cell and flow karyotype damage. This damage was, however, equal to or less severe than the damage caused by either atrazine or simazine alone. No synergy was observed. When all three herbicideswere combined, three of the four possible combinations gave no observable clastogenic response. [ABSTRACT FROM AUTHOR]