Microcolinearity between a 2-cM region encompassing the grain protein content locus<Emphasis Type="Italic"> Gpc-6B1</Emphasis> on wheat chromosome 6B and a 350-kb region on rice chromosome 2

The conservation of the linear order (colinearity) of genetic markers along large chromosome segments in wheat and rice is well established, but less is known about the microcolinearity between both genomes at subcentimorgan distances. In this study we focused on the microcolinearity between a 2.6-cM interval flanked by markers Xcdo365 and Xucw65 on wheat chromosome 6B and rice chromosome 2. A previous study has shown that this wheat segment includes the Gpc-6B1 locus, which is responsible for large differences in grain protein content (GPC) and is the target of a positional cloning effort in our laboratories. Twenty-one recombination events between Xcdo365 and Xucw65 were found in a large segregating population (935 gametes) and used to map 17 genes selected from rice chromosome 2 in the wheat genetic map. We found a high level of colinearity between a 2.1-cM region flanked by loci Xucw75 and Xucw67 on wheat chromosome 6B and a 350-kb uninterrupted sequenced region in rice chromosome arm 2S. Colinearity between these two genomes was extended to the region proximal to Xucw67 (eight colinear RFLP markers), but was interrupted distal to Xucw75 (six non-colinear RFLP markers). Analysis of different comparative studies between rice and wheat suggests that microcolinearity is more frequently disrupted in the distal region of the wheat chromosomes. Fortunately, the region encompassing the Gpc-6B1 locus showed an excellent conservation between the two genomes, facilitating the saturation of the target region of the wheat genetic map with molecular markers. These markers were used to map the Gpc-6B1 locus into a 0.3-cM interval flanked by PCR markers Xucw79 and Xucw71, and to identify five candidate genes within the colinear 64-kb region in rice.     

Trophic coupling of a testate amoeba and <Emphasis Type="Italic">Microcystis</Emphasis> species in a hypertrophic pond

Seasonal changes in abundance of the testate amoeba Penardochlamys sp. and its food vacuole contents were investigated in relation to blooms of the cyanobacteria Microcystis spp. in a hypertrophic pond from April 1999 to March 2000. The behavior of the amoeba feeding on M. aeruginosa and M. wesenbergii was also observed in the laboratory. The amoeba was detectable from late May to November 1999 during the blooms of Microcystis spp. Cell densities of the amoeba fluctuated between 1.4 and 350 cells ml^–1 with some sporadic peaks, which did not coincide with rapid decreases in the abundance of Microcystis spp. Food vacuoles contained only Microcystis cells; other prey items were not found, suggesting that this amoeba utilized only the cyanobacteria as food. The amoeba was frequently found attached to Microcystis colonies, but was not associated with other suspended particles. Observation of the amoeba feeding revealed the feeding mechanism and that the amoeba was able to graze on both species of Microcystis. These results suggest that the trophic coupling of these organisms is substantial, although grazing by the amoeba is not sufficient to regulate the dynamics of Microcystis populations in this hypertrophic pond.     

AFLP-Based Genetic Linkage Maps of the Pacific Oyster <Emphasis Type="Italic">Crassostrea gigas</Emphasis> Thunberg

Amplified fragment length polymorphisms (AFLPs) were used for genome mapping in the Pacific oyster Crassostrea gigas Thunberg. Seventeen selected primer combinations produced 1106 peaks, of which 384 (34.7%) were polymorphic in a backcross family. Among the polymorphic markers, 349 were segregating through either the female or the male parent. Chi-square analysis indicated that 255 (73.1%) of the markers segregated in a Mendelian ratio, and 94 (26.9%) showed significant (P < 0.05) segregation distortion. Separate genetic linkage maps were constructed for the female and male parents. The female framework map consisted of 119 markers in 11 linkage groups, spanning 1030.7 cM, with an average interval of 9.5 cM per marker. The male map contained 96 markers in 10 linkage groups, covering 758.4 cM, with 8.8 cM per marker. The estimated genome length of the Pacific oyster was 1258 cM for the female and 933 cM for the male, and the observed coverage was 82.0% for the female map and 81.3% for the male map. Most distorted markers were deficient for homozygotes and closely linked to each other on the genetic map, suggesting the presence of major recessive deleterious genes in the Pacific oyster.     

Several regions of the repeat domain of the Staphylococcus caprae autolysin,AtlC, are involved in fibronectin binding

The chromosome of Bacteroides fragilis strain YCH46 was shown to be a single circular DNA molecule of about 5.3 Mb having 16 NotI, seven AscI, and six I-CeuI sites. A physical map of the chromosome was constructed by four independent experimental approaches: linking clone analysis, cross-Southern hybridization, partial restriction digestion, and two-dimensional pulsed-field gel electrophoresis. Six rRNA operons and 10 known genes were localized on the physical map.     

Prediction of coordination number and relative solvent accessibility in proteins

Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding and protein structure and in scoring remote homology searches. We develop ensembles of bidirectional recurrent neural network architectures to improve the state of the art in both contact and accessibility prediction, leveraging a large corpus of curated data together with evolutionary information. The ensembles are used to discriminate between two different states of residue contacts or relative solvent accessibility, higher or lower than a threshold determined by the average value of the residue distribution or the accessibility cutoff. For coordination numbers, the ensemble achieves performances ranging within 70.6-73.9% depending on the radius adopted to discriminate contacts (6A-12A). These performances represent gains of 16-20% over the baseline statistical predictor, always assigning an amino acid to the largest class, and are 4-7% better than any previous method. A combination of different radius predictors further improves performance. For accessibility thresholds in the relevant 15-30% range, the ensemble consistently achieves a performance above 77%, which is 10-16% above the baseline prediction and better than other existing predictors, by up to several percentage points. For both problems, we quantify the improvement due to evolutionary information in the form of PSI-BLAST-generated profiles over BLAST profiles. The prediction programs are implemented in the form of two web servers, CONpro and ACCpro, available at http://promoter.ics.uci.edu/BRNN-PRED/.     

Proteins with class alpha/beta fold have high-level participation in fusion events

Now that complete genome sequences are available for a variety of organisms, the elucidation of potential gene products function is a central goal in the post-genome era. Domain fusion analysis has been proposed recently to infer the functional association of the component proteins. Here, we took a new approach to the analysis of the structural features of the proteins involved in fusion events. An exhaustive survey of fusion events within 30 completely sequenced genomes and subsequent structure annotations to the component proteins at a SCOP superfamily level with hidden Markov models was carried out. A domain fusion map was then constructed. The results revealed that proteins with the class alpha/beta fold are frequently involved in fusion events, around 86% of the total 676 assigned single-domain fusion pairs including at least one component protein belonging to the alpha/beta fold class. Moreover, the domain fusion map in our work may offer an attractive framework for designing chimeric enzymes following Nature's lead, and may give useful hints for exploring the evolutionary history of proteins. (c) 2002 Elsevier Science Ltd.     

Integration of the FISH pachytene and genetic maps of Medicago truncatula

A molecular cytogenetic map of Medicago truncatula (2n = 2x = 16) was constructed on the basis of a pachytene DAPI karyogram. Chromosomes at this meiotic prophase stage are 20 times longer than at mitotic metaphase, and display a well differentiated pattern of brightly fluorescing heterochromatin segments. We describe here a pachytene karyogram in which all chromosomes can be identified based on chromosome length, centromere position, heterochromatin patterns, and the positions of three repetitive sequences (5S rDNA, 45S rDNA and the MtR1 tandem repeat), visualized by fluorescence in situ hybridization (FISH). We determined the correlation between genetic linkage groups and chromosomes by FISH mapping of bacterial artificial chromosome (BAC) clones, with two to five BACs per linkage group. In the cytogenetic map, chromosomes were numbered according to their corresponding linkage groups. We determined the relative positions of the 20 BACs and three repetitive sequences on the pachytene chromosomes, and compared the genetic and cytological distances between markers. The mapping resolution was determined in a euchromatic part of chromosome 5 by comparing the cytological distances between FISH signals of clones of a BAC contig with their corresponding physical distance, and showed that resolution in this region is about 60 kb. The establishment of this FISH pachytene karyotype, with a far better mapping resolution and detection sensitivity compared to those in the highly condensed mitotic metaphase complements, has created the basis for the integration of molecular, genetic and cytogenetic maps in M. truncatula.     

Genetic linkage mapping in Acacia mangium. 2. Development of an integrated map from two outbred pedigrees using RFLP and microsatellite loci

An integrated genetic linkage map, comprised of 219 RFLP and 33 microsatellite loci in 13 linkage groups, was constructed using two outbred pedigrees of Acacia mangium Willd. The linkage groups ranged in size from 23 to 103 cM and the total map length was 966 cM. Individual maps were made for each pedigree and the ordering of loci was consistent with the integrated map. The use of two independent pedigrees allowed a comparison of recombination rates between linked loci in male and female meioses as well as between parents. Differences were confined to specific regions and were not uniform across the male and female genomes or between genotypes. The heterogeneity in recombination frequencies did not result in major differences in the ordering of loci between pedigrees; hence, the integrated map provides a sound basis for QTL detection, leading to marker-assisted selection in A. mangium. It also provides a reference map for comparative genome analysis in acacias. The co-dominant markers used for mapping provide a useful resource in population studies and for quality control in acacia breeding programs. Detection of a relatively high proportion of selfs in pods derived from flowers which were not emasculated (30%), compared with emasculated flowers (0.01%), indicates that emasculation is desirable for efficient delivery of control-crossed seed in acacia breeding programs. Received: 25 March 2000 / Accepted: 30 April 2000     

Application of AFLP, RAPD and ISSR markers to genetic mapping of European and Japanese larch

Genetic linkage maps have been increasingly developed for a wide variety of plants, using segregating populations such as F₂s or backcrosses between inbred lines. These pedigrees are rarely available in outbred species like forest trees which have long generation times. Thus genetic mapping studies have to use peculiar pedigrees and markers in appropriate configurations. We constructed single-tree genetic linkage maps of European larch (Larix decidua Mill.) and Japanese larch [Larix kaempferi (Lamb.) Carr.] using segregation data from 112 progeny individuals of an hybrid family. A total of 266 markers (114 AFLP, 149 RAPD and 3 ISSR loci) showing a testcross configuration, i.e.heterozygous in one parent and null in the other parent, were grouped at LOD 4.0, θ=0.3. The maternal parent map (L. decidua)consisted of 117 markers partitioned within 17 linkage groups (1152 cM) and the paternal parent map (L. kaempferi) had 125 markers assembled into 21 linkage groups (1206 cM). The map distance covered by markers was determined by adding a 34.7-cM independence distance at the end of each group and unlinked marker. It reached 2537 cM and 2997 cM respectively for European larch and Japanese larch, and represented respectively a 79.6% and 80.8% coverage of the overall genome. A few 3:1 segregating markers were used to identify homologous linkage groups between the European larch and the Japanese larch genetic maps. The PCR-based molecular markers allowed the construction of genetic maps, thus ensuring a good coverage of the larch genome for further QTL detection and mapping studies. Received: 15 March 1999 / Accepted: 29 March 1999     

A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5

An integrated molecular marker map of the chickpea genome was established using 130 recombinant inbred lines from a wide cross between a cultivar resistant to fusarium wilt caused by Fusarium oxysporum Schlecht. emend. Snyd. &. Hans f. sp. ciceri (Padwick) Snyd & Hans, and an accession of Cicer reticulatum (PI 489777), the wild progenitor of chickpea. A total of 354 markers were mapped on the RILs including 118 STMSs, 96 DAFs, 70 AFLPs, 37 ISSRs, 17 RAPDs, eight isozymes, three cDNAs, two SCARs and three loci that confer resistance against different races of fusarium wilt. At a LOD-score of 4.0, 303 markers cover 2077.9 cM in eight large and eight small linkage groups at an average distance of 6.8 cM between markers. Fifty one markers (14.4%) were unlinked. A clustering of markers in central regions of linkage groups was observed. Markers of the same class, except for ISSR and RAPD markers, tended to generate subclusters. Also, genes for resistance to races 4 and 5 of fusarium wilt map to the same linkage group that includes an STMS and a SCAR marker previously shown to be linked to fusarium wilt race 1, indicating a clustering of several fusarium-wilt resistance genes around this locus. Significant deviation from the expected 1 : 1 segregation ratio was observed for 136 markers (38.4%, P<0.05). Segregation was biased towards the wild progenitor in 68% of the cases. Segregation distortion was similar for all marker types except for ISSRs that showed only 28.5% aberrant segregation. The map is the most extended genetic map of chickpea currently available. It may serve as a basis for marker-assisted selection and map-based cloning of fusarium wilt resistance genes and other agronomically important genes in future. Received: 17 November 1999 / Accepted: 4 June 2000