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PubMed2001

Defining orthologous groups among multicopy genes prior to inferring phylogeny, with special emphasis on the Triticeae (Poaceae).

Sequence information from multicopy genes has been widely used for phylogenetic inference. Among those sequences analyzed, nuclear 5S rRNA genes, the two internal transcribed spacer regions (ITS1 and ITS2) of the 18S-26S rDNA genes, and the intergenic spacer (IGS) regions of the same 18S-26S rDNA genes have all been used at the specific, generic, familial and tribal levels. Many investigations have used direct sequencing of PCR products to generate sequence data. The merits of an alternate approach, namely, cloning prior to sequencing followed by careful alignment of numerous cloned sequences to discern groups of putative orthologous sequences that may then be useful for the inference of relationships among species and genera, are examined and discussed. This process discerns patterns resulting from several cycles of careful alignment followed by manual editing conducted by eye--an exacting operation especially when sequences are unequal in length due to the presence of additions/deletions. Based upon examples taken from our work on the sequencing of individual 5S rDNA clones from several wheat and barley species (Triticum and Hordeum respectively), and the re-analysis of data of others taken from several studies using the nuclear genes mentioned above, we are able to identify groups of putative orthologous sequences that we have named "unit classes". Furthermore, comparisons between provisional orthologous sequences isolated from different species are required for the inference of phylogenetic relationships between them. Paralogous sequences from different unit classes can be compared to infer evolutionary relationships among repeat types only, i.e. among unit classes. In several cases, the analysis of the sequence diversity obtained from different clones permitted the assignment of unit classes to specific haplomes.

Base Sequence↗
PubMed2001

Differentiation in the Elymus dahuricus complex (Poaceae): evidence from grain proteins, DNA, and crossability.

The status of the taxa Elymus dahuricus Turcz. ex Griseb., E. excelsus Turcz. ex Griseb., E. woroschilowii Probat. and E. tangutorum (Nevski) Hand.-Mazz., all of which are sometimes treated as members of E. dahuricus s.l. or as constituting the E. dahuricus complex, has been investigated using morphological, biochemical (SDS-PAGE of endosperm proteins) and molecular (DNA-AFLP) variation characteristics. Populations include accessions from Siberia, Far East (Russia), Tien-Shan (Kirghizstan), and Tibet and Sichuan Provinces (China). Variation in the morphological characteristics and endosperm proteins patterns have been found in all populations of the complex. DNA variation was very low within populations but was different among populations; this was attributed to genetic drift. Seed fertility of artificial hybrids and F2-F3 progenies in 38 combinations was analyzed. All biotypes studied form a common recombination genepool (RGP). The reproductive compatibility of hybrid combinations decreases with increased geographical separation of the parents. Differences in protein patterns and in genetic variation drawn from DNA-AFLPs and phenotypical segregation in F2 on series of diagnostic characters does not support existing taxonomic treatments of the E. dahuricus complex in Southern Russia, and Central-Asian area. The E. dahuricus complex seems to be a polymorphic species having a wide geographical range and wide genetic variation. The different species need probably be relegated to infraspecific rank. We have refrained from making the necessary combinations pending examination of additional specimens, including specimens of taxa not included in this study and the type specimens of all taxa involved.

Analysis of Variance↗
PubMed2006

Molecular diversity and relationships among Elymus trachycaulus, E. subsecundus, E. virescens, E. violaceus, and E. hyperarcticus (Poaceae: Triticeae) as determined by amplified fragment length polymorphism.

Morphological similarity among E. trachycaulus, E. virescens, E. violaceus, and E. hyperarcticus has often been noted. Taxonomists have tried to discriminate among these taxa using morphological characters and a number of different relationships among them have been suggested. However, the genetic relationships among these taxa are still unknown. AFLP analysis was used to characterize the molecular diversity of these taxa and to examine genetic relationships among them. A high degree of genetic identity was apparent among 7 accessions of E. virescens. The similarity values ranged from 0.90 to 0.99 with an average of 0.94. The mean similarity values among 3 E. hyperarcticus and among 5 E. violaceus accessions were 0.84 (0.81-0.87) and 0.77 (0.66-0.90), respectively. The similarity values among 17 E. trachycaulus accessions ranged from 0.49 to 0.92 with an average of 0.75. The 5 accessions of E. subsecundus displayed high variation, with similarity values between 0.52 and 0.68 and a mean value of 0.59. Both maximum-parsimony (MP) and neighbor-joining (NJ) analyses showed that all 7 accessions of E. virescens formed a clade, indicating a monophyletic origin. On the other hand, Elymus trachycaulus, E. subsecundus, and E. violaceus were each paraphyletic and separated into different genetically distinct groups. Among these 5 taxa, E. virescens was genetically similar to E. trachycaulus, and E. violaceus was genetically similar to E. hyperarcticus.

DNA Fingerprinting↗
PubMed1996

Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence.

The satellite sequence studied was primarily composed of GAA repeats organized in long tracts of heterochromatic DNA. Fluorescent in situ hybridization (FISH) with the GAA satellite (GAA banding) to the chromosomes of barley, wheat, rye, and other Triticeae species produced banding patterns similar to those obtained by N-banding. The GAA-banding patterns of barley are described in detail and those of 12 other Triticeae species are described briefly. In situ hybridization with the GAA-satellite sequence permits identification of all the chromosomes of barley. It is a valuable alternative to other banding techniques, especially in connection with physical gene mapping by FISH. The application of the GAA-satellite sequence for the characterization of genomes in phylogenetic studies of genera containing the sequence is discussed.

Base Sequence↗
PubMed1997

The molecular diversity of the 5S rRNA gene in Kengyilia alatavica (Drobov) J.L. Yang, Yen & Baum (Poaceae:Triticeae): potential genomic assignment of different rDNA units.

5S rRNA sequences from several accessions of Kengyilia alatavica, a member of a tribe that includes wheat and wheat relatives, have been amplified by the polymerase chain reaction, cloned, and sequenced. From an evaluation of the aligned sequences, five 5S unit classes have been discerned. One class consists of short units, while the other four contain longer units. BLAST searches of the GenBank database have allowed us to tentatively assign these to classes found in genomes of other species. For example, the short 5S unit class and one long 5S unit class were designated, respectively, "short P1" and "long P1" because of their match with the comparable sequenced 5S rDNA accessions of Agropyron cristatum, a carrier of the P genome. Another unit class, is coined as "long R1", because of its similarity to the units sequenced from Secale cereale and Secale vavilovii, carriers of the R genome. The third unit class was designated "long S1" and is found also in Elytrigia spicata, a carrier of the S genome. Implications of these findings on the possible association of some unit classes with cytological haplome and on concerted evolution are discussed.

Base Sequence↗
PubMed1999

Tandem repetitive Afa-family sequences from Leymus racemosus and Psathyrostachys juncea (Poaceae)

Tandem repetitive Afa-family sequences of 340 bp are known to occur in wheat and related species of tribe Triticeae. We isolated six and three Afa-family sequences from Leymus racemosus and Psathyrostachys juncea, respectively, both of which are perennial species. The sequences account for 0.5% and 0.2% of L. racemosus and P. juncea genomes, respectively, and using in situ hybridization were located in subtelomeric and interstitial regions of L. racemosus chromosomes. These sequences are clustered with those of Elymus trachycaulus in the phylogenetic tree. Our findings indicate that the Afa-family sequences have been amplified at least twice in the lineage of L. racemosus, P. juncea, and E. trachycaulus.

Journal Article↗
PubMed2000

The 5S rRNA gene diversity in Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen, and Baum (Poaceae: Triticeae): possible contribution of the H genome to the origin of Kengyilia.

Fifty-three units of 5S rDNA sequences from five accessions of Kengyilia rigidula, a member of the tribe Triticeae that also includes wheat, barley, rye, and their wild relatives, have been amplified by the polymerase chain reaction (PCR), cloned, and sequenced. The genome of K. rigidula consists of three haplomes, St, P, and Y. An evaluation of the aligned sequences of the diverse 53 different 5S DNA units yielded three 5S-unit classes. One unit class, Long S1, was assignable to the St haplome, one unit class, the Long P1, was assignable to the P haplome, and a third unit class, Long H1, was assignable to the H haplome. The last was expected to be assignable to the Y haplome, based on previous knowledge. Evolutionary scenarios are put forward to explain this finding. Among those possibilities is that the number of copies of units assignable to the Y haplome is very small and difficult to detect. Short units, reported earlier in K. alatavica, were not found in K. rigidula.

Base Sequence↗
PubMed2005

The genetic basis for inflorescence variation between foxtail and green millet (poaceae).

Grass species differ in many aspects of inflorescence architecture, but in most cases the genetic basis of the morphological difference is unknown. To investigate the genes underlying the morphology in one such instance, we undertook a developmental and QTL analysis of inflorescence differences between the cereal grain foxtail millet and its presumed progenitor green millet. Inflorescence differences between these two species are the result of changes in primary branch number and density, spikelet number, and bristle (sterile branchlet) number; these differences also account for inflorescence variation within the clade of 300+ species that share the presence of bristles in the inflorescence. Fourteen replicated QTL were detected for the four inflorescence traits, and these are suggested to represent genes that control differences between the species. Comparative mapping using common markers from rice and maize allowed a number of candidate genes from maize to be localized to QTL regions in the millet genome. Searches of regions of the sequenced rice genome orthologous to QTL regions on foxtail millet identified a number of transcription factors and hormone pathway genes that may be involved in control of inflorescence branching.

Chromosome Mapping↗
PubMed2006

Low variability of internal transcribed spacer rDNA and trnL (UAA) intron sequences of several taxa in the Festuca ovina aggregate (POACEAE).

Identification and classification of numerous Festuca species is still a difficult problem due to the close morphological resemblance. The most difficult fine fescues to identify belong to the Festuca ovina aggregate, which is the largest group in the genus Festuca. Many taxons are considered to be separate species based on quantitative taxonomic characters, differences in ploidy level or the structure of sclerenchyma cells. In order to evaluate the taxonomic value of DNA-based markers, sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and the chloroplast trnL (UAA) intron was performed in the ten most problematic fine fescues belonging to the Festuca ovina aggregate. Intraspecific ITS variants were found in a single case while in other cases only intragenomic ITS polymorphisms were detected with 1-2 ambiguous positions. Among the sequences of the trnL (UAA) intron even intragenomic polymorphisms were not detected in any of the Festuca species studied. Thus, the results do not support the species status of these ten taxa.

Base Sequence↗
PubMed1996

Nutritional and chemical evaluation of pearl millet grains (Pennisetum typhoides (Burm. f.) Stapf & Hubbard, Poaceae) grown in the Gizan area of Saudi Arabia.

The proximate composition, minerals, amino acid profiles, grain protein contents of Pennisetum typhodies (Burm.f.) Stapf & Hubbard were analysed. The crude protein was 12.3%, fat 5.3% and ash 2.4%. The grains contained similar amounts of phosphorus, calcium and iron as compared to some Indian and African millets. Amino acid analysis indicated the presence of at least 17 amino acids including most of the essential ones. They were also characterized by the presence of sufficient quantities of essential amino acids and limiting amino acids. Comparisons were made with the results reported by FAO/WHO, the seed proteins showed the essential amino acid leucine was highest, while isoleucine and valine were within the range, but threonine, lysine and the sulphur containing amino acids were lower. In general the results indicate that this grain has a good nutritive value.

Amino Acids↗
PubMed2025

The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae).

The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed.

Phylogeny↗
PubMed1999

Floral development and the formation of unisexual spikelets in the Andropogoneae (Poaceae).

We investigated spikelet development in four distantly related species of the grass tribe Andropogoneae to determine whether spikelet development and the formation of unisexual florets are uniform throughout the tribe. We studied development in Bothriochloa bladhii, Coelorachis aurita, Heteropogon contortus, and Hyparrhenia hirta, and compared these with Panicum, a member of the sister tribe Paniceae. Many aspects of spikelet development in the species we have studied correlate with what is already known for Tripsacum and maize (both Andropogoneae), despite variation in how unisexual florets are distributed on the plant. The formation of unisexual spikelets is also uniform. All florets initiate both pistil and stamen primordia. In florets destined to be male, cell death occurs in the subepidermal layers of the gynoecium after the formation of a gynoecial ridge. In florets destined to be female, there is no apparent cell death in the stamens, but growth ceases after anther formation. The similarity in spikelet development and the formation of unisexual florets point to a common genetic mechanism for sex determination throughout the Andropogoneae and possibly the entire Panicoideae. Use of a cell death pathway to cause gynoecial abortion may be the basis of one morphological character that defines the subfamily.

Journal Article↗
PubMed1999

Evolution of a new ecotype of Spartina alterniflora (Poaceae) in San Francisco Bay, California, USA.

We report the discovery and spread of a dwarf ecotype of Spartina alterniflora in San Francisco Bay. Relative to typical S. alterniflora, this dwarf ecotype has one-fifth the tiller height (∼21 cm), tenfold the tiller density (∼4000 tillers/m(2)), and is restricted to growth in the upper intertidal zone. Chromosome counts of the dwarfs are identical to typical smooth cordgrass (2n = 62), and smooth cordgrass-specific random amplified DNA markers confirm the species identity of the dwarf. Field-collected clonal fragments of the dwarf grown for 2 yr under high-nutrient conditions maintained the dwarf syndrome, as did plants grown from the seed of a dwarf. The dwarf condition is not caused by endophytic fungi. The first dwarf smooth cordgrass patch was discovered in 1991, and by 1996 five separate dwarf patches had appeared within 200 m of the original. Since 1991, total area covered by the dwarf ecotype has increased sixfold to 140 m(2). The ecological range of the dwarf smooth cordgrass ecotype is similar to that of S. patens, a competitor on the Atlantic coast. We suggest that the absence of S. patens from most of San Francisco Bay has allowed the dwarf ecotype of smooth cordgrass to survive and spread.

Journal Article↗
PubMed1999

Effects of drainage and soil organic content on growth of Spartina alterniflora (Poaceae) in an artificial salt marsh mesocosm.

An artificial salt marsh mesocosm was constructed using 680-L polypropylene tanks to determine the effect of soil drainage depth and organic content on growth and rhizome proliferation of the salt marsh smooth cordgrass Spartina alterniflora. Soil drainage depth had no effect on accumulation of aerial or subsurface plant tissue, but tanks that had 2.5% soil organic content supported enhanced aerial tissue and rhizome growth compared to tanks that contained sand alone. We propose a mathematical model for predicting the mass of photosynthetically significant leaf tissue without cutting and drying leaves. Implications of these findings for salt marsh creation projects are discussed.

Journal Article↗
PubMed1999

Impact of saltwater spray andsand deposition on the coastal annualTriplasis purpurea (Poaceae).

Pioneer coastal plants occur in areas where sand movement and airborne salt are common. The objectives of this study were to (1) quantify natural levels of salt and sand deposition in relation to distance from the shoreline of Staten Island, New York, and (2) experimentally determine the impact of saltwater sprays and partial sand burial on growth and reproduction of the native dunegrass Triplasis purpurea. This summer annual matures most seeds in cleistogamous spikelets on leaf sheath-enclosed axillary panicles along culm internodes. Levels of salt deposition onto T. purpurea shoots over 6 d were determined with a conductivity meter to be 175 μg/cm(2) at 39 m from shore in 1997, but declined rapidly with increasing distances to 90 m. Sand deposition over 1 mo in the summer averaged 30 mm at 72-90 m from shore. In a greenhouse factorial experiment, seedlings were unburied, buried to 50% height, or buried to 75% height and simultaneously subjected to no sprays, two sprays/wk, or six sprays/wk of seawater over the summer. Sand deposition increased plant size and seed production, but seawater sprays were mostly detrimental, reducing plant size, seed production, and seed mass. However, T. purpurea tolerated moderate levels of salt deposition. The stimulation of growth and reproduction in partially buried plants is adaptive on the sandy soils. Prolific seed production and tolerance to moderate levels of airborne salt allow this annual to maintain high population densities close to shore.

Journal Article↗
PubMed1999

Inheritance of resistance to anti-microtubule dinitroaniline herbicides in an "intermediate" resistant biotype of Eleusine indica (Poaceae).

Inheritance of resistance to the anti-microtubule dinitroaniline herbicides was investigated in a goosegrass biotype displaying an intermediate level of resistance (I). Reciprocal crosses were made between the I biotype and previously characterized susceptible (S) or resistant (R) biotypes. Eight F(1) hybrids were identified, and F(2) populations were produced by selfing. The dinitroaniline-herbicide response phenotype (DRP) of F(1) plants, and F(2) seedlings was determined using a root-growth bioassay. The DRP of F(1) plants of S × I was "susceptible" (i.e., identical to the S parental plants), and the DRP of F(1) plants of I × R was "intermediate" (i.e., identical to the I parental plants). Nonparental phenotypes were not observed in F(1) plants. Results indicated susceptibility to be dominant over intermediate resistance and intermediate resistance to be dominant over high resistance. Analysis of reciprocal crosses ruled out any role for cytoplasmic inheritance. When treated at the discriminating concentration (e.g., 0.28 ppm oryzalin), F(2) seedlings of S × I were classified as either S or I phenotype, and F(2) seedlings of I × R were classified as either I or R phenotype. Again, nonparental phenotypes were not observed. The 3:1 (S:I or I:R) segregation ratios in F(2) seedlings were consistent across all eight F(2) families. The results show that dinitroaniline herbicide resistance in the I biotype of goosegrass is inherited as a single, nuclear gene. Furthermore, it suggests that dinitroaniline resistance in goosegrass is controlled by three alleles at a single locus (i.e., Drp-S, Drp-i, and Drp-r).

Journal Article↗
PubMed1999

Comparison of common cytotypesof Andropogon gerardii(Andropogoneae, Poaceae).

Many plant species contain populations with more than one polyploid cytotype, but little is known of the mechanisms maintaining several cytotypes in a population. Andropogon gerardii cytotypes were compared to evaluate different models of autopolyploid cytotype coexistence. The enneaploid (90 chromosome, 9x) cytotype was found to be larger and taller than the hexaploid (60 chromosome, 6x) cytotype. Seed production is significantly more efficient in hexaploids, but seed production per area was not significantly different. The two cytotypes are not exomorphologically separable in the field because of great plasticity in response to environmental variation and wide variation within each cytotype. These data suggest cytotypic variation is maintained by natural selection.

Journal Article↗
PubMed1999

Distribution of native legumes (Leguminoseae) in frequently burned longleaf pine (Pinaceae)-wiregrass (Poaceae) ecosystems.

Legume species distribution and abundance and selected environmental variables were quantified across a complex gradient (varying in both water-holding capacity and fertility) for frequently burned longleaf pine (Pinus palustris)-wiregrass (Aristida stricta) ecosystems. Legumes were present in all months; however, abundance peaked in June and was minimal after killing frosts in October. Legume species were prominent in the flora (43 species encountered) ubiquitous (94% of 2-m(2) subplots had at least one legume species), and abundant (nearly 120 000 stems/ha). Although most species were widely distributed throughout the gradient, Lespedeza angustifolia was distinctly associated with the more hydric end of the gradient, while both Petalostemon pinnatum and Galactia microphylla were located in the more xeric extreme. The percentage variation in species that could be accounted for by environmental variation was low (27%). Of the variation that could be accounted for, a number of environmental variables were important, including soil moisture, pine basal area (i.e., light), and bivalent base cations (e.g., Ca(2+)). Although gradients in resource availability among sites did not affect the distribution of species or abundance of legumes strongly, variation in resources are likely to regulate N(2)-fixation rates of the various native legume species, and thereby affect ecological functions such as maintenance of N capital and productivity.

Journal Article↗