Molecular aspects of the environmental induction of heritable changes in flax

PARENTAL EFFECTS IN PLANTAGO LANCEOLATA L. I.: A GROWTH CHAMBER EXPERIMENT TO EXAMINE PRE- AND POSTZYGOTIC TEMPERATURE EFFECTS

In spite of the potential evolutionary importance of parental effects, many aspects of these effects remain inadequately explained. This paper explores both their causes and potential consequences for the evolution of life-history traits in plants. In a growth chamber experiment, I manipulated the pre- and postzygotic temperatures of both parents of controlled crosses of Plantago lanceolata. All offspring traits were affected by parental temperature. On average, low parental temperature increased seed weight, reduced germination and offspring growth rate, and accelerated onset of reproduction by 7%, 50%, 5%, and 47%, respectively, when compared to the effects of high parental temperature. Both pre- and postzygotic parental temperatures (i.e., prior to fertilization vs. during fertilization and seed set, respectively) influenced offspring traits but not always in the same direction. In all cases, however, the postzygotic effect was stronger. The prezygotic effects were more often transmitted paternally than maternally. Growth and onset of reproduction were influenced both directly by parental temperature as well as indirectly via the effects of parental temperature on seed weight and germination. Significant interactions between parental genotypes and prezygotic temperature treatment (G × E interactions) show that genotypes differ in their intergenerational responses to temperature with respect to germination and growth. The data suggest that temperature is involved in both genetically based and environmentally induced parental effects and that parental temperature may accelerate the rate of evolutionary change in flowering time in natural populations of P. lanceolata. The environmentally induced temperature effects, as mediated through G × (prezygotic) E interactions are not likely to affect the rate or direction of evolutionary change in the traits examined because postzygotic temperature effects greatly exceed prezygotic effects.

RNA-mediated epigenetic regulation of DNA copy number

Increasing evidence suggests that parentally supplied RNA plays crucial roles during eukaryotic development. This epigenetic contribution may regulate gene expression from the earliest stages. Although present in a variety of eukaryotes, maternally inherited characters are especially prominent in ciliated protozoa, in which parental noncoding RNA molecules instruct whole-genome reorganization. This includes removal of nearly all noncoding DNA and sorting the remaining fragments, producing extremely gene-rich somatic genomes. Chromosome fragmentation and extensive replication produce variable DNA copy numbers in the somatic genome. Understanding the forces that drive and regulate copy number change is fundamental. We show that RNA molecules present in parental cells during sexual reproduction can regulate chromosome copy number in the developing nucleus of the ciliate Oxytricha. Experimentally induced changes in RNA abundance can both increase and decrease the levels of corresponding DNA molecules in progeny, demonstrating epigenetic inheritance of chromosome copy number. These results suggest that maternal RNA, in addition to controlling gene expression or DNA processing, can also program DNA amplification levels.

Compounds from plants that regulate or participate in disease resistance

Disease resistance is multifactorial. The response phase includes: synthesis of phytoalexins, i.e. low molecular weight antimicrobial compounds which accumulate at sites of infection; systemically produced enzymes which degrade pathogens, e.g. chitinases, beta-1,3-glucanases and proteases; systemically produced enzymes which generate antimicrobial compounds and protective biopolymers, e.g. peroxidases and phenoloxidases; biopolymers which restrict the spread of pathogens, e.g. hydroxyproline-rich glycoproteins, lignin, callose; and compounds which regulate the induction and/or activity of the defence compounds, e.g. elicitors of plant and microbial origin, immunity signals from immunized plants and compounds which release immunity signals. Disease resistance in plants is not determined by the presence or absence of genes for resistance mechanisms, it is determined by the speed and degree of gene expression and the activity of the gene products. It is likely, therefore, that all plants have the genetic potential for resistance. This potential can be expressed systemically (immunization) after restricted inoculation with pathogens, attenuated pathogens or selected non-pathogens, or treatment with chemical substances that are produced by immunized plants or chemicals which release such signals. Immunization is effective against diseases caused by fungi, bacteria and viruses, and it has been successfully tested in the laboratory and field. Advances in science have provided information and technology to enhance resistance to plant pests. Pesticides are part of this technology, but they also contribute to a complex world problem which threatens our environment and hence our survival. The future will see the restriction of pesticide use and a greater reliance on resistant plants generated using immunization and other biological control technologies, genetic engineering and classical plant breeding. However, as with past and current technology, we will have created unique problems. The survival of our planet depends upon anticipating these problems and meeting the challenge of their solution.

A site-specific insertion sequence in flax genotrophs induced by environment

A single-copy 5.7 kilobase (kb) DNA fragment, termed Linum Insertion Sequence 1 (LIS-1), has been identified and characterized. This is one of the DNA changes associated with the environmentally induced heritable changes resulting in stable lines termed genotrophs in flax (Linum usitatissimum). The insertion sequence and its insertion site have been cloned from genomic libraries and sequenced. PCR products across the insertion and surrounding regions have also been cloned and sequenced. The 5.7 kb DNA fragment is inserted into a 3.7 kb EcoRI fragment in the plastic line (Pl) with the generation of a 3 base pair duplication at the insertion site, as well as additional sequence changes. The identical insertion was also found in other genotrophs and flax varieties. The intact element was not present in Pl but appeared to be generated by a reproducible series of complex rearrangements or insertion events. LIS-1 is the result of a targeted, highly specific, complex insertion event that occurs during the formation of some of the genotrophs, and occurs naturally in many flax and linseed varieties.

Carryover effects on the clonal growth of the grass Holcus lanatus L

The effects of clipping and daylength treatments and their carryover effects on the clonal growth of the perennial grass Holcus lanatus L. were investigated. Plants from ten clones were grown in six combinations of two daylength and three clipping treatments. Both clipping and low daylength reduced the tillering rate of all the clones but the clones differed in their degree of response to these treatments. After eight weeks, the treatments were discontinued and plants were grown in a common environment for seven weeks. Four-week-old tillers from the plants were repotted and grown in a common environment to examine the possibility of 'carryover' effects of the parental environments. After 8 wk of growth, there were main and interaction carryover effects of daylength and clipping on the tillering rates, biomass and tiller extension rates of the plants, which, however, differed greatly among clones. These differences among clones in both direct and carryover treatment effects, on clonal growth, indicate how the effects of many different environmental variables may interact to produce an environment that is highly heterogeneous in space and time, influencing the coexistence of genotypes and species.

The flax ribosomal RNA-encoding genes are arranged in tandem at a single locus interspersed by 'non-rDNA' sequences

The ribosomal RNA (rRNA)-encoding genes (rDNA) in flax, estimated to be present in about 2400 copies per diploid nucleus, have been reported as a single homogeneous repeat unit of 8.6 kb. In situ hybridization analysis indicated that these genes were located at a single site on one pair of chromosomes. However, an analysis of a flax variety, CI 1303, has revealed heterogeneity in the intergenic spacer of the rDNA repeat unit. A genetic analysis of rDNA inheritance in two flax lines, Stormont Cirrus and CI 1303, has again supported the observation that there is a single rDNA locus in this plant species. Screening of four different genomic libraries made in methylation-sensitive and -insensitive systems, and the analysis of 40 phage clones, demonstrate a much higher number than that expected of junctions between rDNA and non-rDNA. Direct evidence of rRNA-encoding genes being present in tandem comes from a few phage clones that contain more than two rDNA repeats. The evidence presented here indicates that rDNA, although present at a single locus in tandem arrays, may be interrupted frequently by other non-rDNA sequences, thus giving rise to questions about their organization into long tandem arrays.

The ubiquitin-encoding multigene family of flax, Linum usitatissimum

Ubiquitin (Ubq), a 76-amino acid (aa) protein, is found in all eukaryotic organisms and is one of the most conserved proteins so far studied. It is implicated in many cellular processes. The Ubq-encoding genes (ubq) are generally present as a multigene family. In flax, we have estimated that this multigene family contains at the most ten members. The initial flax ubq sequences were isolated from a flax genomic library in lambda EMBL4 using a heterologous Arabidopsis thaliana ubq probe. An 916-bp fragment from one of the phage clones was subcloned and sequenced. The aa sequence derived from the nucleotide sequence of this fragment is identical to that of other plant Ubqs. This fragment was then used to isolate additional flax ubq clones. In all, eleven phage lambda clones, which represent six members of the gene family, were restriction-mapped and characterized. These six members are represented as three monomers, three poly-Ubqs, one hexamer and two tetramers. They can be present at either a single locus (two of the monomers and one of the poly-Ubqs) or at two loci (the remaining three genes). The other four members of the family are yet to be cloned and characterized.

Chromosomal and molecular analysis of 5S RNA gene organization in the flax, Linum usitatissimum

The 5S rRNA genes (5S DNA) comprise up to 3% of the flax genome. Large copy-number changes in 5S DNA have been observed in flax genotrophs. We have characterized the chromosomal and molecular organization of this large gene family. In situ hybridization studies indicate the 5S DNA is distributed over many chromosomes, unlike most plants studied to date. Eleven genomic clones were isolated and characterized. All but one of the clones contain both 5S DNA and non-5S DNA. The homology of the 5S DNA of each clone, to a previously isolated flax 5S plasmid clone (pBG13), was determined. Five groups of 5S DNA were identified based on shared identity and repeat unit size. Group-1 and group-2 clones are the most abundant in terms of genomic representation. The remaining groups are significantly different from the previously described flax 5S DNA and are in low representation in comparison to group-1 and group-2 5S DNA. The results establish the presence of several groups of 5S DNA which are distributed over many chromosomes. The extent of identity shared among these groups to pBG13, indicates a high degree of divergence between the different groups.

Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer

Ribosomal RNA genes in plants are highly variable both in copy number and in intergenic spacer (IGS) length. This variability exists not only between distantly related species, but among members of the same genus and also among members of the same population of a single species. Analysis of inheritance indicates that copy number change is rapid, occurring even among somatic cells of individual plants, and that up to 90% or more of the gene copies are superfluous. Subrepetitive sequences within the IGS appear to be changing rapidly as well. They are not only variable in sequence from one species to the next, but can vary in number between neighboring gene repeats on the chromosome. In all species examined in detail they are located in the same region of the IGS and contain sequences that can be folded into stem-loop structures flanked by a pyrimidine-rich region. It has been suggested that these subrepeats function in transcriptional enhancement, termination or processing, or in recombination events generating the high multiplicity of ribosomal genes.

Possible posttranslational modification, and its genetic control, in flax genotroph isozymes

Environmentally induced flax genotrophs L and S show heritable shifts in the relative mobilities of peroxidase, esterase, and acid phosphatase isozymes, plus a number of nonspecific glycoproteins. All L isozymes migrated faster than corresponding S isozymes in 10% acrylamide gels. Various aspects of these shifts are reviewed here; it is proposed that posttranslational modification, probably of the carbohydrate moieties of these glycoproteins, underlies the shifts. This proposal is discussed in relation to the switch model for genotroph induction.

The chloroplast DNAs of flax genotrophs

The chloroplast DNA of L. usitatissimum var. "Stormont Cirrus" has been mapped with respect to the recognition sites for the enzymes SalP1, Sst1 and SalG1. It is a circular molecule of about 160 kilobasepairs, with an inverted repeat containing the rDNA. Comparisons between chloroplast DNA of uninduced and induced flax genotrophs show there to be no major structural differences.

DNA sequence organization in the flax genome

The complexity of the flax genome has been determined by reassociation kinetics. The total complexity of one constituent genome was 3.5 . 10(8) nucleotide pairs. The single copy sequences comprised 44% of the genome and showed a long period interspersion pattern with the repetitive sequences. The repetitive sequences occurred in clusters which stretched for at least 10 000 base pairs. Within these clusters the individual repetitive elements were about 650 base pairs. These elements themselves showed little interspersion of different frequency classes in lengths less than 3000 base pairs. The repetitive sequence duplexes formed on reassociation, except for the satellite DNA, showed a high thermal stability. The fold-back DNA comprised 1% of the total genome, and was itself clustered in a small fraction of the genome.

Segregation of the isozymes of flax genotrophs

The segregation of isozymes of peroxidase and acid phosphatase in progenies of crosses between large (L) and small (S and L6) flax genotrophs has been determined. The peroxidase isozymes segregated as expected on a simple Mendelian model with a dominant and a recessive allele and with the L genotroph being a homozygous dominant. All the peroxidase isozymes which differed segregated together, so the isozymes are controlled by either a single locus or closely linked loci. The acid phosphatase isozymes in the F1 were all L type, but the segregations observed in the F2 were not always consistent with a simple Mendelian model.

Isozymes, plant population genetic structure and genetic conservation

The exploration, conservation and use of the genetic resources of plants is a contemporary issue which requires a multidisciplinary approach. Here the role of population genetic data, particularly those derived from electrophoretic analysis of protein variation, is reviewed. Measures of the geographic structure of genetic variation are used to check on sampling theory. Current estimates justify the contention that alleles which have a highly localised distribution, yet are in high frequency in some neighbourhoods, represent a substantial fraction of the variation. This class, which is the most important class in the framing of sampling strategies, accounts for about 20-30% of variants found in 12 plant species. The importance of documenting possible coadapted complexes and gene-environment relationships is discussed. Furthermore, the genetic structure of natural populations of crop relatives might suggest the best structure to use in the breeding of crops for reduced vulnerability to pest and disease attack, or for adaptation to inferior environments. The studies reported to date show that whilst monomorphic natural populations do occur, particularly in inbreeding colonisers, or at the extreme margins of the distribution, polymorphism seems to be the more common mode. It is stressed here that the genetic resources of the wild relatives of crop plants should be systematically evaluated. These sources will supplement, and might even rival, the primitive land races in their effectiveness in breeding programmes. We may look forward to a wider application of gel electrophoresis in the evaluation of plant genetic resources because this technique is currently the best available for detecting genetic differences close to the DNA level on samples of reasonable size.