A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

Background: \ud The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species.\ud \ud Results: \ud A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map.\ud \ud Conclusions: \ud Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/

The genomic Make-Up of a Hybrid Species - Analysis of the Invasive Cottus Lineage (Pisces, Teleostei) in the River Rhine system

In the past years a new invasive lineage of sculpins (Cottus species complex) has been studied that is currently expanding in the Lower River Rhine. Molecular analysis showed that this lineage has originated through hybridization of Cottus perifretum from the River Scheldt and Cottus rhenanus from the Lower River Rhine system. The emergence of the hybrid lineage is correlated with new habitat adaptations that allow the expansion along river habitats that have previously not been used by Cottus. Thus the question arises, if the hybridization event facilitated the invasion of and the adaptation to such a new environment. To start tackling this question an estimate is required how much each of the parental species contributed to the hybrid genome and which chromosomal fragments became fixed. Several genomic resources had to be developed in order to map the ancestries of chromosomal fragments in the hybrid genome. As a basic genomic resource for Cottus a genetic map based on already established microsatellite markers was created. This map was compared with the physical maps of sequenced fish genomes and a high degree of conserved synteny between Cottus and Tetraodon nigroviridis and between Cottus and Gasterosteus aculeatus could be detected. These model fish genomes could then be used as a reference in the further analysis of the Cottus genome. Finally, a set of ancestry-informative markers was developed in order to determine the ancestries of chromosomal fragments in the hybrid lineage. These tools allowed to map the hybrid genome and to assess the contribution of each parental species to the hybrid lineage. 25 genomic fragments could be identified that were fixed for material from only one parental species and thus might harbor genes that are relevant for the specific adaptations in the hybrid species

The genome of Apis mellifera: dialog between linkage mapping and sequence assembly

Two independent genome projects for the honey bee, a microsatellite linkage map and a genome sequence assembly, have interactively produced an almost complete organization of the euchromatic genome

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny

published_or_final_versio

A High density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. (Résumé d'auteur

GENE MAPPING: BASICS, TECHNIQUES AND SIGNIFICANCE

Watson says, "Like the system of interstate highways spanning our country, the map of the human genome will be completed stretch by stretch". It may be possible to use genetic information to diagnose the disease accurately and to predict a patient\u27s likely response to a particular medicine or treatment. For whole genome mapping development and application of mapping, sequencing and computational tools are very essential and also linkage, physical and sequence maps are required to put the information together. For most genome mapping projects involve markers consisting of a unique site in the genome and should be independent of any particular experimental resource. For mapping purpose the DNA and RNA identification is essential. These genes are identified by hybridizing DNA clones against Northern blot, cDNA libraries, Zoo blot, Western blot and Southern blot of genomic DNA digested with rare cutter restriction endonuclease. The various experimental studies of gene mapping have extended our understanding of the genetics. This has allowed the investigators to detect a particular gene, which is responsible for the disease. Recent studies have shown the various effective and scientific gene mapping techniques and gene identification methods, which are helpful to diagnose a particular disease. It is easy for the doctor to give right medicine to the right patient to cure the disease when he can identify the defective gene responsible for disease. This article reviews the details of identification techniques of genes, gene mapping with broad applications. KEY WORDS: Gene mapping; Restriction mapping; Fluorescent in situ hybridization (FISH); Sequenced tagged site (STS) mapping; Somatic cell hybridization

Gene Mapping: Basics, Techniques and Significance

Watson says, "Like the system of interstate highways spanning our country, the map of the human genome will be completed stretch by stretch". It may be possible to use genetic information to diagnose the disease accurately and to predict a patient's likely response to a particular medicine or treatment. For whole genome mapping development and application of mapping, sequencing and computational tools are very essential and also linkage, physical and sequence maps are required to put the information together. For most genome mapping projects involve markers consisting of a unique site in the genome and should be independent of any particular experimental resource. For mapping purpose the DNA and RNA identification is essential. These genes are identified by hybridizing DNA clones against Northern blot, cDNA libraries, Zoo blot, Western blot and Southern blot of genomic DNA digested with rare cutter restriction endonuclease. The various experimental studies of gene mapping have extended our understanding of the genetics. This has allowed the investigators to detect a particular gene, which is responsible for the disease. Recent studies have shown the various effective and scientific gene mapping techniques and gene identification methods, which are helpful to diagnose a particular disease. It is easy for the doctor to give right medicine to the right patient to cure the disease when he can identify the defective gene responsible for disease. This article reviews the details of identification techniques of genes, gene mapping with broad applications. KEY WORDS: Gene mapping; Restriction mapping; Fluorescent in situ hybridization (FISH); Sequenced tagged site (STS) mapping; Somatic cell hybridization

A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

<p>Abstract</p> <p>Background</p> <p>Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH).</p> <p>Results</p> <p>First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps <it>in silico </it>anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map.</p> <p>Conclusions</p> <p>The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.</p

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

BACKGROUND: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. RESULTS: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. CONCLUSION: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations