Biomedical subjects

O Panaud

Publications and source records attributed to O Panaud.

11 recordsLinked to original sources

PubMed2005

LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model.

Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.

Flowers↗

PubMed2004

Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.).

The origin of rice domestication has been the subject of debate for several decades. We have compared the transpositional history of 110 LTR retrotransposons in the genomes of two rice varieties, Nipponbare (Japonica type) and 93-11 (Indica type) whose complete sequences have recently been released. Using a genomic paleontology approach, we estimate that these two genomes diverged from one another at least 200,000 years ago, i.e., at a time which is clearly older than the date of domestication of the crop (10,000 years ago, during the late Neolithic). In addition, we complement and confirm this first in silico analysis with a survey of insertion polymorphisms in a wide range of traditional rice varieties of both Indica and Japonica types. These experimental data provide additional evidence for the proposal that Indica and Japonica rice arose from two independent domestication events in Asia.

Base Sequence↗

PubMed2003

Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L.

We studied the dynamics of hopi, Retrosat1, and RIRE3, three gypsy-like long terminal repeat (LTR) retrotransposons, in Oryza sativa L. genome. For each family, we assessed the phenetic relationships of the copies and estimated the date of insertion of the complete copies through the evaluation of their LTR divergence. We show that within each family, distinct phenetic groups have inserted at significantly different times, within the past 5 Myr and that two major amplification events may have occurred during this period. We show that solo-LTR formation through homologous unequal recombination has occurred in rice within the past 5 Myr for the three elements. We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.

Animals↗

PubMed2002

Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis (RDA).

Representational Difference Analysis was applied to characterize genomic differentiations between rice ( Oryza sativa) and foxtail millet ( Setaria italica) and subsequently to identify rice transposable elements. Rice was used as the tester and millet as the driver. A total of eleven, non-redundant, positive clones were isolated from the library. Their analysis revealed that they all represent dispersed repetitive DNA sequences. In addition, homology searches using the BLAST procedure showed that they correspond to seven distinct rice transposable elements. Three had been previously identified as gypsy-like retroelements ( Retrosat1, RIRE3 and RIRE8). The remaining four are novel: we named them hipa (a CACTA-like transposon), houba (a copia-like retroelement), hopi and dagul (two gypsy-like retroelements). The RDA clones were used as probes in Southern hybridization experiments with genomic DNAs of several species from the family Poaceae. The results suggest that the genomic differentiations associated with the activity of these transposable elements are of relatively recent origin. In addition, comparison of the hybridization patterns obtained for several Oryza species suggests that several independent amplifications of these transposable elements might have occurred within the genus.

Base Sequence↗

PubMed2001

Representational difference analysis reveals genomic differences between Q. robur and Q. suber: implications for the study of genome evolution in the genus Quercus.

Very similar genome sizes, similar karyotypes and heterochromatin organisation, and identical number/position of ribosomal loci characterise the common oak (Q. robur) and the cork oak (Q. suber), two distantly related oak species. Representational Difference Analysis (RDA) was used to subtract the genome of Q. suber from the genome of Q. robur in order to search for genome differentiation. A library of 400 clones (bearing RDA fragments) representing genome differences between the two species was obtained. Seven Q. robur-specific DNA sequences were analysed with respect to their molecular and chromosome organisation. All belong to the dispersed repetitive component of the genome, as revealed by Southern hybridisation and in situ hybridisation. They are present in the Q. robur genome in between 100 and 700 copies, and are distributed along the length of almost all chromosomes. A search for homologies between RDA fragments and sequences in Genbank revealed similarities of all RDA fragments with known retrotransposons. The RDA fragments were also tested for their presence/absence in the genomes of six additional oak species belonging to different phylogenetic groups, in order to examine the evolutionary dynamics of these DNA sequences.

Base Sequence↗

PubMed2001

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system.

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.

Alleles↗

PubMed2000

Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers.

Despite the urgent need to conserve domesticated plant genetic resources, and developing 'on farm' strategies of conservation, the impact of traditional farming practices and of their interaction with ecological factors on the structure and evolutionary dynamics of the genetic variability of crop populations has been little documented. We assessed the genetic variability of 31 varieties of cassava (M. esculenta Crantz) traditionally grown by Makushi Amerindians from Guyana, using AFLP markers. We used a sample of 38 varieties from an ex situ core collection as a reference. Accessions of wild cassava were also included. While clonality of the varieties was expected due to the vegetative propagation of cassava, 21 varieties presented intravarietal polymorphism. Among the varieties from a single site in Guyana, genetic diversity was the same as that in the accessions from the core collection. We suggest that incorporation of volunteer seedlings, produced by sexual reproduction, into the stock of varieties grown by the Makushi plays a major role in explaining both intravarietal polymorphism and the high level of genetic diversity. No correspondence was found between the structure of molecular diversity and variation observed for agronomic traits that are targets for selection by cultivators. As found in previous studies, all wild forms of cassava clustered together and separately from the cultivated varieties in a Neighbour-Joining dendrogram. These results are consistent with the hypothesis of a limited domestication event in a restricted area, followed by rapid diffusion of cultivated phenotypes and convergent evolution. Our results show that local varieties are an important source of genetic diversity, and highlight the importance of the interaction between human and ecological factors in the dynamics of this diversity.

Evolution, Molecular↗

PubMed1997

Microsatellite marker development, mapping and applications in rice genetics and breeding.

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10,000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trail locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.

Breeding↗

PubMed1996

Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.).

Microsatellite markers containing simple sequence repeats (SSR) are a valuable tool for genetic analysis. Our objective is to augment the existing RFLP map of rice with simple sequence length polymorphisms (SSLP). In this study, we describe 20 new microsatellite markers that have been assigned to positions along the rice chromosomes, characterized for their allelic diversity in cultivated and wild rice, and tested for amplification in distantly related species. Our results indicate that the genomic distribution of microsatellites in rice appears to be random, with no obvious bias for, or clustering in particular regions, that mapping results are identical in intersubspecific and interspecific populations, and that amplification in wild relatives of Oryza sativa is reliable in species most closely related to cultivated rice but becomes less successful as the genetic distance increases. Sequence analysis of SSLP alleles in three related indica varieties demonstrated the clustering of complex arrays of SSR motifs in a single 300-bp region with independent variation in each. Two microsatellite markers amplified multiple loci that were mapped onto independent rice chromosomes, suggesting the presence of duplicated regions within the rice genome. The availability of increasing numbers of mapped SSLP markers can be expected to increase the power and resolution of genome analysis in rice.

Alleles↗

PubMed1996

Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels.

An efficient technique for cloning DNA from silver-stained denaturing polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of 32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding 32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome.

Base Sequence↗

PubMed1995

Frequency of microsatellite sequences in rice (Oryza sativa L.).

This study was undertaken to estimate the relative frequencies of 13 microsatellite motifs in the rice genome as a basis for efficient development of a microsatellite map. Two dinucleotide, seven trinucleotide, and four tetranucleotide repeat motifs were end labelled and used as hybridization probes to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing temperatures for identification of clones containing specific microsatellite motifs were estimated based on washing temperatures near Td (dissociation temperature; Td = Tm - 7.6 degrees C). Sequencing of 20 putatively positive clones corresponding to each of 4 microsatellite motifs suggested that while Td provides a useful predictor of washing stringency for most of the repeats studied, those with a very high GC or AT content were most prone to error. The results from screening the rice genomic library suggest that there are an estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome, and that the relative frequency of different repeats decreased with increasing size of the motif. The most frequently observed microsatellites in the cDNA library were the same as for genomic library, but no poly(CGG)n, poly(ATC)n, or tetranucleotide motifs were observed among cDNA in this study.

Base Composition↗