DNA Rearrangements in Response To Environmental Stress

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters

Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.

In Search of Darwin's Imaginary Gemmules

Darwin's gemmules were supposed to be "thrown off" by cells and were "inconceivably minute and numerous as the stars in heaven." They were capable of self-propagation and diffusion from cell to cell, and circulation through the system. The word "gene" coined by Wilhelm Johannsen, was derived from de Vries's term "pangen," itself a substitute for "gemmule" in Darwin's Pangenesis. Johannsen resisted the "morphological" conception of genes as particles with a certain structure. Morgan's genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string. In the late 1940s, McClintock challenged the concept of the stability of the gene when she discovered that some genes could move within a chromosome and between chromosomes. In 1948, Mandel and Metais reported the presence of cell-free nucleic acids in human blood for the first time. Over the past several decades, it has been universally accepted that almost all types of cells not only shed molecules such as cell-free DNA (including genomic DNA, tumor DNA and fetal DNA), RNAs (including mRNA and small RNAs) and prions, but also release into the extracellular environment diverse types of membrane vesicles (known as extracellular vesicles) containing DNA, RNA and proteins. Thus Darwin's speculative gemmules of the 19th century have become the experimentally demonstrated circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles.

Transposition of IS elements induced by electroporation of suicide plasmid in Acidithiobacillus caldus

Transposition insertional mutagenesis of the insertion sequences (IS elements) was discovered for the first time in Acidithiobacillus caldus (A. caldus), when A. caldus MTH-04 hsdM (type I restriction-modification system M-subunit) mutant was constructed by electroporation of a suicide plasmid. The IS element, specifically inserting into hsdM gene, was analyzed, identified, and named ISAtc2. The transposition frequency of ISAtc2 was ranged from 4% to 7%, and no reverse mutation occurred in the mutants after 50 generations of proliferation without selective pressure. These results revealed that transposition of IS elements on A. caldus chromosome could regulate the gene expression and metabolic pathways by gene inactivation, gene loss and gene acquisition. Therefore, the transposition of IS elements in A. caldus may be an important and unique regulation mechanism for adaptation to the living condition.

SSR-marker analysis of the intracultivar phenotypic variation discovered within 3 soybean cultivars

Genetic variation within homogeneous gene pools in various crops is assumed to be very limited. One objective of this study was to use 144 simple sequence repeat (SSR) markers to determine if the single-plant lines selected at ultra-low plant density in honeycomb designs within the soybean cultivars Benning, Haskell, and Cook had unique SSR genetic fingerprints. Another objective was to investigate if the variation found was the result of residual genetic heterozygosity that could be detected in the original gene pool where selection initiated. Our results showed that the phenotypic variation for seed protein content and seed weight has a genotypic component identified by the SSR band variation. The 7 lines from Haskell had a total of 63 variant alleles, the 5 lines from Benning had 34 variant alleles, and the 7 lines from Cook had 34 variant alleles, therefore, possessing unique genetic fingerprints. Most of the intracultivar SSR band variation discovered was the result of residual heterozygosity in the initial plant selected to become the cultivar. More specifically, 82% of the SSR variant alleles were traced in the Benning Foundation seed source, 93% in the Haskell seed source, and 82% in the Cook seed source. The remaining variant bands (18% for Benning, 7% for Haskell, and 18% for Cook) could not be detected in the Foundation seed source and were likely the result of mutation or some other mechanism generating de novo variation. These results provide evidence that genetic variation among individual plants is present even in homogeneous gene pools and can be further utilized in breeding programs.

Intraspecific genotypic diversity in plants

Variations in the nuclear DNA, mainly as a result of quantitative modulations of DNA repeats belonging to different sequence families of satellite DNA and to the activity of transposable elements, have been assessed within several angiosperm species. These variations alter the amount and organization of the DNA and therefore the genotype, rather than the genome proper. They take place on an evolutionary time scale as the result of selection processes after the occurrence of uncontrolled events in the genome or may be due to direct responses of plant genomes to environmental stimuli that occur under plant-level control within a short developmental period of a single generation. These DNA changes are correlated to changes in the developmental dynamics and phenotypic characteristics of the plants, and the capability to carry out genotypic variation is an evolutionary trait that allows plant species to adapt to different environmental conditions, as well as to the variability of conditions in a given environment. The link between developmental and environmental stimuli and repetitive DNA that elicits the intraspecific diversity of plant genotypes may provide models of evolutionary change that extend beyond the conventional view of evolution by allelic substitution and take into account epigenetic effects of the genome structure.

The chromosome number, karyotype and genome size of the desert plant diploid Reaumuria soongorica (Pall.) Maxim

Extreme drought and salt resistant plant Reaumuria soongorica is of great potential for revealing genetic bases unique to naturally stress-tolerant plants. A preliminary genome survey, including chromosome number, karyotype, chromosomal localization of 45S rDNA loci and genome size was conducted with R. soongorica collected from Lanzhou, China. Chromosome counting showed that R. soongorica is diploid with chromosome number of 22. Karyotypical analysis illustrated that the chromosomes size ranges from 3.38 to 5.51 μm, and the chromosomal formula is 2n = 2x = 22 = 4 m + 14sm + 4st. Fluorescence in situ hybridization revealed that four pairs of 45SrDNA signals were detected at the end of R. soongorica chromosomes. The flow cytometry analysis indicated that the mean C value of R. soongorica is 0.806 pg with predicted genome size of about 778 Mb. The results indicate that the extreme drought and salt resistance of R. soongorica was not attributed to a big and complicate genome and also offer some clues in resolving the problems of taxonomy and evolution in Tamaricaceae.

Meiotic behavior and DNA content in alloplasmic lines of maize

The cytoplasm of Zea mays ssp. mexicana (teosinte) affects several inherited traits when combined with genotypes of maize (Zea mays ssp. mays). The meiotic behavior and the total DNA content of four lines of maize with teosinte cytoplasm were compared with those of the parental lines. The results obtained suggest that the cytoplasm of teosinte promotes an increase in total nuclear DNA content, perhaps through an increase of highly repetitive DNA in the knob zones. The analysis of meiotic behavior indicates that the cytoplasm of teosinte can alter the spatial distribution of the genomes, since two groups of five bivalents each were observed at a high frequency. During prophase I - anaphase I, each group of five bivalents behaves in a slightly asynchronous way with respect to the other group and, moreover, two nucleoli were observed in 10% of the cells. These results suggest that the cytoplasm of teosinte could induce changes affecting genomic structure and function in some maize genotypes. These changes are of potential importance for breeding programs and evolutionary studies.

Genome size microscale divergence of Cyclamen persicum in Evolution Canyon, Israel

Using DAPI flow cytometry, we examined genome size divergence of the Persian violet, Cyclamen persicum (Primulaceae) (2n=48) on close opposite slopes of Evolution Canyon (EC), Mt. Carmel, Israel. The range of genome size variation detected among measured cyclamens was 6.41% in relation to the smallest measured DNA content. Our data on C. persicum at EC showed that local variability in the 2C-value exists. Significantly less DNA was recorded in plants growing in one station of the African savannah-like south-facing slope (AS) but not in the remaining two stations of the same slope. We were not able to reject the null hypothesis that there are no significant interslope differences in the genome size between the temperate European garrigue-like north-facing slope (ES) and the drier AS. In spite of the nonsignificant interslope trend for the higher genome size in C. persicum, the data-fusion (meta-analysis) test using correlations between C-values in C. persicum, and earlier studied carob tree (Ceratonia siliqua), trifoil (Lotus peregrinus) and a beetle (Oryzaephilus surinamensis) and their distribution along the aridity gradient indicates a positive relationship between drought and genome size at the microsite.

Genomic stability in Arabidopsis thaliana transgenic plants obtained by floral dip

The occurrence of DNA modification is an undesired phenomenon accompanying plant cell transformation. The event has been correlated with the stress imposed by the presently utilised transformation procedures, all depending on plant differentiation from in vitro cell culture, but other causes have not been excluded. In this work, transgenic Arabidopsis thaliana plants have been produced by an approach that does not require cell dedifferentiation, being based on in planta Agrobacterium-mediated gene transfer by flower infiltration, which is followed by recovery and selection of transgenic progeny. Genomic DNA changes in transgenic and control plants have been investigated by AFLP and RAMP analysis. Results show no statistically relevant genomic modifications in transgenic plants, as compared with control untreated plants. Variations were observed in callus-derived A. thaliana plants, thus supporting the conclusion that somaclonal variation is essentially correlated with the stress imposed by the in vitro cell culture, rather than with the integration of a foreign gene.

Evolutionary DNA variation in the genus hypochaeris

The genome size and the base composition (GC%) of eight Hypochaeris species were determined by flow cytometry in order to establish the pattern of nuclear DNA variation within the genus. The species analysed showed an almost fivefold range of variation from 1.68 pg in H. cretensis to 8.10 pg in H. uniflora. This variation in DNA content is greater between taxonomic sections of Hypochaeris species than within a section. There was no correlation between 2C DNA content and GC% indicating that neither the GC fraction nor the AT fraction were preferentially associated with variation in genome size. Because there is little heterochromatin, these results show that it is interspersed repeated sequences that are most probably implicated in this variation. From phylogenetic analysis, it is likely that genome size has evolved by loss of DNA content in some lineages and by gain in one lineage from an ancestral genome which was probably similar to genomes of intermediate size in Hypochaeris.

A complex adaptive syndrome in Drosophila caused by microclimatic contrasts

Temperature and humidity are among the most important environmental factors affecting insect adaptive strategies and evolution. Here, we report multiple adaptive differences between Drosophila melanogaster isofemale lines derived from the opposite slopes of Lower Nahal Oren canyon at Mount Carmel, Israel. The slopes are separated by 100 m at the bottom and 400 m at the top, and contrast sharply in physical and biotic factors. The multivariate fitness complex analysed in D. melanogaster included oviposition temperature preferences, viability and longevity changes, caused by short-term and lifetime temperature treatments, and resistance to drought stress at different temperatures. Some of these measures were obtained for the sibling species, D. simulans, and gave results that paralleled those of D. melanogaster. We conclude that strong microclimatic natural selection overrides migration in Drosophila at this microsite.

The organisations of hereditary information

The meaning of hereditary information is not simple. It includes not only what a system receives and transmits but particularly what it makes. The syntactic basis to hereditary information is also not straightforward. For example, is DNA instructions, or data, or both? The answer to this question requires an appreciation of the meaning of the information yet there are a number of possible semantic systems for describing hereditary information including proteins and development. The descriptive boundaries of hereditary information are examined by locating some general organising themes including hierarchy, ecology, regulation, epigenetic systems and talkback. Though metaphors have limits in terms of their explanatory power a number have influenced the development of biological thinking and biosystems have variously been represented as chemical laboratories, computers, electromechanical machines and societies. In this article a further metaphor is discussed, that of life-as-a-play or dance in which the trio of script (genome), cast (metabolism) and stage (cellular structure) co-exist and pre-exist the phenotypic life history which inherits them. A fuller examination of this trio provides an important perspective on the study of the organisations of information processing in hereditary systems.

Nuclear DNA content of Vitis species, cultivars, and other genera of the Vitaceae

The nuclear DNA content was analyzed in Vitis species, hybrid cultivars, and genera of the Vitaceae using flow cytometry. Significant variation was found among Vitis species, hybrids, and other genera of the Vitaceae (Ampelopsis and Parthenocissus). DNA content was estimated to range from 0.98 to 1.05 pg/2C within V. labrusca (ns) and 0.86 to 1.00 pg/2C within V. vinifera (ns). Genotypes from Vitis and Parthenocissus were similar in nuclear DNA content (approximately 1.00 pg/2C) whereas they differed significantly from Ampelopsis (1.39 pg/2C). No correlation between DNA content and the center of origin of genotypes of the Vitaceae was noted. Based on the present study, the Vitis genome size is 475 Mbp, 96% of which is non-coding. Knowledge of DNA content is useful in order to understand the complexity of the Vitis genome and to establish a relationship between the genetic and physical map for map-based cloning.

Transposition of IST2 in Thiobacillus ferrooxidans

The genome of Thiobacillus ferrooxidans contains at least two different repetitive DNA elements. One of these elements, termed IST2 has been sequenced and shown to exhibit the characteristics of a typical prokaryotic insertion sequence. Furthermore, preliminary evidence has implicated IST2 in genomic rearrangements, although the mechanism of rearrangement, whether by transposition or recombination, has not been established. In this report we provide evidence from detailed restriction enzyme analyses and DNA sequencing data that support a model of transposition, consistent with the notion that IST2 is a mobile insertion sequence.

Molecular markers in plant ecology

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. PCR-based methods, especially arnitrary-primer-based RAPDs, are likely to be most widely used and receive most attention. The limited use of DNA markers for overall quantitative (phenetic) comparisons of 'genetic variability' and 'generic distance' is stressed and fheir power as qualitative markers for any and all relevant regions in the genome is emphasized. Specific applications relevant to plant ecology are illustrated. These are: identification of organism and genotype even where morphology is of little help, as in mycorrhiza; identification of clones in asexually-reproducing species, even when they are widespread and intermingled; determining if genetic variation in elonal populations comes from mutations within elonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of elonal (apomicuc) and inbred selling organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing reeombinant genotypes in hybrid zones relative to differential adaptive responses: tracing the phylogenetic origin and extent of ecologically differentiated races or species; characterizing the genetic basis, mapping and isolating the genes responsible for special adaptive responses. In a final outlook, 1 speculate about unconventional sources of genetic variation affecting the ecological characteristics of plants that will become accessible to experimental analysis with the new molecular methods. Contents Summary 403 I. Introduction 404 II. Most ecological applications concern markers in the nuclear geonome 404 III. DNA polymorphisms differ from allozyme pohmorphisms 404 IV. Types of molecular marker 405 V. The application of markers in ecology 409 VI. From marker to character 413 VII. Outlook 414 References 414.

Trans-activation and stable integration of the maize transposable element Ds cotransfected with the Ac transposase gene in transgenic rice plants

To develop an efficient gene tagging system in rice, a plasmid was constructed carrying a non-autonomous maize Ds element in the untranslated leader sequence of a hygromycin B resistance gene fused with the 35S promoter of cauliflower mosaic virus. This plasmid was cotransfected by electroporation into rice protoplasts together with a plasmid containing the maize Ac transposase gene transcribed from the 35S promoter. Five lines of evidence obtained from the analyses of hygromycin B-resistant calli, regenerated plants and their progeny showed that the introduced Ds was trans-activated by the Ac transposase gene in rice. (1) Cotransfection of the two plasmids is necessary for generation of hygromycin B resistant transformants. (2) Ds excision sites are detected by Southern blot hybridization. (3) Characteristic sequence alterations are found at Ds excision sites. (4) Newly integrated Ds is detected in the rice genome. (5) Generation of 8 bp target duplications is observed at the Ds integration sites on the rice chromosomes. Our results also show that Ds can be trans-activated by the transiently expressed Ac transposase at early stages of protoplast culture and integrated stably into the rice genome, while the cotransfected Ac transposase gene is not integrated. Segregation data from such a transgenic rice plant carrying no Ac transposase gene showed that four Ds copies were stably integrated into three different chromosomes, one of which also contained the functional hph gene restored by Ds excision. The results indicate that a dispersed distribution of Ds throughout genomes not bearing the active Ac transposase gene can be achieved by simultaneous transfection with Ds and the Ac transposase gene.

Nuclear DNA changes within Helianthus annum L.: changes within single progenies and their relationships with plant development

The variations in the basic nuclear DNA content, which previous results indicated to occur within one and the same progeny of Helianthus annuus, were studied in detail and correlated with certain developmental features of the plants. The size and organization of the genome of seedlings obtained from seeds (achenes) collected at the periphery (P-seedlings) or in the middle (M-seedlings) of the flowering heads of plants belonging to a line selfed for 10 years were compared. Cytophotometric determinations indicated that the nuclear DNA content of P-seedlings is 14.7% higher than that of M-seedlings. Thermal denaturation and reassociation kinetics of extracted DNAs showed that variations in the redundancy of repetitive DNA, in particular of a family of medium repeated sequences with a Cot range of 2-100, account for the differences in genome size. These findings were confirmed by the results of molecular hybridizations (slot blots), which also indicated a higher amount of ribosomal DNA in the P-seedlings than in the M-seedlings. Cell proliferation is affected by DNA content, and mitotic cycle time is 1h30' longer in the P-seedlings. By studying mature plants, positive correlations were also found between genome size and both the surface area of leaf epidermal cells (P≤0.01) and flowering time (P≤0.001). It is suggested that the variations of nuclear DNA content and organization observed play a role in determining developmental variability in plant populations, which may be of importance in buffering the effects of changing environmental conditions.

Evidence for de novo rearrangements of Drosophila transposable elements induced by the passage to the cell culture

The genomic distribution and the number of elements of eleven transposon families have been compared by the Southern technique between permanent cultured cells, larval salivary glands and the brains and whole flies of an inbred Drosophila line (inb-c) from which the cells were established. In cultured cells, changes in restriction patterns consistent with various types of rearrangements such as amplification, transposition and excision of the elements of copia, 1731, 412, 297 and mdg-4 transposon families are detected whereas B 104, G and blood elements appear stable. In previous reports these rearrangements were not detected among individuals of the inb-c line or among samples of somatic tissues, or in samples spanning years of maintenance of cultured cells. Hence, we believe that they have been induced de novo during the passage to the cell culture.