H. James Price

Evolution of DNA content in higher plants

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Range of Variability of DNA Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 DNA Variation in Higher Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Angiosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Mechanisms of Change in DNA Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Cellular and Organismic Correlations with DNA Content . . . . . . . . . . . . . . . . . . . . . . . . 40 Functions of DNA Sequences Duplicated or Deleted during Evolution . . . . . . . . . . . . . 41 Prospects for Future Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Literature Cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Feast and famine in plant genomes

Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a ‘one-way ticket to genomic obesity’, as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.

Detection of Intraspecific Variation in Nuclear DNA Content in Microseris douglasii

A precise technique to measure DNA content in Microseris douglasii is reported. Relative absorbancy (560 nm) of Feulgen-stained spherical nuclei, arrested at the 2C DNA level, was measured microspectrophotometrically. Relative DNA contents were determined by placing epidermis of an inbred line on the same slide with epidermis from the unknown sample prior to hydrolysis and staining. The DNA values were adjusted to the internal standard; direct comparisons were made of values collected from different slides and staining batches. Differences among individual plant specimens in the 2.5%-5% range are detectable with this procedure. Intraspecific variation up to 20% in DNA content was apparent

Somatic embryogenesis in suspension cultures of Gossypium klotzschianum anderss.

Somatic embryoids differentiated in suspension cultures of G. klotzschianum after 3–4 weeks of culture in a liquid medium containing glutamine (optimally, 10–15 mM). Embryogenesis occurred after a preculture of callus on a medium containing 10 mg/l of the cytokinin, 2iP. The embryoids had meristematic regions, a well formed epidermis, and formed roots and vestigial leaves. Asparagine was much less effective than glutamine in promoting embryoid differentiation. The presence of 2,4-D in the medium resulted in increased vigor of the suspension cultures and subsequently in the formation of many embryoids, but does not seem to be necessary for somatic embryogenesis in cotton.

Geographic and Ecological Distribution of Genomic DNA Content Variation in Microseris douglasii (Asteraceae)

We measured nuclear 2C DNA content (Feulgen absorbancy) of 222 plants of Microseris douglasii representing 24 geographically, ecologically, and morphologically diverse populations in California. The DNA content among plants varied more than 20% and was not correlated with morphological traits. Mean DNA contents of populations varied about 14%. For most populations, the DNA content was relatively uniform, even when the biotypes were morphologically diverse. Populations with higher DNA contents were restricted to the more mesic sites, generally with well-developed soil. A correlation between the amount of precipitation and DNA content was temporally observed within a single population near Jolon, California, over a 15-yr interim. Natural selection may be responsible, at least in part, for the observed distributional pattern of DNA content.

Evolution of interspersed repetitive elements in Gossypium (Malvaceae)

Very little is known regarding how repetitive elements evolve inpolyploid organisms. Here we address this subject by fluorescent insitu hybridization (FISH) of 20 interspersed repetitive elements tometaphase chromosomes of the cotton AD-genome tetraploid Gossypiumhirsutum and its putative A- and D-genome diploid ancestors. Theseelements collectively represent an estimated 18% of the G.hirsutum genome, and constitute the majority of high-copyinterspersed repetitive elements in G. hirsutum. Seventeen ofthe elements yielded FISH signals on chromosomes of both G.hirsutum subgenomes, while three were A-subgenome specific. Hybridization of eight selected elements, two of which were A-subgenomespecific, to the A(2) genome of G. arboreum yielded asignal distribution that was similar to that of the G. hirsutumA-subgenome. However, when hybridized to the D(5) genome ofG. raimondii, the putative diploid ancestor of the G.hirsutum D-subgenome, none of the probes, including elements thatstrongly hybridized to both G. hirsutum subgenomes, yieldeddetectable signal. The results suggest that the majority, although notall, G. hirsutum interspersed repetitive elements haveundergone intergenomic concerted evolution following polyploidizationand that this has involved colonization of the D-subgenome byA-subgenome elements and/or replacement of D-subgenome elements byelements of the A-subgenometype.

Genome Size Variation in Diploid Microseris Bigelovii (Asteraceae)

Variation in nuclear 2C DNA content (Feulgen absorbancy) up to 25% was detected among plants from four populations of diploid Microseris bigelovii, 2n = 18. The lower DNA values were from geographically disjunct populations growing at the latitudinal extremes of the species range. These smaller genomes may have resulted from selection for low DNA content in stressful and/or time-limited environments. These data add M. bigelovii to the short list of taxa in which intraspecific variation in DNA content has been detected.

Ty1-copia-retrotransposon behavior in a polyploid cotton.

Retrotransposons constitute a ubiquitous and dynamic component of plant genomes. Intragenomic and intergenomic comparisons of related genomes offer potential insights into retrotransposon behavior and genomic effects. Here, we have used fluorescent in-situ hybridization to determine the chromosomal distributions of a Ty1-copia-like retrotransposon in the cotton AD-genome tetraploid Gossypium hirsutum and closely related putative A- and D-genome diploid ancestors. Retrotransposon clone A108 hybridized to all G. hirsutum chromosomes, approximately equal in intensity in the A- and D-subgenomes. Similar results were obtained by hybridization of A108 to the A-genome diploid G. arboreum, whereas no signal was detected on chromosomes of the D-genome diploid G. raimondii. The significance and potential causes of these observations are discussed.

Defined conditions for the initiation on growth of cotton callus in vitro I.Gossypium arboreum

SummaryDefined in vitro conditions for callus initiation byGossypium arboreum L. were determined, and different tissues were evaluated as explant sources. Environmental conditions tested included light versus dark, and low light versus high light. Different nutrient media as well as carbohydrate sources were examined. Our data show that hypocotyl tissue was superior to cotyledon or leaf tissue as the explant source for callus proliferation; the Murashige-Skoog inorganic formulation with (in mg per 1) 100 myo-inositol, 0.4 thiamine·HCl, 2 indoleacetic acid (IAA), 1 kinetin, and 3% glucose solidified by agar was the best medium to initiate callus. Cultures with sucrose as a carbohydrate source browned rapidly. Callus proliferation was superior under high light (8000 to 9000 lux) conditions at 29±1°C. Various combinations of auxins and cytokinins were tested for their ability to improve callus proliferation and subsequent growth of subcultures. Although the MS medium containing IAA and kinetin was found superior for obtaining rapid proliferation of callus from hypocotyl explants, a second medium containing 2 mg per 1 naphthalenacetic acid (NAA) and 0.5 to 1 mg per 1 benzyladenine (BA) was found necessary for vigorous growth of subcultured callus. A MS medium with 5 to 10 mg per 1 {ie329-1} (2iP) and 1 mg per 1 NAA was also favorable for continued subculturing.

Genome size variation among north american minnows (Cyprinidae). I. Distribution of the variation in five species.

Genome sizes (nuclear DNA contents) were examined spectrophotometrically from ten individuals of each of five species of North American cyprinid fishes (minnows). The distributions of DNA values both within and between the five species were essentially continuous and normal. Differences between individuals within populations were significant and contributed to approximately 16 per cent of the total variation. Variation between individuals within species ranged from 4·7–13·5 per cent and averaged ca. 7·4 per cent. Variation between species ranged from 0–9·5 per cent and the average difference between any species pair was ca. 4·per cent. Statistical analyses showed that the methodology used was sufficient to detect significant differences in genome size as small as 2–3 per cent. Consideration of these data lead to the following tentative conclusions: (i) changes in genome size in cyprinids appear small in amount, frequent in occurrence, to involve both gains and losses of DNA, and to be cumulative and independent in effect; (ii) differences within and between cyprinid taxa are likely the result of accumulations of small changes in DNA quantity; and (iii) the primary focus of quantitative DNA variation in cyprinids is between individuals within populations. The extent of DNA quantity variation which occurs within species would appear to preclude any direct relationship between genome size variation and many of the organismal parameters (including speciation) which differentiate the five species. In short, the data suggest that a significant fraction of the cyprinid genome, perhaps more than 10 per cent, is free to vary quantitatively without phenotypic constraint or biological consequence. This fraction is considerably larger than that theoretically needed for the structural gene component.