Search

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes ( NADH dehydrogenase ( NADHdh) and retinoid and fatty acid binding protein ( RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field. [ABSTRACT FROM AUTHOR]

Eucalyptus globulus subsp. globulus Labill. (Tasmanian Blue Gum), native to southeast Australia, is a benchmark species for the pulp and paper industry. We genotyped 397 trees from 16 populations of E. globulus representing the native diversity in Australia using 24 microsatellite loci. Eight genetically distinct groups were detected, consistent with genetic groupings detected in previous quantitative and molecular studies. A sample of 29 Portuguese individuals was added to help clarify the origin of the Portuguese landrace. The results suggest a southern and eastern Tasmania origin for the Portuguese landrace. This genetic framework will enable researchers to investigate the provenance of individuals of unknown pedigree and assess the levels of representation of E. globulus natural variation in the Portuguese landrace. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis (Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression. [ABSTRACT FROM AUTHOR]

Polygonatum cyrtonema Hua is a traditional Chinese herb medicine, and it is widely distributed in China. The intrageneric taxonomy and phylogenetic relationships within Polygonatum have long been controversial due to their morphological similarity and lacking special DNA barcodes. In this paper, the complete chloroplast genome is a relatively conserved quadripartite structure including a large single copy region of 84 711 bp, a small single copy region of 18 210 bp, and a pair of inverted repeats region of 26 142 bp. A total of 342 simple sequence repeats were identified, and most of them were found to be composed of A/T, including 126 mono-nucleotides and 179 di-nucleotides. Nucleotide diversity was analyzed and eight highly variable regions (psbl∼trnT-CGU, atpF∼atpH, trnT-GGU∼psbD, psaJ∼rps20, trnL-UAG∼ndhD, ndhG∼ndhl, ndhA, and rpl32∼ccsA) were identified as potential molecular markers. Phylogenetic analysis based on the whole chloroplast genome showed that P. cyrtonema, within the family Asparagaceae, is closely related to Polygonatum sibiricum and Polygonatum kingianum. The sequence matK, trnT-GGU & ccsA, and ndhG∼ndhA were identified as three DNA barcodes. The assembly and comparative analysis of P. cyrtonema complete chloroplast genome will provide essential molecular information about the evolution and molecular biology for further study. [ABSTRACT FROM AUTHOR]

The article presents lists of papers published in the August 2013 and September 2013 issue which include papers on topics such as genome size diversity in sponges, distribution of transposable element the genome of the domestic cow Bos taurus, and genome size diversity patterns in bats.

The article lists the research papers related to genetics, published in the August 2013 and September 2013 issue of the journal.

The cumulative reproductive cost of multi-locus selection has been considered to be a potentially limiting factor on the rate of adaptive evolution. In this paper, we show that Haldane's arguments for the accumulation of reproductive costs over multiple loci are valid only for a clonally reproducing population of asexual genotypes. We show that a sexually reproducing population avoids this accumulation of costs. Thus, sex removes a perceived reproductive constraint on the rate of adaptive evolution. The significance of our results is twofold. First, the results demonstrate that adaptation based on multiple genes—such as selection acting on the standing genetic variation—does not entail a huge reproductive cost as suggested by Haldane, provided of course that the population is reproducing sexually. Second, this reduction in the cost of natural selection provides a simple biological explanation for the advantage of sex. Specifically, Haldane's calculations illustrate the evolutionary disadvantage of asexuality; sexual reproduction frees the population from this disadvantage. [ABSTRACT FROM AUTHOR]

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales. [ABSTRACT FROM AUTHOR]

Mendel is credited for discovering Laws of Heredity, but his work has come under criticism on three grounds: for possible falsification of data to fit his expectations, for getting undue credit for the laws of heredity without having ideas of segregation and independent assortment, and for being interested in the development of hybrids rather than in the laws of heredity. I present a brief review of these criticisms and conclude that Mendel deserved to be called the father of genetics even if he may not, and most likely did not, have clear ideas of segregation and particulate determiners as we know them now. I argue that neither Mendel understood the evolutionary significance of his findings for the problem of genetic variation, nor would Darwin have understood their significance had he read Mendel's paper. I argue that the limits to imagination, in both cases, came from their mental framework being shaped by existing paradigms-blending inheritance in the case of Darwin, hybrid development in the case of Mendel. Like Einstein, Darwin's natural selection was deterministic; like Niels Bohr, Mendel's Laws were probabilistic-based on random segregation of trait-determining 'factors'. Unlike Einstein who understood quantum mechanics, Darwin would have been at a loss with Mendel's paper with no guide to turn to. Geniuses in their imaginations are like heat-seeking missiles locked-in with their targets of deep interests and they generally see things in one dimension only. Imagination has limits; unaided imagination is like a bird without wings - it goes nowhere. [ABSTRACT FROM AUTHOR]

For commercial oyster aquaculture, triploidy has significant advantages. To produce triploids, the principal technology uses diploid × tetraploid crosses. The development of tetraploid brood stock for this purpose has been successful, but as more is understood about tetraploids, it seems clear that chromosome instability is a principal feature in oysters. This paper is a continuation of work to investigate chromosome instability in polyploid Crassostrea virginica. We established families between tetraploids-apparently stable (non-mosaic) and unstable (mosaic)-and normal reference diploids, creating triploid groups, as well as tetraploids between mosaic and non-mosaic tetraploids. Chromosome loss was about the same for triploid juveniles produced from either mosaic or non-mosaic tetraploids or from either male or female tetraploids. However, there was a statistically significant difference in chromosome loss in tetraploid juveniles produced from mosaic versus non-mosaic parents, with mosaics producing more unstable progeny. These results confirm that chromosome instability, as manifested in mosaic tetraploids, is of little concern for producing triploids, but it is clearly problematic for tetraploid breeding. Concordance between the results from cytogenetics and flow cytometry was also tested for the first time in oysters, by assessing the ploidy of individuals using both techniques. Results between the two were non-concordant. [ABSTRACT FROM AUTHOR]

Aegilops columnaris is a tetraploid species originated from Ae. umbellulata (2 n=2 x=14, UU) and a yet unknown diploid grass species. Although Ae. columnaris possesses some agronomically valuable traits, such as heat and drought tolerance and resistance to pests, it has never been used in wheat breeding because of difficulties in producing hybrids and a lack of information on the relationships between Ae. columnaris and common wheat chromosomes. In this paper, we report the development of 57 wheat - Ae. columnaris introgressive lines covering 8 of the14 chromosomes of Aegilops. Based on substitution spectra of hybrids and the results of FISH analysis of the parental Ae. columnaris line with seven DNA probes, we have developed the genetic nomenclature of the Uc and Xc chromosomes. Genetic groups and genome affinities were established for 11 of 14 chromosomes; the classification of the remaining three chromosomes remains unsolved. Each Ae. columnaris chromosome was characterized on the basis of C-banding pattern and the distribution of seven DNA sequences. Introgression processes were shown to depend on the parental wheat genotype and the level of divergence of homoeologous chromosomes. We found that lines carrying chromosome 5Xc are resistant to leaf rust; therefore, this chromosome could possess novel resistance genes that have never been utilized in wheat breeding. [ABSTRACT FROM AUTHOR]

To transfer multiple desirable alien genes into common wheat, we previously reported a new trigeneric hybrid synthesized by crossing a wheat - Thinopyrum intermedium partial amphiploid with wheat - Psathyrostachys huashanica amphiploid. Here, the meiotic behavior, chromosome constitution, and stripe rust resistance of F5 derivatives from the wheat - Th. intermedium - P. huashanica trigeneric hybrid were studied. Cytological analysis indicated the F5 progenies had chromosome numbers of 42-50 (average 44.96). The mean meiotic configuration was 1.28 univalents, 21.74 bivalents, 0.04 trivalents, and 0.02 tetravalents per pollen mother cell. In 2 n = 42 lines, the average pairing configuration was 0.05 I + 19.91 II (ring) + 1.06 II (rod) + 0.003 IV, suggesting these lines were cytologically stable. Most lines with 2 n = 43, 44, 46, 48, or 50, bearing a high frequency of univalents or multivalents, showed abnormal meiotic behavior. Genomic in situ hybridization karyotyping results revealed that 25 lines contained 1-7 Th. intermedium chromosomes, but no P. huashanica chromosomes were found among the 27 self-pollinated progenies. At meiosis, univalents (1-5) possessing Th. intermedium hybridization signals were detected in 19 lines. Bivalents (1-3) expressing fluorescence signals were observed in 12 lines. Importantly, 21 lines harbored wheat - Th. intermedium chromosomal translocations with various alien translocation types. Additionally, two homozygous lines, K13-668-10 and K13-682-12, possessed a pair of wheat - Th. intermedium small fragmental translocations. Compared with the recurrent parent Zhong 3, most lines showed high resistance to the stripe rust ( Puccinia striiformis f. sp. tritici) pathogens prevalent in China, including race V26/Gui22. This paper reports a highly efficient technical method for inducing alien translocation between wheat and Th. intermedium by trigeneric hybridization. These lines might be potentially valuable germplasm resources for further wheat improvement. [ABSTRACT FROM AUTHOR]

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%-4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region. [ABSTRACT FROM AUTHOR]

Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica. [ABSTRACT FROM AUTHOR]

Clubroot disease, caused by Plasmodiophora brassicae, is a threat to the production of Brassica crops including oilseed B. napus. In Canada, several pathotypes of this pathogen, such as pathotypes 2, 3, 5, 6, and 8, were identified, and resistance to these pathotypes was found in a rutabaga ( B. napus var. napobrassica) genotype. In this paper, we report the genetic basis and molecular mapping of this resistance by use of F2, backcross (BC1), and doubled haploid (DH) populations generated from crossing of this rutabaga line to a susceptible spring B. napus canola line. The F1, F2, and BC1 populations were evaluated for resistance to pathotype 3, and the DH population was evaluated for resistance to pathotypes 2, 3, 5, 6, and 8. A 3:1 segregation in F2 and a 1:1 segregation in BC1 were found for resistance to pathotype 3, and a 1:1 segregation was found in the DH population for resistance to all pathotypes. Molecular mapping by using the DH population identified a genomic region on chromosome A8 carrying resistance to all five pathotypes. This suggests that a single gene or a cluster of genes, located in this genomic region, is involved in the control of resistance to these pathotypes. [ABSTRACT FROM AUTHOR]

Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications. [ABSTRACT FROM AUTHOR]

By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal. [ABSTRACT FROM AUTHOR]

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents. [ABSTRACT FROM AUTHOR]

The fundamental question about Dioscorea trifida (Dioscoreaceae), the most important Amerindian yam, that remains unresolved concerns its evolutionary origin, since no wild relative has been reported. In this paper we report the existence of D. trifida’s wild relative for the first time. The diploidy of wild D. trifida (2n = 40) is clearly demonstrated by flow cytometry, chromosome counts, and microsatellite pattern analysis, whereas the cultivated form was previously shown to be autotetraploid (2n = 80). In the coastal region where the wild and cultivated forms are sympatric, tetraploid and triploid cytotypes coexist within the same populations. In the sites where the wild and cultivated forms are allopatric, the wild diploid cytotype predominates. AFLP (amplified fragment length polymorphism) analyses gave an initial idea of the position of the wild forms in relation to the cultivated forms. All the wild and cultivated types form a monophyletic group structured into two major subgroups corresponding to the tetraploid cytotype of the cultivated form and the diploid cytotype of the wild form. The triploid cytotypes of the wild form are in an intermediary position. Wild accessions are grouped on the basis of their geographic origin. The data presented in this paper are significant for the effective breeding and conservation of D. trifida and to assess its genetic diversity and population structure for the general understanding of the evolution and domestication of the species. La question fondamentale et toujours irrésolue au sujet du Dioscorea trifida (Dioscoréacées), la plus importante espèce d’igname amérindienne, est son origine évolutive puisque aucun ancêtre sauvage ne lui est connu. Dans ce travail, les auteurs rapportent pour la première fois l’existence d’un ancêtre sauvage du D. trifida. La diploïdie du D. trifida sauvage (2n = 40) est démontrée clairement par cytométrie en flux, comptage des chromosomes et par analyse de microsatellites, tandis que la forme cultivée est connue pour être autotétraploïde (2n = 80). Dans les régions côtières où les formes sauvages et cultivées sont sympatriques, des cytotypes tétraploïdes et triploïdes sont observés au sein des mêmes populations. Dans les sites où les formes sauvages et cultivées sont allopatriques, le cytotype diploïde sauvage prédomine. Des analyses AFLP (« amplified fragment length polymorphism ») ont fourni une première indication de la position des formes sauvages par rapport aux formes cultivées. Tous les types sauvages et cultivés forment un groupe monophylétique composé de deux sous-groupes majeurs correspondant au cytotype tétraploïde de la forme cultivée et au cytotype diploïde de la forme sauvage. Les cytotypes triploïdes de la forme sauvage occupent une position intermédiaire. Les accessions sauvages sont groupées sur la base de leur origine géographique. Les données présentées ici sont significatives dans le contexte des efforts de sélection et de conservation du D. trifida ainsi que pour la mesure de la diversité génétique et de la structure de la population en vue d’une meilleure compréhension de l’évolution et de la domestication de l’espèce. [ABSTRACT FROM AUTHOR]

A previous paper reported the development of disomic addition lines (2H, 3H, 4H, and 1HS isochromosomic) from hybrids between the winter wheat ‘Martonvásári 9 kr1’ and the two-rowed winter barley cultivar ‘Igri’. The present paper describes the isolation of two new additions, the 7H disomic and 6HS ditelosomic additions, using fluorescence in situ hybridization with the repetitive DNA probes Afa-family and HvT01. The identification of the barley chromosomes in the wheat genome was confirmed with simple sequence repeat markers. The morphological characterization of the new addition lines is also discussed. Studies of the genetic stability of the whole set (2H, 3H, 4H, 7H, 1HS iso, 6HS) of ‘Martonvásári 9 kr1’ - ‘Igri’ additions revealed that the most stable disomic additions are 2H and 3H and the most unstable line is the 1HS isochromosomic addition. [ABSTRACT FROM AUTHOR]

We comment on a recent paper by Rama Singh, who concludes that Mendel deserved to be called the father of genetics, and Darwin would not have understood the significance of Mendel's paper had he read it. We argue that Darwin should have been regarded as the father of genetics not only because he was the first to formulate a unifying theory of heredity, variation, and development - Pangenesis, but also because he clearly described almost all genetical phenomena of fundamental importance, including what he called 'prepotency' and what we now call 'dominance' or 'Mendelian inheritance'. The word 'gene' evolved from Darwin's imagined 'gemmules', instead of Mendel's so-called 'factors'. [ABSTRACT FROM AUTHOR]

Based on paper I in this series, our goals in this paper were to determine the relationship between prebombardment pretreatments and temperatures, microspore cell cycle when bombarded, and the frequencies of homozygous and hemizygous transgenic progeny in barley (Hordeum vulgare L.). Of the 104 fluorescent plants selected when using the GFP fluorescence transgene, 28 were albino and 76 plants were green. Thirty-one green plants were confirmed to be transgenic; the others were either transient green fluorescent protein expression or selected due to autofluorescence. Of the 31 plants, 23 came from embryos expressing a high level of fluorescence during selection and eight from 51 plants exhibiting a low level of fluorescence. Of the two pretreatments used to induce embryogenesis, 24 of 31 plants were from the cold pretreatment for 21 days (C) versus seven from the 4 day cold plus mannitol pretreatment. Following pretreatment, the microspores were subjected to a high-osmotic period (0.5 mol/L mannitol plus sorbitol) of 4 h prebombardment and 18 h postbombardment at either 25 or 4 °C. Of the 31 transgenic plants, 19 were produced following the 25 °C 4 h prebombardment. Sixteen of the 19 were doubled haploid plants (seven being homozygous for the transgene) and the other three plants were haploid. Of the remaining 12 plants recovered following the 4 h 4 °C prebombardment treatment, nine were haploid and three were doubled haploid plants, two of the latter being homozygous for the transgene. All 12 haploid plants obtained were treated with colchicine and produced homozygous transgenic doubled haploids. Of the two promoters compared, 30 plants had the actin promoter and only one had the 35S promoter. The use of arabinogalactan protein in the culture medium was very beneficial, giving rise to 29 of the 31 plants. The best procedure for obtaining transgenic barley plants from this study was pretreatment C, leaving the cultures at either 4 or 25 °C during the 4 h prebombardment high-osmotic period, using the actin promoter and having arabinogalactan protein in the microspore culture medium. With this procedure, the transgenic frequency was improved 8- to10-fold over previous reports on bombardment of microspores. It yielded about one transgenic plant per Petri dish and is comparable with Agrobacterium frequencies on structures derived from microspores. Suite aux résultats présentés dans l’article I de cette série, les objectifs de cet article étaient d’établir la relation entre les prétraitements et les températures employés avant le bombardement biolistique, le stade du cycle cellulaire auquel se trouvaient les microspores au moment du bombardement et les fréquences de plantes transgénetiques homozygotes et hemizygotes d’orge (Hordeum vulgare L.). Des 104 plantes fluorescentes sélectionnées à l’aide du transgène GFP, 28 plantes étaient albinos et 76 plantes étaient vertes. Trente et une plantes vertes ont été confirmées transgéniques; les autres présentaient une expression transitoire de la protéine fluorescente verte ou de l’auto fluorescence. De ces 31 plantes, 23 provenaient d’embryons exprimant un haut niveau de fluorescence, et huit provenaient des 51 plantules à faible niveau de fluorescence. Des deux prétraitements utilisés pour induire l’embryogenèse, 24 des 31 plantes ont été produites après 21 jours à 4 °C, alors que seulement sept l’ont été après 4 jours à 4 °C en présence de mannitol. Lors des phases à forte pression osmotique (0,5 mol/L mannitol plus sorbitol) de 4 h avant et 18 h après le bombardement, deux régimes de température ont été évalué, soit 4 et 25 °C. Sur les 31 plantes transgéniques, 19 ont été produites suite au prétraitement à 25 °C pendant 4 h. Seize de ces plantes étaient haploïdes doublées (sept homozygotes pour le transgène), tandis que les autres trois étaient haploïdes. Des 12 plantes produites après le prétraitement de 4 h à 4 °C précédent le bombardement, neuf étaient haploïdes et trois haploïdes doublées, deux de ces dernières étant homozygotes. Les 12 plantes haploïdes ont été traitées à la colchicine pour produire des plantes haploïdes doublées transgéniques. Des deux promoteurs comparés, 30 plantes avaient le promoteur de l’actine et seulement une plante avait le promoteur 35S. L’utilisation de protéine arabinogalactan en milieu de culture a été très bénéfique puisque 29 des 31 plantes ont été obtenues en sa présence. Le meilleur procédé pour [ABSTRACT FROM AUTHOR]

Cotton is one of the most economically important cultivated crops. It is the major source of natural fiber for the textile industry and an important target for genetic modification for both biotic stress and herbicide tolerance. Therefore, the characterization of genes and regulatory regions that might be useful for genetic transformation is indispensable. The isolation and characterization of new regulatory regions is of great importance to drive transgene expression in genetically modified crops. One of the major drawbacks in cotton production is pest damage; therefore, the most promising, cost-effective, and sustainable method for pest control is the development of genetically resistant cotton lines. Considering this scenario, our group isolated and characterized the promoter region of a MCO (multicopper oxidase) from Gossypium hirsutum, named GhAO-like1 (ascorbate oxidase-like1). The quantitative expression, together with the in vivo characterization of the promoter region reveals that GhAO-like1 has a flower- and fruit-specific expression pattern. The GUS activity is mainly observed in stamens, as expected considering that the GhAO-like1 regulatory sequence is enriched in cis elements, which have been characterized as a target of reproductive tissue specific transcription factors. Both histological and quantitative analyses in Arabidopsis thaliana have confirmed flower (mainly in stamens) and fruit expression of GhAO-like1. In the present paper, we isolated and characterized both in silico and in vivo the promoter region of the GhAO-like1 gene. The regulatory region of GhAO-like1 might be useful to confer tissue-specific expression in genetically modified plants. [ABSTRACT FROM AUTHOR]

This paper proposes a set of recommendations for the return of research results and incidental findings in paediatrics. The Network of Applied Genetic Medicine of Quebec spearheaded the initiative to develop the Statement of Principles on the Return of Research Results and Incidental Findings, which was the result of a consultation process with clinical and research experts in the field. To formulate the Statement of Principles, the authors ( i) reviewed empirical and grey literature on the return of research results and incidental findings in Europe and Canada, ( ii) conducted a qualitative study of stakeholder groups, ( iii) developed, and ( iv) validated the recommendations through consultations with the stakeholder groups. The Statement of Principles provides a useful disclosure tool for deciding when, and under what circumstances to return research results and incidental findings. It addresses the issue of return of results in genetic research generally, and has also specific principles for various research contexts, including paediatric research. It delineates ethical issues unique to paediatric research, and provides a framework to guide research ethics committees as well as the research community in addressing these issues. [ABSTRACT FROM AUTHOR]

Mycobacterium leprae is an intracellular obligate parasite that causes leprosy in humans, and it leads to the destruction of peripheral nerves and skin deformation. Here, we report an extensive analysis of the hypothetical proteins (HPs) from M. leprae strain Br4923, assigning their functions to better understand the mechanism of pathogenesis and to search for potential therapeutic interventions. The genome of M. leprae encodes 1604 proteins, of which the functions of 632 are not known (HPs). In this paper, we predicted the probable functions of 312 HPs. First, we classified all HPs into families and subfamilies on the basis of sequence similarity, followed by domain assignment, which provides many clues for their possible function. However, the functions of 320 proteins were not predicted because of low sequence similarity with proteins of known function. Annotated HPs were categorized into enzymes, binding proteins, transporters, and proteins involved in cellular processes. We found several novel proteins whose functions were unknown for M. leprae. These proteins have a requisite association with bacterial virulence and pathogenicity. Finally, our sequence-based analysis will be helpful for further validation and the search for potential drug targets while developing effective drugs to cure leprosy. [ABSTRACT FROM AUTHOR]

Domestic animals represent an extremely useful model for linking genotypic and phenotypic variation. One approach involves identifying allele frequency differences between populations, using FST, to detect selective sweeps. While simple to calculate, FST may generate false positives due to aspects of population history. This prompted the development of hapFLK, a metric that measures haplotype differentiation while accounting for the genetic relationship between populations. The focus of this paper was to apply hapFLK in sheep with available SNP50 genotypes. The hapFLK approach identified a known selective sweep on chromosome 10 with high precision. Further, five regions were identified centered on genes with strong evidence for positive selection ( COL1A2, NCAPG, LCORL, and RXFP2). Estimation of global FST revealed many more genomic regions, providing empirical data in support of published simulation-based results concerning elevated type I error associated with FST when it is being used to characterize sweep regions. The findings, while conducted using sheep SNP data, are likely to be applicable across those domestic animal species that have undergone artificial selection for desirable phenotypic traits. [ABSTRACT FROM AUTHOR]

The hermaphroditic, facultatively selfing, land snail Rumina decollata is a common, widespread species that is indigenous to the Mediterranean region and that has been introduced to many other regions of the world. However, recent DNA sequence analyses have indicated that R. decollata is a complex of several phylogenetic species, two of which correspond to previously distinguished allozyme strains with different body colors (light vs. dark) and life history characteristics. Against this background, this paper attempts to identify which of these phylogenetic species have been introduced elsewhere in the world. Based on a comparative DNA sequence analysis of putatively introduced populations from South America, North America, Japan, and the North Atlantic Islands versus native Mediterranean populations, it is shown that all putatively introduced populations belong to a single phylogenetic species that was previously recognized as the dark morph. Hence, the colonizing and invasive character of R. decollata seems to be due to this phylogenetic species. Nevertheless, in its native area the dark morph is supposed to be outcompeted when sympatric with the light morph of R. decollata. This issue is briefly discussed and the Iberian Peninsula is tentatively proposed as an important source for introduced R. decollata populations outside Europe. [ABSTRACT FROM AUTHOR]

Identification of individual chromosomes in a complement is usually a difficult task in the case of most plant species, especially for those with small, numerous, and morphologically uniform chromosomes. In this paper, we demonstrate that the landmarks produced by cross-species fluorescence in situ hybridisation (FISH) of Brachypodium distachyon derived bacterial artificial chromosome (BAC) clones can be used for discrimination of Brachypodium pinnatum (2 n = 18) chromosomes. Selected sets of clones were hybridised in several sequential experiments performed on exactly the same chromosome spreads, using reprobing of cytological preparations. Analysis of the morphometric features of B. pinnatum chromosomes was performed to establish their total length, the position of centromeres, and the position of BAC-based landmarks in relation to the centromere, thereby enabling their effective karyotyping, which is a prerequisite for more complex study of the grass genome structure and evolution at the cytomolecular level. [ABSTRACT FROM AUTHOR]

In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in genomic DNA provide unequivocal evidence of cis-acting polymorphisms. This paper describes experiments designed to demonstrate that stochastic variation in low copy number of targets in PCR reactions give variable allelic ratios even when starting with the same copy numbers of the two alleles. These significant departures from an expected 1:1 ratio provide an explanation to the lack of reproducibility observed for our cDNA measurements. [ABSTRACT FROM AUTHOR]

Serine proteinases including trypsins and chymotrypsins play various important roles in insects, including food digestion, immune defense, and zymogen activation. Studies on insect serine proteinases could reveal their feeding preference (polyphagous and monophagous) and facilitate identification of protease inhibitors, which can be engineered for pest management. In this paper, 11 transcripts encoding trypsin- and chymotrypsin-like proteins were cloned from the striped rice stem borer, (Walker). All the predicted proteins share high sequence similarity with known trypsin- and chymotrypsin-like proteins from either lepidopterans or dipterans, and most of the proteins have conserved motifs that are characteristics of serine proteinases. Among the 11 cloned genes, six were expressed predominantly and one exclusively in the midgut of the insect, three were expressed relatively evenly in examined tissues, and one was not expressed in either the gut or hemolymph based on RT-PCR results. The seven genes that were predominantly or exclusively expressed in the gut were also affected by feeding on different host plants. The genes that were expressed in the gut and were affected by host plants are likely to encode digestive proteinases. The identification of trypsin- and chymotrypsin-like genes in this insect species is the first step towards further comparative studies and for identification of insect-specific proteinase inhibitors, which might be engineered to protect rice plants against the striped rice stem borer, which is one of the destructive pests of rice. [ABSTRACT FROM AUTHOR]

Phylogenetic inferences of the polyploid taxa were drawn based upon the analysis of 909 nuclear 5S rDNA sequences obtained from 15 Aegilops polyploid taxa (531 sequences new to this paper) and 378 sequences from our previous study on the diploid taxa. The 531 sequences can be split into two orthologous groups (unit classes), the long AE1 and short AE1 previously identified in the diploid set. An examination of the relationships between unit classes and their associated haplomes suggests that U haplome sequences found in Ae. umbellulata are the closest to the T sequences found in Amblyopyrum muticum and that sequences of the polyploid species expected to be the M type found in Ae. comos are more similar to the T haplome sequences, except in the three hexaploids Ae. glumiaristata, Ae. juvenalis, and Ae. vavilovii and the tetraploid Ae. crassa where they are found to be similar to the M haplome sequences. These three hexaploid taxa likely originated from the tetraploid Ae. crassa ( DM), while the closest taxon to the fourth hexaploid, Ae. recta, is the tetraploid Ae. neglecta ( UM). Based upon the distribution of the unit classes, several reticulate phylogenies depicting evolutionary relationships among diploid, tetraploid, and hexaploid taxa were constructed; however, none of these widely used methods could depict the expected reticulate relationship as previously drawn from cytogenetic analyses in this group of allopolyploid species. These results suggest that evolutionary relationships derived from models based upon the assumption of bifurcating species require careful interpretation when these same models are applied to species with reticulate evolution. [ABSTRACT FROM AUTHOR]

Monoacylglycerol acyltransferase (MGAT3, also known as MOGAT3) catalyzes the synthesis of diacylglycerol (DAG) using 2-monoacylglycerol and fatty acyl coenzyme A. This enzymatic reaction is believed to be an essential and rate-limiting step for the absorption of dietary fat in the small intestine. However, similar research for the bovine MOGAT3 gene is lacking. Therefore, in this paper, polymorphisms of the bovine MOGAT3 gene were detected in 1145 individuals from five cattle breeds by DNA pooling, PCR-RFLP, and DNA sequencing methods. The results showed that 26 novel SNPs were identified, which included 16 mutations in the coding region and the others in the introns. Additionally, association analysis between two missense mutations, g.A229G and g.G1627A, and growth traits in Nanyang cattle up to 2 years of age and adult Qinchuan cattle was performed. The results indicated that polymorphisms were significantly associated with Nanyang cattle, but no convincing associations were observed for Qinchuan cattle for the studied traits. [ABSTRACT FROM AUTHOR]

Core histones are subjected to various post-translational modifications, and one of them, most intensively studied in plants, is the methylation of histone H3. In the majority of analyzed plant species, dimethylation of H3 at lysine 9 (H3K9me2) is detected in heterochromatin domains, whereas methylation of H3 at lysine 4 (H3K4me2) is detected in euchromatin domains. The distribution of H3K9me2 in the interphase nucleus seems to be correlated with genome size, chromatin organization, but also with tissue specificity. In this paper, we present the analysis of the pattern and level of histone H3 methylation for two allotetraploid and one diploid Brassica species. We have found that the pattern of H3K9me2 in interphase nuclei from root meristematic tissue is comparable within the analyzed species and includes both heterochromatin and euchromatin, but the level of modification differs not only among species but even among nuclei in the same phase of the cell cycle within one species. Moreover, the differences in the level of H3K9me2 are not directly coupled with DNA content in the nuclei and are probably tissue specific. [ABSTRACT FROM AUTHOR]

Production of high-lutein maize grain is of particular interest as a value-added feed source to produce high-lutein eggs. In this paper, it is demonstrated that heterosis for total carotenoid concentration and for the ratio of lutein to zeaxanthin (L:Z ratio), or profile type, exists infrequently in yellow dent crosses. However, yellow dent inbred maize lines A619 and CG102, both possessing high-lutein profiles, produce F1 seed with a classic overdominant expression of lutein levels (i.e., 49 µg/g dry weight (DW) above the high-parent value). Reciprocal crosses of A619 and CG102 with one another and with two high-zeaxanthin (i.e., low lutein), high-carotenoid lines both suggest that the A619 and CG102 high-lutein phenotypes are achieved by different and complementary genotypes. The contribution of CG102 to the heterotic response was examined using a QTL-based approach that involved phenotyping the mapping population in a testcross to A619. Significant QTL were found at loci known to be involved in the carotenoid pathway but also at loci proximate to, but separate from, known carotenoid pathway steps. Exploiting an overdominant heterotic response for lutein and total carotenoids should be given strong consideration as a viable method of producing high-carotenoid hybrid maize lines. [ABSTRACT FROM AUTHOR]

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL1, trnL2, and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of Ka/Ks in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 × 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda. [ABSTRACT FROM AUTHOR]

The estimation of recombination frequencies is a crucial step in genetic mapping. For the construction of linkage maps, nonadditive recombination fractions must be transformed into additive map distances. Two of the most commonly used transformations are Kosambi's and Haldane's mapping functions. This paper reports on the calculation of the bias associated with estimation of recombination fractions, Kosambi's distances, and Haldane's distances. I calculated absolute and relative biases numerically for a wide range of recombination fractions and sample sizes. I assumed that the ratio of recombinant gametes to the total number of gametes can be adequately represented by a binomial function. I found that the bias in recombination fraction estimates is negative, i.e., the estimator is an underestimate. However, significant values were only obtained when recombination fractions were large and sample sizes were small. The relevant estimates of recombination fractions were, therefore, nearly unbiased. Haldane's and Kosambi's distances were found to be strongly biased, with positive bias for the most interesting values of recombination fractions and sample sizes. The bias of Kosambi's distance was considerably smaller than the bias of Haldane's distance. L'estimation de la fréquence de recombinaison est une étape cruciale lors de la cartographie génétique. Lors de la construction de cartes génétiques, des fractions non-additives de recombinants sont transformées en distances génétiques additives. Deux des transformations parmi les plus employées sont les fonctions cartographiques de Kosambi et de Haldane. Ce travail porte sur la détermination des biais survenant lors de l'estimation des fractions de recombinants, des distances de Kosambi et des distances de Haldane. L'auteur a calculé les biais numériques absolus et relatifs pour une grande gamme de fractions de recombinants et de tailles d'échantillons. L'auteur a présumé que le ratio de gamètes recombinants versus le nombre total de gamètes était adéquatement représenté par une fonction binomiale. L'auteur a observé que les biais dans l'estimation des fractions de recombinants étaient négatifs, c'est-à-dire que l'estimateur était sous-évalué. Cependant, des valeurs significatives ont été obtenues seulement lorsque les fractions de recombinants étaient grandes et que les échantillons étaient de petite taille. Les estimés des fractions de recombinants sont donc généralement presque sans biais. Les distances de Kosambi et de Haldane présentaient de forts biais, des biais positifs étant observés pour les valeurs les plus intéressantes en matière de fractions de recombinants et de taille des échantillons. Le biais pour la distance de Kosambi était considérablement plus petit que le biais pour la distance de Haldane. [ABSTRACT FROM AUTHOR]

In this paper multiplicative mixed models have been used for the analysis of multi-environment trial (MET) data for canola oil and grain yield. Information on pedigrees has been included to allow for the modelling of additive and nonadditive genetic effects. The MET data set included a total of 19 trials (synonymous with sites or environments), which were sown across southern Australia in 2007 and 2008. Each trial was designed as a p-rep design using DiGGeR with the default prespecified spatial model. Lines in their first year of testing were unreplicated, whereas there were two or three replications of advanced lines or varieties. Pedigree information on a total of 578 entries was available, and there were 69 entries that had unknown pedigrees. The degree of inbreeding varied from 0 (55 entries) to nearly fully inbred (337 entries). Subsamples of 2 g harvested grain were taken from each plot for determination of seed oil percentage by near infrared reflectance spectroscopy. The MET analysis for both yield and oil modelled genetic effects in different trials using factor analytic models and the residual plot effects for each trial were modelled using spatial techniques. Models in which pedigree information was included provided significantly better fits to both yield and oil data. [ABSTRACT FROM AUTHOR]

In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5′ and 3′ long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5′ LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last ~84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions. [ABSTRACT FROM AUTHOR]

Coffea canephora Pierre ex Frohener is a perennial plant originated from Africa. Two main groups, Guinean and Congolese, have already been identified within this species. They correspond to main refugia in western and central Africa. In this paper we present the analysis of a region that has not yet been studied, Uganda. Two wild, one feral (once cultivated but abandoned for many years), and two cultivated populations of C. canephora from Uganda were evaluated using 24 microsatellite markers. Basic diversity, dissimilarity and genetic distances between individuals, genetic differentiation between populations, and structure within populations were analysed. Expected heterozygosity was high for wild compartments (0.48 to 0.54) and for cultivated and feral ones (0.57 to 0.59), with the number of private alleles ranging from 12 for cultivated genotypes to 37 for a wild compartment. The Ugandan samples show significant population structuring. We compared the Ugandan populations with a representative sample of known genetic diversity groups within the species using 18 markers. Coffea canephora of Ugandan origin was found to be genetically different from previously identified diversity groups, implying that it forms another diversity group within the species. Given its large distribution and extremely recent domestication, C. canephora can be used to understand the effect of refugia colonization on genetic diversity. [ABSTRACT FROM AUTHOR]

The objective of this study was to determine when DNA synthesis occurred during pretreatments of cultured barley (Hordeum vulgare L.) microspores and during their preparation for particle bombardment. Based on this information, an investigation of the influence of cell cycle stage on the ability to obtain homozygous transgenic plants by particle bombardment will be presented in paper II of this series. It was hypothesized that the introduction of foreign genes at the G1 cell cycle stage in cultured uninucleate microspores would produce homozygous transgenic plants. Experiments were conducted with two different commonly used pretreatments to induce microspore embryogenesis: cold (4 °C) for 21days and cold plus 0.3 mol/L mannitol for 4 days. After pretreatment, the microspores were placed in a higher osmotic medium for 4 h prior to and for 18 h following bombardment. It was confirmed that during the cold plus mannitol pretreatment, there was no apparent change in the cell cycle stage, with the majority of the microspores remaining at the G1 stage. While in the cold for 21 days, the microspores progressed slowly through to G2, with a few progressing further into the mitosis and binucleate stages. Hourly DNA density measurements that were taken during the 4 h osmotic adjustment period following the cold plus mannitol pretreatment indicated that DNA synthesis began during this period at 25 °C, while at 4 °C, there was no apparent change in cell cycle stage or in DNA density. Thus, one might expect to find a higher frequency of homozygous doubled haploids by maintaining the temperature low during the 4 h osmotic adjustment period following the cold plus mannitol pretreatment than following the 21 day cold pretreatment. However, it is also not known what effect the temperatures during the whole high-osmotic treatments will have on the rate and time of incorporation of the transgene. Le but de cette étude était de déterminer le moment de la synthèse de l’ADN au cours du prétraitement en culture de microspores d’orge (Hordeum vulgare L.) et de leur conditionnement en vue d’un bombardement biolistique. Avec de telles données, il est possible d’étudier l’influence du stade du cycle cellulaire sur la capacité de générer des plantes transgéniques homozygotes par bombardement et les résultats d’une telle analyse sont présentés dans l’article II de cette série. L’hypothèse proposée était que l’introduction de transgènes au stade G1 du cycle cellulaire chez des microspores uninucléées produirait des plantes transgéniques homozygotes. Deux prétraitements couramment utilisés pour induire l’embryogénèse chez les microspores ont été comparés : 4 °C pendant 21 jours et 4 °C et 0,3 mol/L mannitol pendant 4 jours. Après le prétraitement, les microspores ont été placées sur un milieu à forte pression osmotique 4 h avant le bombardement et jusqu’à 18 h après. Nous avons confirmé qu’aucune progression dans le cycle cellulaire n’était apparente au cours du traitement mannitol plus froid; la majorité des microspores restant au stade G1. Par contre, pendant 21 jours au froid, les microspores progressent lentement jusqu’au stade G2, certaines atteignant même les stades mitose et de microspore binucléée. Des mesures de la densité de l’ADN, répétées à chaque heure suivant la passage du prétraitement mannitol plus froid au traitement osmotique de 4 h précédant le bombardement ont indiqué que la synthèse de l’ADN commence lors de cette phase à 25 °C, tandis qu’à 4 °C, aucun changement apparent du cycle cellulaire ou de la densité d’ADN n’a été observé. Ainsi, une fréquence plus élevée d’haploïdes doublés homozygotes serait attendue en maintenant la température à 4 °C lors du traitement osmotique de 4 h faisant suite au prétraitement mannitol plus froid, que suite au prétraitement de 21 jours au froid. Cependant, l’effet de la température durant le traitement osmotique sur le taux et le moment d’incorporation du transgène est inconnu. [ABSTRACT FROM AUTHOR]

Responses to allopolyploidy include unequal expression of duplicated genes, gene silencing, and sometimes genomic rearrangements. In plants, the relationship between allelic expression differences arising from changes in regulatory regions and the resulting phenotype is poorly understood because of the complexity of their genomes and lack of efficient methodology to identify regulatory variation. Identifying functionally important regulatory variation in crops such as hexaploid wheat (Triticum aestivum) is in its infancy. More knowledge is required about the contribution of participatory genomes to its transcriptome. In this paper, we demonstrate the use of allelic imbalance assays to quantify relative expression levels across tissues and growth regimes of homoeologous transcripts of the A, B, and D genomes. Polymorphisms in the type I thionins have been used as an example. We show that expression levels vary markedly and interactively over all factors. For this gene, the B genome is the smallest contributor to the transcriptome and the D genome the largest. As additional sequence information is accumulated across genomes, this assay will allow the simple study of relative expression across multiple homeologous loci. Les changements observés en réponse à l’allopolyploïdie comprennent une expression inégale des gènes dupliqués, l’inactivation génique et, parfois, des réarrangements génomiques, Chez les plantes, les relations entre les différences d’expression allélique en réponse à des changements dans les régions régulatrices et le phénotype qui en résulte sont peu connus en raison de la complexité de leurs génomes et de l’absence de méthode efficace pour identifier la variation dans la régulation. L’identification de la variation dans la régulation qui est importante sur le plan fonctionnel chez des espèces cultivées comme le blé hexaploïde (Triticum aestivum) en est à ses tout premiers débuts. Davantage de connaissances sur la participation des génomes à l’élaboration du transcriptome sont nécessaires. Dans ce travail, les auteurs illustrent l’utilisation d’analyses de déséquilibre allélique pour quantifier les niveaux d’expression relative des transcrits homéologues des génomes A, B et D selon les tissus et les conditions de croissance. Les polymorphismes au sein des thionines de type I sont employés pour les fins de l’exemple. Les auteurs montrent que les niveaux d’expression varient de façon marquée et interactive pour l’ensemble des conditions. Pour ce gène, le génome B est le plus faible contributeur au transcriptome tandis que le génome D est le plus important. Avec l’accumulation d’informations additionnelles sur des séquences chez l’ensemble des génomes, cette analyse permettra d’étudier aisément l’expression relative sur de multiples locus homéologues. [ABSTRACT FROM AUTHOR]

This paper investigates the bias (the difference between the expectation (mean) of an estimator and its true value) of genetic distances for small samples. Exact results on this bias have not received much attention in genetic mapping literature. We show that bias drops quickly with increasing sample size for both a backcross population and an F2 in coupling. By contrast, bias may be substantial even for larger sample size for an F2 when markers are in repulsion. It is concluded that Karlin’s map function should be used with care when mapping is done using an F2 population. The same note of caution applies to other map functions such as Haldane’s and Kosambi’s. Finite-sample bias of these latter functions cannot be assessed because of the nonexistence of an expected value, but their median bias is similar to that of Karlin’s function. Ce travail examine le biais (i.e., la différence entre la valeur attendue (moyenne) d’un estimateur et sa vraie valeur) dans la mesure de distances génétiques au moyen de petits effectifs. Des résultats exacts concernant ce biais n’ont pas reçu beaucoup d’attention dans la littérature portant sur la cartographie génétique. Les auteurs montrent que le biais diminue rapidement avec l’accroissement de la taille de l’effectif, tant chez des populations issues d’un rétrocroisement que chez une F2 en couplage. Par contre, ce biais peut être substantiel, même avec de grands effectifs, pour une F2 lorsque les marqueurs sont en répulsion. Les auteurs en concluent qu’il faut être prudent lorsqu’on utilise la fonction de Karlin sur une population F2. La même prudence est de mise lorsqu’on utilise d’autres fonctions comme celles de Haldane ou de Kosambi. Dans ces derniers cas, le biais occasionné par la taille finie de l’effectif ne peut être mesuré en raison de l’absence d’une valeur attendue, mais leur biais médian est semblable à celui obtenu avec la fonction de Karlin. [ABSTRACT FROM AUTHOR]

There have been many studies of the morphology, behavioral audiograms, and population structure of the false killer whale (Pseudorca crassidens), but sequencing, mapping, and functional and comparative genomics studies are still largely unknown. In this paper, we sequenced three novel BAC clones corresponding to a total length of 308 kb and spanning the PRNP, PRND, and RASSF2 loci, and conducted comparative genomic analysis to examine the genomic structure of the false killer whale PRNP locus. We determined that the three genes show a high degree of conservation in their syntenic regions with respect to gene order, gene orientation, and the predicted coding sequence (CDS) between human and whale, whereas PRNT was not detected in whale. Interestingly, the predicted CDS in whale PRNP contained a novel type of 4-copy octarepeat resulting from a 24 bp deletion when compared with the human sequence. In addition, we identified a novel 1869 bp repeat unit in a region that is non-syntenic to human and cow sequences and is therefore considered to be whale-specific sequence. Our results will provide novel insights into the genomic changes that have occurred during evolution of mammalian PRNP loci, and may also have implications for research into prion disease. [ABSTRACT FROM AUTHOR]

In a previous phylogeographic study of the rodent Calomys musculinus, 24 haplotypes of the mitochondrial DNA D-loop region were detected using the restriction fragment length polymorphism technique (PCR-RFLP). Seven percent of the individuals showed patterns in which the sum of the sizes of the restriction fragments exceeded the size of the original PCR product. In the present paper we analyze possible causes of these atypical haplotypes. PCR products were cloned, and two or three different clones from a single individual were detected by their RFLP patterns. Nine clones with different restriction patterns were selected for sequence analyses. A maximum parsimony phylogenetic analysis revealed two well-supported paraphyletic groups. One group comprised sequences showing low nucleotide divergence compared with the most common haplotypes detected in the phylogeographic study. The other group was basal to the three species of Calomys other than C. musculinus included in the study; the mutations in the short portion of the cytochrome b gene amplified corresponded to 12 amino acid substitutions. The results suggest that two independent insertions of mtDNA sequences into the nucleus occurred; these sequences would co-amplify in the PCR procedure. Identification of pseudogenes is crucial to obtain reliable reconstruction of the intraspecific genealogy in phylogeographic studies. [ABSTRACT FROM AUTHOR]

The DOPA decarboxylase gene (Ddc) belongs to the “early-late” class of ecdysone-inducible genes in Drosophila melanogaster. Its expression is up-regulated in epidermal tissues by the ecdysone receptor acting through a response element, EcRE. In this paper, we show that another member of the nuclear receptor superfamily, DHR38, may act as a repressor of epidermal Ddc while inducing Ddc expression in neuronal cells. DHR38 does not behave as a classical co-repressor of the ecdysone receptor though, since the site through which DHR38 acts is distinct from the EcRE. Ectopic expression of a Dhr38 cDNA from a heat-shock promoter completely repressed transcription from the endogenous Ddc promoter and from an intact reporter construct in the hypoderm and in imaginal discs. Ectopic DHR38 had no effect on the transcription of a reporter driven by a Ddc fragment missing the DHR38 binding site. Neither reporter expression nor endogenous Ddc transcript levels were affected in a Dhr38 mutant background. Because most mutant organisms pupariate apparently normally and many of these survive to eclose, we believe that some functional redundancy exists within the Dhr38 regulatory network operating in epidermal tissues. In contrast to its apparent repressor function in epidermal tissues, DHR38 may act as a positive regulator of neural Ddc expression. Ectopic expression of DHR38 throughout the CNS induced as much as a 20-fold increase in Ddc transcripts in the set of neurons in which DDC normally appears. Le gène codant pour la décarboxylase DOPA (Ddc) appartient à la classe « tôt-tard » des gènes inductibles par l’ecdysone chez le Drosophila melanogaster. Son expression est accrue dans les tissus épidermiques grâce au récepteur d’ecdysone, lequel agit via un élément cis, EcRE. Dans ce travail, les auteurs montrent qu’un autre membre de la superfamille de récepteurs nucléaires, DHR38, agirait comme répresseur de l’expression épidermique de Ddc, tout en induisant l’expression de Ddc dans les cellules neuronales. DHR38 ne se comporte pas comme un co-répresseur classique du récepteur d’ecdysone puisque le site via lequel agit DHR38 est différent de l’élément EcRE. L’expression ectopique d’un ADNc de Dhr38 à partir d’un promoteur induit par les chocs thermiques a complètement réprimé la transcription du promoteur endogène de Ddc ainsi que d’un gène rapporteur dans l’hypoderme et les disques imaginaux. L’expression ectopique de DHR38 n’a eu aucun effet sur la transcription d’un rapporteur sous le contrôle d’un fragment de Ddc dépourvu du site de liaison de DHR38. Ni l’expression du rapporteur, ni celle de la copie endogène de Ddc n’a été affectée chez un mutant Dhr38. Puisque la plupart des mutants complètent leur pupaison normalement et que plusieurs survivent jusqu’à l’éclosion, les auteurs concluent qu’une redondance fonctionnelle existe au sein de circuit de régulation de Dhr38 dans les tissus épidermiques. Contrairement à son rôle apparent de répresseur dans les tissus épidermiques, DHR38 agirait comme régulateur positif de l’expression neuronale de Ddc. L’expression ectopique de DHR38 dans l’ensemble du CNS induirait une augmentation jusqu’à 20 fois du transcrit Ddc au sein des neurones dans lesquels DDC apparaît normalement. [ABSTRACT FROM AUTHOR]

This paper describes a study of the 5S ribosomal RNA genes (5S rDNA) in a group of 6 species belonging to 4 genera of Mugilidae. In these 6 species, the relatively short 5S rDNA repeat units, generated by PCR and ranging in size from 219 to 257 bp, show a high level of intragenomic homogeneity of both coding and spacer regions (NTS-I). Phylogenetic reconstructions based on this data set highlight the greater phylogenetic and genetic diversity of Mugil cephalus and Oedalechilus labeo compared with the genera Liza and Chelon. Comparative sequence analysis revealed significant conservation of the short 5S rDNA repeat units across Chelon and Liza. Moreover, a second size class of 5S rDNA repeat units, ranging from roughly 800 to 1100 bp, was produced in the Liza and Chelon samples. Only short 5S rDNA repeat units were found in M. cephalus and O. labeo. The sequences of the long 5S rDNA repeat units, obtained in Chelon labrosus and Liza ramada, differ owing to the presence of 2 large insertion/deletions (indels) in the spacers (NTS-II) and show considerable sequence identity with NTS-I spacers. Interspecific sequence variation of NTS-II spacers, excluding the indels, is low. Southern-blot hybridization patterns suggest an intermixed arrangement of short and long repeat units within a single chromosome locus. Cet article décrit une étude portant sur les gènes d’ARN ribosomique 5S (ADNr 5S) chez un groupe de 6 espèces appartenant à 4 genres au sein des mugilidés. Chez ces 6 espèces, les répétitions relativement courtes d’ADNr 5S, dont la taille des produits amplifiés par PCR varie entre 219 et 257 pb, présentent une grande homogénéité intragénomique tant au sein des régions codantes qu’au sein des espaceurs (NTS-I). Des reconstructions phylogénétiques sur la base de ces données mettent en relief la plus grande diversité phylogénétique et génétique chez le Mugil cephalus et l’Oedalechilus labeo par rapport aux genres Liza et Chelon. Des analyses comparées de séquences ont révélé une conservation significative des répétitions courtes d’ADNr 5S au sein des genres Chelon et Liza. De plus, une seconde classe d’ADNr 5S, dont la taille variait entre environ 800 et 1100 pb, a été observée chez les échantillons des genres Chelon et Liza. Seules des répétitions courtes ont été trouvées chez le M. cephalus et l’O. labeo. Les séquences de ces longues répétitions d’ADNr 5S, obtenues chez le Chelon labrosus et le Liza ramada, diffèrent en raison de la présence de deux grandes insertions/délétions (indels) dans les espaceurs (NTS-II) et montrent une très grande similarité avec les espaceurs NTS-I. La variation interspécifique de la séquence des espaceurs NTS-II, en dehors des indels, est faible. Les résultats d’hybridations Southern suggèrent la présence au sein d’un même locus chromosomique des répétitions courtes et longues entremêlées. [ABSTRACT FROM AUTHOR]

Legumes are members of the family Fabaceae or Leguminosae and include economically important grain legumes, oilseed crops, forage crops, shrubs, and tropical or subtropical trees. Legumes are a rich source of quality protein for humans and animals. They also enrich the soil by producing their own nitrogen in symbiosis with nitrogen-fixing bacteria. International centers and national institutes collect, maintain, distribute, and produce high-yielding legumes (grain-pulses, oilseeds, forages, nutraceuticals, medicinal shrubs, and trees). Legume breeders are confined within the primary gene pools (GP-1) in their varietal improvement programs and have not exploited secondary gene pools (GP-2), tertiary gene pools (GP-3), or quaternary gene pools (GP-4). Legumes are also an excellent source of timber, medicine, nutraceuticals, tannins, gums, insecticides, resins, varnish, paints, dyes, and eco-friendly by-products such as soy diesel. Three forage crops, Medicago truncatula, Lotus japonicus, and Trifolium pratense, are model legumes for phylogenetic studies and genome sequencing. This paper concludes that a “protein revolution” is needed to meet the protein demands of the world. [ABSTRACT FROM AUTHOR]

This paper describes a series of winter wheat – winter barley disomic addition lines developed from hybrids between winter wheat line Triticum aestivum L. ‘Martonvásári 9 kr1’ and the German 2-rowed winter barley cultivar Hordeum vulgare L. ‘Igri’. The barley chromosomes in a wheat background were identified from the fluorescent in situ hybridization (FISH) patterns obtained with various combinations of repetitive DNA probes: GAA–HvT01 and pTa71–HvT01. The disomic addition lines 2H, 3H, and 4H and the 1HS isochromosome were identified on the basis of a 2-colour FISH with the DNA probe pairs GAA–pAs1, GAA–HvT01, and pTa71–HvT01. Genomic in situ hybridization was used to confirm the presence of the barley chromosomes in the wheat genome. The identification of the barley chromosomes in the addition lines was further confirmed with simple-sequence repeat markers. The addition lines were also characterized morphologically. [ABSTRACT FROM AUTHOR]

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin. [ABSTRACT FROM AUTHOR]