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1.  Evolution of Genome Size in Brassicaceae 
Annals of botany  2005;95(1):229-235.
Background and Aims
Brassicaceae, with nearly 340 genera and more than 3350 species, anchors the low range of angiosperm genome sizes. The relatively narrow range of DNA content (0·16 pg < 1C < 1·95 pg) was maintained in spite of extensive chromosomal change. The aim of this study was to erect a cytological and molecular phylogenetic framework for a selected subset of the Brassicacae, and use this as a template to examine genome size evolution in Brassicaceae.
Methods
DNA contents were determined by flow cytometry and chromosomes were counted for 34 species of the family Brassicaceae and for ten Arabidopsis thaliana ecotypes. The amplified and sequenced ITS region for 23 taxa (plus six other taxa with known ITS sequences) were aligned and used to infer evolutionary relationship by parsimony analysis.
Key Results
DNA content in the species studied ranged over 8-fold (1C = 0·16–1·31 pg), and 4·4-fold (1C = 0·16–0·71 pg) excluding allotetraploid Brassica species. The 1C DNA contents of ten Arabidopsis thaliana ecotypes showed little variation, ranging from 0·16 pg to 0·17 pg.
Conclusions
The tree roots at an ancestral genome size of approximately 1x = 0·2 pg. Arabidopsis thaliana (1C = 0·16 pg; ~157 Mbp) has the smallest genome size in Brassicaceae studied here and apparently represents an evolutionary decrease in genome size. Two other branches that represent probable evolutionary decreases in genome size terminate in Lepidium virginicum and Brassica rapa. Branches in the phylogenetic tree that represent probable evolutionary increases in genome size terminate in Arabidopsis halleri, A. lyrata, Arabis hirsuta, Capsella rubella, Caulanthus heterophyllus, Crucihimalaya, Lepidium sativum, Sisymbrium and Thlaspi arvense. Branches within one clade containing Brassica were identified that represent two ancient ploidy events (2x to 4x and 4x to 6x) that were predicted from published comparative mapping studies.
doi:10.1093/aob/mci016
PMCID: PMC1950721  PMID: 15596470
Arabidopsis; Brassicaceae; ITS phylogeny; DNA content; genome size; chromosome number
2.  The Emergence of Embryos from Hard Seeds is Related to the Structure of the Cell Walls of the Micropylar Endosperm, and not to Endo-β-mannanase Activity 
Annals of Botany  2005;96(7):1165-1173.
• Background and Aims Seeds of carob, Chinese senna, date and fenugreek are hard due to thickened endosperm cell walls containing mannan polymers. How the radicle is able penetrate these thickened walls to complete seed germination is not clearly understood. The objective of this study was to determine if radicle emergence is related to the production of endo-β-mannanase to weaken the mannan-rich cell walls of the surrounding endosperm region, and/or if the endosperm structure itself is such that it is weaker in the region through which the radicle must penetrate.
• Methods Activity of endo-β-mannanase in the endosperm and embryo was measured using a gel assay during and following germination, and the structure of the endosperm in juxtaposition to the radicle, and surrounding the cotyledons was determined using fixation, sectioning and light microscopy.
• Key Results The activity of endo-β-mannanase, the major enzyme responsible for galactomannan cell wall weakening increased in activity only after emergence of the radicle from the seed. Thickened cell walls were present in the lateral endosperm in the hard-seeded species studied, but there was little to no thickening in the micropylar endosperm except in date seeds. In this species, a ring of thin cells was visible in the micropylar endosperm and surrounding an operculum which was pushed open by the expanding radicle to complete germination.
• Conclusions The micropylar endosperm presents a lower physical constraint to the completion of germination than the lateral endosperm, and hence its structure is predisposed to permit radicle protrusion.
doi:10.1093/aob/mci269
PMCID: PMC4247068  PMID: 16176942
Endo-β-mannanase; lateral endosperm; micropylar endosperm; germination; hard seeded legumes; Phoenix dactylifera
3.  Morphological and Secretory Characterization of Extrafloral Nectaries in Plants of Coastal Veracruz, Mexico 
Annals of Botany  2005;96(7):1175-1189.
• Background and Aims Morphological descriptions of the extrafloral nectaries (EFNs) of certain plant species are common in the literature, but they rarely relate morphology with histology, gland distribution and secretory attributes. In this study a morphological/secretory characterization of EFNs occurring on several plant species in a tropical coastal community is made and the implications of gland attributes discussed from a functional perspective.
• Methods The morphology and nectar secretion of the EFNs of 20 plant species are characterized through scanning electron microscopy, histochemical detection of reducing sugars (Fehling's reagent) and nectar volume/concentration estimates.
• Key Results Sixty-five per cent of plant species in coastal communities had EFNs on vegetative structures and 35 % of species had glands on reproductive and vegetative organs. The Fabaceae is the plant family with the most species with EFNs and most diversity of gland morphologies. Four types of vascularized nectaries and four of glandular trichomes are described; sugar-secreting trichomes are characterized using Fehling's technique, and the first descriptions of unicellular and peltate trichomes functioning as EFNs are provided. Glands of ten plant species and six genera are described for the first time. Four plant species possess more than one morphological type of EFN. Eleven species have EFNs in more than one location or organ. More complex glands secrete more nectar, but are functionally homologous to the aggregations of numerous secretory trichomes on specific and valuable plant organs.
• Conclusion Important diversity of EFN morphology was foundin the coastal plant community studied. Both vascularized and non-vascularized EFNs are observed in plants and, for the latter, previously non-existent morpho-secretory characterizations are provided with a methodological approach to study them. It is recommended that studies relating EFN attributes (i.e. morphology, distribution) with their differential visitation by insects (i.e. ants) and the cost of maintenance to the plants are carried out to understand the evolution of these glands.
doi:10.1093/aob/mci270
PMCID: PMC4247069  PMID: 16227307
Extrafloral nectary morphology; secretory rates; nectary position; histology; taxonomy; ant-plant interactions; coastal plant communities
4.  The Relative Importance of Pre- and Post-germination Determinants for Recruitment of an Annual Plant Community on Moving Sandy Land 
Annals of Botany  2005;96(7):1215-1223.
• Background and Aims The relative importance of pre- and post-germination determinants for recruitment of natural plant communities is rarely explored. An annual plant community on moving sandy land was chosen for a case study. Answers to the following questions were sought: (a) Does recruitment of new individuals within the community of annual plants differ in time and space? (b) Is there spatial concordance between seed deposition, seedling emergence, survival and recruitment? (c) What are the direct and indirect effects of pre- and post-germination determinants on plant recruitment.
• Methods An integrative approach combining investigation of natural recruitment processes with regression, correlation and path analyses was adopted. Data on seed deposition and seedling recruitment were collected by monitoring the number of seeds deposited in the top 5 cm of the soil and the numbers of seedlings emerged and recruited from all annual plants at sites to a range of distances from the existing shrub Artemisia halodendron (Asteraceae) in eight compass directions for two consecutive growing seasons.
• Key Results Community-level recruitment was strongly affected by inter-annual rainfall variation and was highly site- and density-dependent. Low recruitment rate in this system was due to low emergence rate and low post-emergence survival rate. Of the pre- and post-germination determinants studied, it was the number of seedlings which emerged and the post-emergence survival rate that had the greatest direct effects on recruitment, with a combination of both variables explaining the majority of the variance (97 %) in recruitment.
• Conclusions This study suggests that post-germination determinants (emergence and survival) rather than pre-germination determinants (seed deposition) substantially determined the final pattern of recruitment. Although the density of seeds deposited did not have a significant direct effect on recruitment, it contributed to observed variation in recruitment indirectly through density-dependent emergence of seedlings.
doi:10.1093/aob/mci271
PMCID: PMC4247070  PMID: 16199487
Annual plants; community level; Horqin Sandy Land; path analysis; recruitment dynamics; recruitment success; spatial variation; seed deposition; seedling emergence; seedling survival
5.  Aerenchyma Formation and Recovery from Hypoxia of the Flooded Root System of Nodulated Soybean 
Annals of Botany  2005;96(7):1191-1198.
• Background and Aims Flooding results in hypoxia of the root system to which N2 fixation of nodulated roots can be especially sensitive. Morphological adaptions, such as aerenchyma formation, can facilitate the diffusion of oxygen to the hypoxic tissues. Using soybean, the aim of the study was to characterize the morphological response of the nodulated root system to flooding and obtain evidence for the recovery of N metabolism.
• Methods Sections from submerged tissues were observed by light microscopy, while sap bleeding from the xylem was analysed for nitrogenous components.
• Key Results Flooding resulted in the rapid formation of adventitious roots and aerenchyma between the stem (immediately above the water line), roots and nodules. In the submerged stem, taproot, lateral roots and adventitious roots, lysigenous aerenchyma arose initially in the cortex and was gradually substituted by secondary aerenchyma arising from cells derived from the pericycle. Nodules developed aerenchyma from cells originating in the phellogen but nodules situated at depths greater than 7–8 cm showed little or no aerenchyma formation. As a result of aerenchyma formation, porosity of the taproot increased substantially between the 4th and 7th days of flooding, coinciding with the recovery of certain nitrogenous products of N metabolism of roots and nodules transported in the xylem. Thus, on the first day of flooding there was a sharp decline in xylem ureides and glutamine (products of N2 fixation), together with a sharp rise in alanine (product of anaerobic metabolism). Between days 7 and 10, recovery of ureides and glutamine to near initial levels was recorded while recovery of alanine was partial.
• Conclusions N metabolism of the nodulated soybean root system can recover at least partially during a prolonged period of flooding, a process associated with aerenchyma formation.
doi:10.1093/aob/mci272
PMCID: PMC4247071  PMID: 16199486
Glycine max; soybean; secondary aerenchyma; oxygen deficiency; waterlogging; nitrogen metabolism; nitrogen fixation
6.  Epigenetics and its Implications for Plant Biology. 1. The Epigenetic Network in Plants 
Annals of Botany  2005;96(7):1143-1164.
• Background Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, ‘epigenetics’ studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations.
• Context Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves.
• Scope In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system—regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts—may work together.
doi:10.1093/aob/mci273
PMCID: PMC4247072  PMID: 16254022
Epigenetics; DNA methylation; histones; chromatin; RNA; paramutation; transgenes; silencing; gene expression
7.  The Changing Window of Conditions that Promotes Germination of Two Fire Ephemerals, Actinotus leucocephalus (Apiaceae) and Tersonia cyathiflora (Gyrostemonaceae) 
Annals of Botany  2005;96(7):1225-1236.
• Background and Aims Following a period of burial, more Actinotus leucocephalus (Apiaceae) and Tersonia cyathiflora (Gyrostemonaceae) seeds germinate in smoke water. The main aim of this study was to determine whether these fire-ephemeral seeds exhibit annual dormancy cycling during burial. This study also aimed to determine the effect of dormancy alleviation on the range of light and temperature conditions at which seeds germinate, and the possible factors driving changes in seed dormancy during burial.
• Methods Seeds were collected in summer, buried in soil in mesh bags in autumn and exhumed every 6 months for 24 months. Germination of exhumed and laboratory-stored (15 °C) seeds was assessed at 20 °C in water or smoke water. Germination response to light or dark conditions, incubation temperature (10, 15, 20, 25 and 30 °C), nitrate and gibberellic acid were also examined following burial or laboratory storage for 24 months. In the laboratory seeds were also stored at various temperatures (5, 15, 37 and 20/50 °C) for 1, 2 and 3 months followed by germination testing in water or smoke water.
• Key Results The two species exhibited dormancy cycling during soil burial, producing low levels of germination in response to smoke water when exhumed in spring and high levels of germination in autumn. In autumn, seeds germinated in both light and dark and at a broader range of temperatures than did laboratory-stored seeds, and some Actinotus leucocephalus seeds also germinated in water alone. Dormancy release of Actinotus leucocephalus was slow during dry storage at 15 °C and more rapid at higher temperatures (37 and 20/50 °C); weekly wet/dry cycles further accelerated the rate of dormancy release. Cold stratification (5 °C) induced secondary dormancy. By contrast, no Tersonia cyathiflora seeds germinated following any of the laboratory storage treatments.
• Conclusions Temperature and moisture influence dormancy cycling in Actinotus leucocephalus seeds. These factors alone did not simulate dormancy cycling of Tersonia cyathiflora seeds under the conditions tested.
doi:10.1093/aob/mci274
PMCID: PMC4247073  PMID: 16199485
Dormancy cycling; fire ephemeral; germination stimulants; scarification; smoke water; soil burial; storage temperature; Actinotus leucocephalus; Tersonia cyathiflora
8.  Species Distinction in Irish Populations of Quercus petraea and Q. robur: Morphological versus Molecular Analyses 
Annals of Botany  2005;96(7):1237-1246.
• Background and Aims Populations of oak (Quercus petraea and Q. robur) were investigated using morphological and molecular (AFLP) analyses to assess species distinction. The study aimed to describe species distinction in Irish oak populations and to situate this in a European context.
• Methods Populations were sampled from across the range of the island of Ireland. Leaf morphological characters were analysed through clustering and ordination methods. Putative neutral molecular markers (AFLPs) were used to analyse the molecular variation. Cluster and ordination analyses were also performed on the AFLP markers in addition to calculations of genetic diversity and F-statisitcs.
• Key Results A notable divergence was uncovered between the morphological and molecular analyses. The morphological analysis clearly differentiated individuals into their respective species, whereas the molecular analysis did not. Twenty species-specific AFLP markers were observed from 123 plants in 24 populations but none of these was species-diagnostic. Principal Coordinate Analysis of the AFLP data revealed a clustering, across the first two axes, of individuals according to population rather than according to species. High FST values calculated from AFLP markers also indicated population differentiation (FST = 0·271). Species differentiation accounted for only 13 % of the variation in diversity compared with population differentiation, which accounted for 27 %.
• Conclusions The results show that neutral molecular variation is partitioned more strongly between populations than between species. Although this could indicate that the populations of Q. petraea and Q. robur studied may not be distinct species at a molecular level, it is proposed that the difficulty in distinguishing the species in Irish oak populations using AFLP markers is due to population differentiation masking species differences. This could result from non-random mating in small, fragmented woodland populations. Hybridization and introgression between the species could also have a significant role.
doi:10.1093/aob/mci275
PMCID: PMC4247074  PMID: 16199484
Species differentiation; pedunculate oak; sessile oak; AFLP; Quercus petraea; Quercus robur
9.  Floral Ontogeny in Ficinia and Isolepis (Cyperaceae), with Focus on the Nature and Origin of the Gynophore 
Annals of Botany  2005;96(7):1247-1264.
• Background and Aims The generic delimitations of Ficinia and Isolepis, sister genera in the Cypereae, are blurred. Typical Ficinia flowers have a lobed gynophore, which envelops the base of the nutlet, whereas in Isolepis the character is considered to be absent. Some former species of Isolepis, lacking the gynophore, were recently included in Ficinia. The floral ontogeny of representative taxa in Ficinia and Isolepis were investigated with the aim of evaluating the origin and nature of the gynophore in the Cypereae.
• Methods The spikelet and floral ontogeny in inflorescences collected in the field was investigated using scanning electron microscopy (SEM) and light microscopy (LM).
• Key Results SEM images of Isolepis setacea and I. antarctica, Ficinia brevifolia, F. minutiflora, F. zeyheri and F. gracilis, and LM sections of F. radiata, show that the gynoecium in Ficinia is elevated above the flower receptacle by the development of a hypogynous stalk. From its apex, a (often three-)lobed cup is formed, which envelopes the basal part of the later nutlet. In developing flowers of I. antarctica, a rudimentary hypogynous stalk appears. In I. setacea, rudiments of a hypogynous stalk can be observed at maturity. In F. radiata and F. zeyheri, intralocular hairs are present in the micropylar zone. At the surface of developing gynoecia in flowers of F. gracilis, star-shaped cuticular structures appear which disappear again at maturity.
• Conclusions The overall floral ontogeny of all species studied occurs following a typical scirpoid pattern, though no perianth primordia are formed. The gynophore in Ficinia originates as a hypogynous stalk, from which the typical gynophore lobes develop. The gynophore is not homologous with the perianth.
doi:10.1093/aob/mci276
PMCID: PMC4247075  PMID: 16216820
Ficinia; floral ontogeny; gynophore; Isolepis; scanning electron microscopy
10.  Genetic Consequence of Restricted Habitat and Population Decline in Endangered Isoetes sinensis (Isoetaceae) 
Annals of Botany  2005;96(7):1265-1274.
• Background and Aims Isoetes sinensis (Isoeteaceae) is a critically endangered aquatic quillwort in eastern China. Rapid decline of extant population size and local population extinction have occurred in recent years and have raised great concerns among conservationists.
• Methods Amplified fragment length polymorphisms (AFLPs) were used to investigate the genetic variation and population structure of seven extant populations of the species.
• Key Results Eight primer combinations produced a total of 343 unambiguous bands of which 210 (61·2 %) were polymorphic. Isoetes sinensis exhibited a high level of intra-population genetic diversity (HE = 0·118; hs = 0·147; I = 0·192; P = 35·2 %). The genetic variation within each of the populations was not positively correlated with their size, suggesting recent population decline, which is well in accordance with field data of demographic surveys. Moreover, a high degree of genetic differentiation (FST = 0·535; GST = 0·608; θB = 0·607) was detected among populations and no correlation was found between geographical and genetic distance, suggesting that populations were in disequilibrium of migration-drift. Genetic drift played a more important role than gene flow in the current population genetic structure of I. sinensis because migration of I. sinensis is predominantly water-mediated and habitat range was highly influenced by environment changes.
• Conclusions Genetic information obtained in the present study provides useful baseline data for formulating conservation strategies. Conservation management, including both reinforcement for in situ populations and ex situ conservation programmes should be carefully designed to avoid the potential risk of outbreeding depression by admixture of individuals from different regions. However, translocation within the same regional population should be considered as a measure of genetic enhancement to rehabilitate local populations. An ex situ conservation strategy for conserving all extant populations to maximize genomic representation of the species is also recommended.
doi:10.1093/aob/mci277
PMCID: PMC4247076  PMID: 16216819
AFLP; genetic diversity; genetic differentiation; population structure; Isoetes sinensis; pteridophyte
11.  Genecology of Douglas Fir in Western Oregon and Washington 
Annals of Botany  2005;96(7):1199-1214.
• Background and Aims Genecological knowledge is important for understanding evolutionary processes and for managing genetic resources. Previous studies of coastal Douglas fir (Pseudotsuga menziesii var. menziesii) have been inconclusive with respect to geographical patterns of variation, due in part to limited sample intensity and geographical and climatic representation. This study describes and maps patterns of genetic variation in adaptive traits in coastal Douglas fir in western Oregon and Washington, USA.
• Methods Traits of growth, phenology and partitioning were measured in seedlings of 1338 parents from 1048 locations grown in common gardens. Relations between traits and environments of seed sources were explored using regressions and canonical correlation analysis. Maps of genetic variation as related to the environment were developed using a geographical information system (GIS).
• Key Results Populations differed considerably for adaptive traits, in particular for bud phenology and emergence. Variation in bud-set, emergence and growth was strongly related to elevation and cool-season temperatures. Variation in bud-burst and partitioning to stem diameter versus height was related to latitude and summer drought. Seedlings from the east side of the Washington Cascades were considerably smaller, set bud later and burst bud earlier than populations from the west side.
• Conclusions Winter temperatures and frost dates are of overriding importance to the adaptation of Douglas fir to Pacific Northwest environments. Summer drought is of less importance. Maps generated using canonical correlation analysis and GIS allow easy visualization of a complex array of traits as related to a complex array of environments. The composite traits derived from canonical correlation analysis show two different patterns of variation associated with different gradients of cool-season temperatures and summer drought. The difference in growth and phenology between the westside and eastside Washington Cascades is hypothesized to be a consequence of the presence of interior variety (P. menziessii var. glauca) on the eastside.
doi:10.1093/aob/mci278
PMCID: PMC4247077  PMID: 16246849
Pseudotsuga menziesii; genecology; geographical variation; adaptation; growth; phenology
12.  Cluster Roots of Leucadendron laureolum (Proteaceae) and Lupinus albus (Fabaceae) Take Up Glycine Intact: An Adaptive Strategy to Low Mineral Nitrogen in Soils? 
Annals of Botany  2005;96(7):1275-1282.
• Background and Aims South African soils are not only low in phosphorus (P) but most nitrogen (N) is in organic form, and soil amino acid concentrations can reach 2·6 g kg−1 soil. The Proteaceae (a main component of the South African Fynbos vegetation) and some Fabaceae produce cluster roots in response to low soil phosphorus. The ability of these roots to acquire the amino acid glycine (Gly) was assessed.
• Methods Uptake of organic N as 13C–15N-Gly was determined in cluster roots and non-cluster roots of Leucadendron laureolum (Proteaceae) and Lupinus albus (Fabaceae) in hydroponic culture, taking account of respiratory loss of 13CO2.
• Key Results Both plant species acquired doubly labelled (intact) Gly, and respiratory losses of 13CO2 were small. Lupin (but not leucadendron) acquired more intact Gly when cluster roots were supplied with 13C–15N-Gly than when non-cluster roots were supplied. After treatment with labelled Gly (13C : 15N ratio = 1), lupin cluster roots had a 13C : 15N ratio of about 0·85 compared with 0·59 in labelled non-cluster roots. Rates of uptake of label from Gly did not differ between cluster and non-cluster roots of either species. The ratio of C : N and 13C : 15N in the plant increased in the order: labelled roots < rest of the root < shoot in both species, owing to an increasing proportion of 13C translocation.
• Conclusions Cluster roots of lupin specifically acquired more intact Gly than non-cluster roots, whereas Gly uptake by the cluster and non-cluster roots of leucadendron was comparable. The uptake capacities of cluster roots are discussed in relation to spatial and morphological characteristics in the natural environment.
doi:10.1093/aob/mci279
PMCID: PMC4247078  PMID: 16223736
Amino acid; cluster roots; 13C–15N-Gly; Leucadendron laureolum; Lupinus albus; Fynbos; Proteaceae; organic nitrogen
13.  Genetic Fingerprinting of Germplasm Accessions as an Aid for Species Conservation: A Case Study with Borderea chouardii (Dioscoreaceae), One of the Most Critically Endangered Iberian Plants 
Annals of Botany  2005;96(7):1283-1292.
• Background and Aims Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain.
• Methods Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers.
• Key Results The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples).
• Conclusions The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.
doi:10.1093/aob/mci280
PMCID: PMC4247079  PMID: 16230324
Borderea chouardii; endangered plants; ex situ conservation strategies; genetic diversity; germplasm stocks; microsatellites; polyploids; population structure; SSRs
14.  Nuclear DNA Variation, Chromosome Numbers and Polyploidy in the Endemic and Indigenous Grass Flora of New Zealand 
Annals of Botany  2005;96(7):1293-1305.
• Background and Aims Little information is available on DNA C-values for the New Zealand flora. Nearly 85 % of the named species of the native vascular flora are endemic, including 157 species of Poaceae, the second most species-rich plant family in New Zealand. Few C-values have been published for New Zealand native grasses, and chromosome numbers have previously been reported for fewer than half of the species. The aim of this research was to determine C-values and chromosome numbers for most of the endemic and indigenous Poaceae from New Zealand.
• Scope To analyse DNA C-values from 155 species and chromosome numbers from 55 species of the endemic and indigenous grass flora of New Zealand.
• Key Results The new C-values increase significantly the number of such measurements for Poaceae worldwide. New chromosome numbers were determined from 55 species. Variation in C-value and percentage polyploidy were analysed in relation to plant distribution. No clear relationship could be demonstrated between these variables.
• Conclusions A wide range of C-values was found in the New Zealand endemic and indigenous grasses. This variation can be related to the phylogenetic position of the genera, plants in the BOP (Bambusoideae, Oryzoideae, Pooideae) clade in general having higher C-values than those in the PACC (Panicoideae, Arundinoideae, Chloridoideae + Centothecoideae) clade. Within genera, polyploids typically have smaller genome sizes (C-value divided by ploidy level) than diploids and there is commonly a progressive decrease with increasing ploidy level. The high frequency of polyploidy in the New Zealand grasses was confirmed by our additional counts, with only approximately 10 % being diploid. No clear relationship between C-value, polyploidy and rarity was evident.
doi:10.1093/aob/mci281
PMCID: PMC4247080  PMID: 16243852
Chromosome number; C-value; distribution; New Zealand; Poaceae; polyploidy; rarity; taxonomy
15.  NADP-Malate Dehydrogenase Gene Evolution in Andropogoneae (Poaceae): Gene Duplication Followed by Sub-functionalization 
Annals of Botany  2005;96(7):1307-1314.
• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4; Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C4; Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C4 isoform has evolved over a broader range of panicoid grasses.
• Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach.
• Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II.
• Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C4 isoform as previously suggested. Nevertheless, some C4 species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C4 photosynthesis but are not required in every case.
doi:10.1093/aob/mci282
PMCID: PMC4247081  PMID: 16243851
C4 photosynthesis; gene duplication; multigene family; NADP-MDH; Poaceae; positive selection; sub-functionalization
16.  First Nuclear DNA C-values for 18 Eudicot Families 
Annals of Botany  2005;96(7):1315-1320.
• Background and Aims A key target set at the second Plant Genome Size Workshop, held at the Royal Botanic Gardens, Kew in 2003, was to produce first DNA C-value data for an additional 1 % of angiosperm species, and, within this, to achieve 75 % familial coverage overall (up from approx. 50 %) by 2009. The present study targeted eudicot families for which representation in 2003 (42·5 %) was much lower than monocot (72·8 %) and basal angiosperm (69·0 %) families.
• Methods Flow cytometry or Feulgen microdensitometry were used to estimate nuclear DNA C-values, and chromosome counts were obtained where possible.
• Key Results First nuclear DNA C-values are reported for 20 angiosperm families, including 18 eudicots. This substantially increases familial representation to 55·2 % for angiosperms and 48·5 % for eudicots.
• Conclusions The importance of targeting specific plant families to improve familial nuclear DNA C-value representation is reconfirmed. International collaboration will be increasingly essential to locate and obtain material of unsampled plant families, if the target set by the second Plant Genome Size Workshop is to be met.
doi:10.1093/aob/mci283
PMCID: PMC4247082  PMID: 16239248
Angiosperm families; chromosome counts; DNA amounts; eudicots; genome size; nuclear DNA C-values
17.  The Relationship Between Nuclear DNA Content and Leaf Strategy in Seed Plants 
Annals of Botany  2005;96(7):1321-1330.
• Background and Aims Species' 2C-values (mass of DNA in G1 phase 2n nuclei) vary by at least four orders of magnitude among seed plants. The 2C-value has been shown to be co-ordinated with a number of other species traits, and with environmental variables. A prediction that species 2C-values are negatively related to leaf life span (LL) and leaf mass per area (LMA) is tested. These leaf traits are components of a major dimension of ecological variation among plant species.
• Methods Flow cytometry was used to measure the 2C-values for 41 Australian seed plant species, 40 of which were new to the literature. Where possible, LL and LMA data from the global literature were combined with 2C-values from our data set and online C-value databases.
• Key Results Across all species, weak positive relationships were found between 2C-values and both LL and LMA; however, these did not reflect the relationships within either angiosperms or gymnosperms. Across 59 angiosperm species, there were weak negative relationships between 2C-values and both LL (r2 = 0·13, P = 0·005) and LMA (r2 = 0·15, P = 0·002). These relationships were the result of shifts to longer LL and greater LMA in woody compared with herbaceous growth forms, with no relationships present within growth forms. It was not possible to explain a positive relationship between 2C-values and LMA (r2 = 0·30, P = 0·024) across 17 gymnosperm species. The 2C-value was not related to LL or LMA either across species within orders (except for LMA among Pinales), or as radiation divergences in a model phylogeny.
• Conclusions Gymnosperms appear to vary along a spectrum different from angiosperms. Among angiosperms, weak negative cross-species relationships were associated with growth form differences, and traced to a few divergences deep in the model phylogeny. These results suggest that among angiosperms, nuclear DNA content and leaf strategy are unrelated.
doi:10.1093/aob/mci284
PMCID: PMC4247083  PMID: 16230323
Genome size; C-value; leaf life span; leaf mass per area; LMA; SLA; angiosperms; gymnosperms; correlated divergence analysis; standardized major axis
21.  Investigations into Seed Dormancy in Grevillea linearifolia, G. buxifolia and G. sericea: Anatomy and Histochemistry of the Seed Coat 
Annals of Botany  2005;96(6):965-980.
• Background and Aims Seeds of east Australian Grevillea species generally recruit post-fire; previous work showed that the seed coat was the controller of dormancy in Grevillea linearifolia. Former studies on seed development in Grevillea have concentrated on embryology, with little information that would allow testing of hypotheses about the breaking of dormancy by fire-related cues. Our aim was to investigate structural and chemical characteristics of the seed coat that may be related to dormancy for three Grevillea species.
• Methods Seeds of Grevillea linearifolia, Grevillea buxifolia and Grevillea sericea were investigated using gross dissection, thin sectioning and histochemical staining. Water movement across the seed coat was tested for by determining the water content of embryos from imbibed and dry seeds of G. sericea. Penetration of intact seeds by Lucifer Yellow was used to test for internal barriers to diffusion of high-molecular-weight compounds.
• Key Results Two integuments were present in the seed coat: an outer testa, with exo-, meso- and endotestal (palisade) layers, and an inner tegmen of unlignified sclerenchyma. A hypostase at the chalazal end was a region of structural difference in the seed coat, and differed slightly among the three species. An internal cuticle was found on each side of the sclerenchyma layer. The embryos of imbibed seeds had a water content six times that of dry seeds. Barriers to diffusion of Lucifer Yellow existed at the exotestal and the endotestal/hypostase layers.
• Conclusions Several potential mechanisms of seed coat dormancy were identified. The embryo appeared to be completely surrounded by outer and inner barriers to diffusion of high-molecular-weight compounds. Phenolic compounds present in the exotesta could interfere with gas exchange. The sclerenchyma layer, together with strengthening in the endotestal and exotestal cells, could act as a mechanical constraint.
doi:10.1093/aob/mci250
PMCID: PMC4247087  PMID: 16157632
Seed coat structure; Grevillea linearifolia; Grevillea buxifolia; Grevillea sericea; histochemistry; seed dormancy
22.  Co-ordination between Leaf Initiation and Leaf Appearance in Field-grown Maize (Zea mays): Genotypic Differences in Response of Rates to Temperature 
Annals of Botany  2005;96(6):997-1007.
• Background and Aims In maize (Zea mays), early flowering date, which is a valuable trait for several cropping systems, is associated with the number of leaves per plant and the leaf appearance rate. Final leaf number depends upon the rate and duration of leaf initiation. The aims of this study were to analyse the genotypic variation in the response to temperature of leaf appearance rate and leaf initiation rate, and to investigate the co-ordination between these processes under field conditions.
• Methods Sixteen hybrids of different origins were grown under six contrasting environmental conditions. The number of appeared leaves was measured twice a week to estimate leaf appearance rate (leaves d−1). Plants were dissected at four sampling dates to determine the number of initiated leaves and estimate leaf initiation rate (leaves d−1). A co-ordination model was fitted between the number of initiated leaves and the number of appeared leaves. This model was validated using two independent data sets.
• Key Results Significant (P < 0·05) differences were found among hybrids in the response to temperature of leaf initiation rate (plastochron) and leaf appearance rate (phyllochron). Plastochron ranged between 24·3 and 36·4 degree days (°Cd), with a base temperature (Tb) between 4·0 and 8·2 °C. Phyllochron ranged between 48·6 and 65·5 °Cd, with a Tb between 2·9 and 5·0 °C. A single co-ordination model was fitted between the two processes for all hybrids and environments (r2 = 0·96, P < 0·0001), and was successfully validated (coefficient of variation < 9 %).
• Conclusions This work has established the existence of genotypic variability in leaf initiation rate and leaf appearance rate in response to temperature, which is a promising result for maize breeding; and the interdependence between these processes from seedling emergence up to floral initiation.
doi:10.1093/aob/mci251
PMCID: PMC4247088  PMID: 16126778
Zea mays; maize; co-ordination; leaf initiation; leaf appearance; plastochron; phyllochron; Tb; genotypic variability; temperature; modelling
23.  A New Method for in-situ Monitoring of the Underground Development of Orobanche cumana in Sunflower (Helianthus annuus) with a Mini-rhizotron 
Annals of Botany  2005;96(6):1137-1140.
• Aims To develop an in-situ, non-destructive method for observation and monitoring of the underground developmental stages of the root parasite Orobanche cumana.
• Scope The parasitic weed Orobanche causes severe damage to vegetables and field crops. Most of the damage caused to the crops occurs during the underground, unobservable parasitism stage. Sunflower (Helianthus annuus ‘Adi’) plants were planted in soil that was artificially inoculated with O. cumana seeds. Clear Plexiglas mini-rhizotron plastic observation tubes were inserted into the soil. Seed germination, early stage of penetration, and formation of tubercles and spikes were observed non-destructively and were monitored throughout the growing season by mean of a mini-rhizotron camera. Use of this technology enabled the complete individual parasite life cycle from the very early development (including germination) to Orobanche shoot to be monitored. In addition, the effect of the systemic herbicide Cadre (imazapic) on the development of O. cumana was inspected and quantified.
• Conclusions This novel methodology facilitates the in-situ study of major aspects of the host–parasite interaction and of parasite suppression, such as parasitism dynamics, parasite growth rate, and the effect of chemical treatments on the parasite.
doi:10.1093/aob/mci252
PMCID: PMC4247089  PMID: 16157627
Orobanche cumana; broomrape; mini-rhizotron; chemical control; image analysis
24.  Change in Spatial Distribution Patterns of a Biennial Plant between Growth Stages and Generations in a Patchy Habitat 
Annals of Botany  2005;96(6):1009-1017.
• Background and Aims The aim of the study was to evaluate factors causing change in spatial distribution patterns of plants between growth stages and generations for a monocarpic biennial plant, Lysimachia rubida. It was assumed that habitat heterogeneity was a primary factor determining spatial patterns of plants, and a randomization procedure was developed for testing the null hypothesis that only spatial association with ground surface conditions determined spatial patterns of plants.
• Methods A 5-year demographic census was conducted on an open dry habitat that was heterogeneous with regard to the ground surface conditions.
• Key Results There was significant habitat association in that plants at vegetative and reproductive stages were denser in areas with smaller gravel than with larger gravel. Point process analyses rejected the null hypothesis of the spatial association with ground surface conditions.
• Conclusions The results suggest that other factors, such as patchy seed dispersal, secondary dispersal of the seeds and life-history variation at various spatial scales, also affected spatial patterns of individuals in a population of L. rubida. Spatial structures and dynamics of a local population in a patchy habitat represent various performances of plants within patches and seed dispersal within a patch and beyond the patch.
doi:10.1093/aob/mci253
PMCID: PMC4247090  PMID: 16126777
Monocarpic biennial; generations; environmental heterogeneity; ground surface conditions; growth stages; life history variation; Lysimachia rubida; patch dynamics; point process analysis; randomization test; seed dispersal; spatial patterns
25.  A Model for the Circadian Oscillations in Expression and Activity of Nitrate Reductase in Higher Plants 
Annals of Botany  2005;96(6):1019-1026.
• Background and Aims Nitrate is the major nitrogen source for many plants. The first step of the nitrate assimilation pathway is the reduction of nitrate to nitrite, catalysed by nitrate reductase (NR). Circadian oscillations in expression and activity of NR have been demonstrated in many plant species. The pathway by which this circadian behaviour is regulated remains to be elucidated. In this study, based on recent experimental observations, a mathematical model is proposed to explain the origin of diurnal and circadian oscillations in NR gene expression and enzyme activity.
• Methods The dynamic model is based on the feedback interconnections between NR and its substrate, nitrate. In the model, NR activity is regulated at the transcriptional level, in response to the balance between nitrate influx and reduction, and at the post-translational levels in response to signals from carbon assimilation. Conditions for the model system to generate self-sustained circadian oscillations are investigated by numerical simulations.
• Key Results and Conclusions Under light/dark cycles, the simulation results are in agreement with the observed diurnal pattern of changes in leaf nitrate concentration, NR transcript level and NR activity. Within a range of kinetic parameter values, circadian oscillation behaviour persists even under constant light, with periods of approx. 24 h. These simulation results suggest that sustained circadian oscillations can originate from the feedback interactions between NR and its substrate, nitrate, without the need to postulate the existence of an endogenous ‘circadian clock’.
doi:10.1093/aob/mci254
PMCID: PMC4247091  PMID: 16126776
Nitrate reductase; model; nitrate reduction; circadian rhythms; diurnal oscillations; nitrogen metabolism

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