Development of an in silico coding gene SNP map in pigs

A total of 5450 sequences obtained from the NCBI pig SNP database were consolidated into 465 unique sequences (189 singleton sequences and 276 contigs). These 465 sequences contained 1787 putative SNPs and had strong sequence homology to 433 human protein-coding genes based on blast analyses. These genes were assigned to the pig QTL maps ( http://www.animalgenome.org/QTLdb/pig.html ) via the human and pig comparative maps established by a pig radiation hybrid (RH) map. The SNP information characterized from this study provides a useful functional gene variation resource to facilitate QTL data mining in the pig genome.     

A QTL resource and comparison tool for pigs: PigQTLDB

During the past decade, efforts to map quantitative trait loci (QTL) in pigs have resulted in hundreds of QTL being reported for growth, meat quality, reproduction, disease resistance, and other traits. It is a challenge to locate, interpret, and compare QTL results from different studies. We have developed a pig QTL database (PigQTLdb) that integrates available pig QTL data in the public domain, thus, facilitating the use of this QTL data in future studies. We also developed a pig trait classification system to standardize names of traits and to simplify organization and searching of the trait data. These steps made it possible to compare primary data from diverse sources and methods. We used existing pig map databases and other publicly available data resources (such as PubMed) to avoid redundant developmental work. The PigQTLdb was also designed to include data representing major genes and markers associated with a large effect on economically important traits. To date, over 790 QTL from 73 publications have been curated into the database. Those QTL cover more than 300 different traits. The data have been submitted to the Entrez Gene and the Map Viewer resources at NCBI, where the information about markers was matched to marker records in NCBI’s UniSTS database. Having these data in a public resource like NCBI allows regularly updated automatic matching of markers to public sequence data by e-PCR. The submitted data, and the results of these calculations, are retrievable from NCBI via Entrez Gene, Map Viewer, and UniSTS. Efforts were undertaken to improve the integrated functional genomics resources for pigs.     

Identification of quantitative trait loci for dry-matter,starch, and β-carotene content in sweetpotato

Development of orange-fleshed sweetpotatoes (OFSP) is desired for the improvement of the food supply and nutritional status of millions of people in developing countries, particularly in sub-Saharan Africa. However, sweetpotato [Ipomoea batatas (L.) Lam] breeding is challenging due to its genetic complexity, and marker-assisted breeding tools are needed to facilitate crop improvement. We identified quantitative trait loci (QTL) for dry-matter, starch, and β-carotene content in a hexaploid sweetpotato mapping population derived from a cross between Tanzania, a white-fleshed, high dry-matter African landrace, and Beauregard, an orange-fleshed, low dry-matter sweetpotato cultivar popular in the USA. Two parental maps were constructed using a population of 240 clones. Strong correlations were observed between starch and dry-matter content (r > 0.8, P < 0.0001) in the storage roots, while moderate correlations (r = –0.6, P < 0.0001) were observed for β-carotene and starch content. In both parental maps, QTL analysis revealed the presence of 13 QTL for storage root dry-matter content, 12 QTL for starch content, and 8 QTL for β-carotene content. Multiple QTL regression models developed for segregation of alleles in each parent explained 15–24% of the variation in dry-matter content, 17–30% of the starch content, and 17–35% of β-carotene content. To the best of our knowledge, this research presents the only QTL mapping study published to date for dry-matter, starch, and β-carotene content in sweetpotato. This work improves our understanding of the inheritance of these important traits in sweetpotato, and represents a first step toward the long-term goal of developing marker-assisted breeding tools to facilitate sweetpotato breeding efforts.     

Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits

New microsatellites markers [simple sequence repeat (SSR)] have been isolated from rose and integrated into an existing amplified fragment-length polymorphism genetic map. This new map was used to identify quantitative trait locus (QTL) controlling date of flowering and number of petals. From a rose bud expressed sequence tag (EST) database of 2,556 unigenes and a rose genomic library, 44 EST-SSRs and 20 genomic-SSR markers were developed, respectively. These new rose SSRs were used to expand genetic maps of the rose interspecific F₁ progeny. In addition, SSRs from other Rosaceae genera were also tested in the mapping progeny. Genetic maps for the two parents of the progeny were constructed using pseudo-testcross mapping strategy. The maps consist of seven linkage groups of 105 markers covering 432 cM for the maternal map and 136 markers covering 438 cM for the paternal map. Homologous relationships among linkage groups between the maternal and paternal maps were established using SSR markers. Loci controlling flowering traits were localised on genetic maps as a major gene and QTL for the number of petals and a QTL for the blooming date. New SSR markers developed in this study will provide tools for the establishment of a consensus linkage map for roses that combine traits and markers in various rose genetic maps.     

Gramene,a tool for grass genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.     

Identification of quantitative trait loci controlling winter hardiness in an annual × perennial ryegrass interspecific hybrid population

Winter hardiness is a quantitative trait and the lack of it limits geographic distribution of ryegrass. Improving winter hardiness is an important breeding goal in ryegrass breeding programs. An understanding of the genetic basis for the component traits of winter hardiness would allow more efficient selection. A three-generation interspecific population of an annual × perennial ryegrass consisting of 152 progenies was used to map quantitative trait loci (QTL) that control winter hardiness-related traits including fall growth (FG), freezing tolerance (FT), and winter survival (WS) over 2 years. A total of 39 QTL were identified for the three traits from both the female parental (MFA) and the male parental (MFB) maps, of which 13 were for FG, 6 for FT, and 20 for WS. The proportion of phenotypic variation explained by individual QTL ranged from 10.4 to 22.1%. Both FG and FT were positively correlated with WS. Common QTL were detected between FG, FT, and WS. The QTL associated with WS on linkage groups (LGs) 4 and 5, and the QTL for FT on LG 5 were consistently identified over years and maps. These consistent QTL might serve as potential tools for marker-assisted selection to improve ryegrass winter hardiness.     

The Organelle Genome Database Project (GOBASE).

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data.     

A grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) genetic map integrating the position of 139 expressed genes

Grapevine molecular maps based on microsatellites, AFLP and RAPD markers are now available. SSRs are essential to allow cross-talks between maps, thus upgrading any growing grapevine maps. In this work, single nucleotide polymorphisms (SNPs) were developed from coding sequences and from unique BAC-end sequences, and nested in a SSR framework map of grapevine. Genes participating to flavonoids metabolism and defence, and signal transduction pathways related genes were also considered. Primer pairs for 351 loci were developed from ESTs present on public databases and screened for polymorphism in the “Merzling” (a complex genotype Freiburg 993–60 derived from multiple crosses also involving wild Vitis species) × Vitis vinifera (cv. Teroldego) cross population. In total 138 SNPs, 108 SSR markers and a phenotypic trait (berry colour) were mapped in 19 major linkage groups of the consensus map. In specific cases, ESTs with putatively related functions mapped near QTLs previously identified for resistance and berry ripening. Genes related to anthocyanin metabolism mapped in different linkage groups. A myb gene, which has been correlated with anthocyanin biosynthesis, cosegregated with berry colour on linkage group 2. The possibility of associating candidate genes to known position of QTL is discussed for this plant. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Marzia Salmaso and Giulia Malacarne contributed equally to the present work.     

Rearranged gene order between pig and human in a quantitative trait loci region on SSC3

A quantitative trait locus (QTL) for ovulation rate on chromosome 3 that peaks at 36 cM has been identified in a Meishan-White composite resource population with an additive effect of 2.2 corpora lutea. As part of an effort to identify the responsible gene(s), typing of additional genes on the INRA-University of Minnesota porcine radiation hybrid (IMpRH) map of SSC3 and comparative analysis of gene order was conducted. We placed 52 known genes and expressed sequence tags, two BAC-end sequences and one microsatellite (SB42) on a framework map that fills gaps on previous RH maps. Data were analysed for two-point and multipoint linkage with the IMpRH mapping tool and were submitted to the IMpRH database (http://imprh.toulouse.inra.fr/). Gene order was confirmed for 42 loci residing in the QTL region (spanning c. 17 Mb of human sequence) by using the high-resolution IMpRH2 panel. Carthagène (http://www.inra.fr/internet/departments/MIA/T/CarthaGene) was used to estimate multipoint marker distance and order using all public markers on SSC3 in the IMpRH database and those typed in this study. For the high-resolution map, only data for markers typed in both panels were used. Comparative analysis of human and porcine maps identified conservation of gene order for SSC3q and multiple blocks of conserved segments for SSC3p, which included six distinct segments of HSA7 and two segments of HSA16. The results of this study allow significant refinement of the SSC3p region that contains an ovulation rate QTL.     

New molecular tools to improve the efficiency of breeding for increased drought resistance

The advent of molecular markers (particularly RFLP- and PCR-derived) for use as probes for genomic DNA has revolutionized the genetic analysis of crop plants and provided not only geneticists, but also physiologists, agronomists and breeders with valuable new tools to identify traits of importance in improving resistance to abiotic stresses. For the breeder, a genetic map saturated with molecular markers allows selection for certain characters to be carried out much more efficiently and effectively than was possible previously. Two areas of molecular marker technology that are proving particularly useful in identifying traits of value for stress resistance and introducing them into improved varieties are in situ hybridization with fluorescent-labelled molecular probes and quantitative trait locus (QTL) analysis with either radioactively- or cold-labelled probes. Fluorescence in situ hybridization (FISH) takes out much of the cytological tedium previously associated with monitoring the introgression of chromosomes and DNA fragments from one species to another. Labelled DNA can be prepared that is specific to a particular species and used to visualize in chromosome preparations the presence of chromosomes or chromosomal fragments from that species amongst the recipient's chromosomes. This is being used to help transfer genes for drought resistance and salt tolerance from alien species into Graminaceous crops. DNA probes showing polymorphism between the donor and recipient species can also be used to monitor the incorporation of alien genes from chromosome addition lines into the recipient species. High density molecular maps allow the location of all major genes regulating the expression of a particular trait to be determined. Statistical methods have been developed to allow QTL for the trait to be identified. Not only does this allow the complexity of genetic control of any trait to be determined, but by comparing the extent to which confidence intervals of QTL for different traits overlap it is possible to examine the likelihood that traits are pleiotropically linked. Thus, the traits most likely to be important in determining yield under droughted conditions can be identified. Examples are given of traits that could be incorporated into breeding programmes to improve drought resistance using techniques of marker-assisted selection.     

New microsatellite markers in chicken optimized for automated fluorescent genotyping

We have isolated and developed 180 new polymorphic chicken microsatellite markers. In addition, primers have been developed for 91 microsatellites derived from the GenBank sequence database (isolated by the laboratory of Terry Burke, Leicester University), of which 89 were polymorphic, and six existing polymorphic markers (HUJ) have been modified. The primer sequences were designed to allow optimal performance of the markers, in sets containing multiple microsatellites, on ABI sequencers. The average number of alleles for the 275 polymorphic markers described was 4·0. Of these markers, 93% were polymorphic in the Wageningen resource population whereas 57% of the markers were polymorphic in the East Lansing reference population and only 44% could be mapped in the Compton reference population. The microsatellite markers described in this paper, in combination with the microsatellite markers published previously, are particularly well suited for performing a total genome scan for the detection of quantitative trait loci (QTL).     

Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database

With the availability of two-dimensional (2-D) gel electrophoresis databases that have many characterized proteins, it may be possible to compare a researcher’s gel images with those in relevant databases. This may lead to the putative identification of unknown protein spots in a researcher’s gel with those characterized in a given database, saving the researcher time and money by suggesting monoclonal antibodies to try in confirming these identifications. We have developed two tools to help with this comparison: (1) Flicker, http://www.lecb.ncifcrf.gov/flicker/, a Java applet program running in the researcher’s Web browser, to visually compare their gels against gels on the Internet; and (2) the 2DWG meta-database, http://www.lecb.ncifcrf.gov/2dwgDB/, a searchable database of locations of 2-D electrophoretic gel images found on the Internet. Recent additions to Flicker allow users to click on a protein spot in a gel that is linked to a federated 2D gel database, such as SWISS-2DPAGE, and have it retrieve a report from that Web database for that protein.     

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs

During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community. Furthermore, the working group recommended that all data models and software source code should be made visible in public repositories to allow a coordinated effort on the use of common data structures and file formats.     

MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments

Background  

Integration of multiple results from Quantitative Trait Loci (QTL) studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database developers to facilitate the storage, compilation and visualization of multiple QTL mapping experiment results. However, studying the congruency between these results still remains a complex task. Presently, the few computational and statistical frameworks to do so are mainly based on empirical methods (e.g. consensus genetic maps are generally built by iterative projection).     

TGB: the tobacco genetics and breeding database

The germplasm of the genus Nicotiana contains more than 5,000 accessions and plays an important role in modern biological research. Tobacco can be used as a model system to develop methodologies for plant transformation and for investigating gene function. In order to develop the study of Nicotiana, a large quantity of data on germplasm, sequences, molecular markers and genetically modified tobacco was required for in-depth and systematic collation and research. It became necessary to establish a special database for tobacco genetics and breeding. The tobacco genetics and breeding (TGB, http://yancao.sdau.edu.cn/tgb) database was developed with the aim of bringing together tobacco genetics and breeding. The database has three main features: (1) a materials database with information on 1,472 Nicotiana germplasm accessions, as well as updated genomic and expressed sequence tag (EST) data available from the public database; (2) a molecular markers database containing a total of 12,388 potential intron polymorphisms 10,551 EST-simple sequence repeat (EST-SSR) and 66,297 genomic-SSR markers; and (3) an applications database with genetic maps and some genetically modified studies in tobacco. The TGB database also makes Basic Local Alignment Search Tool and primer designing tools publicly available. As far as can be ascertained, the TGB database is the first tobacco genetics and breeding database to be created, and all this comprehensive information will aid basic research into Nicotiana and other related plants. It will serve as an excellent resource for the online tobacco research community.     

Editor's choice: High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method—2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.     

Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling

Background

Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm.

Results

A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2.

Conclusions

The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.     

Selection of a core set of RILs from Forrest × Williams 82 to develop a framework map in soybean

Soybean BAC-based physical maps provide a useful platform for gene and QTL map-based cloning, EST mapping, marker development, genome sequencing, and comparative genomic research. Soybean physical maps for “Forrest” and “Williams 82” representing the southern and northern US soybean germplasm base, respectively, have been constructed with different fingerprinting methods. These physical maps are complementary for coverage of gaps on the 20 soybean linkage groups. More than 5,000 genetic markers have been anchored onto the Williams 82 physical map, but only a limited number of markers have been anchored to the Forrest physical map. A mapping population of Forrest × Williams 82 made up of 1,025 F₈ recombinant inbred lines (RILs) was used to construct a reference genetic map. A framework map with almost 1,000 genetic markers was constructed using a core set of these RILs. The core set of the population was evaluated with the theoretical population using equality, symmetry and representativeness tests. A high-resolution genetic map will allow integration and utilization of the physical maps to target QTL regions of interest, and to place a larger number of markers into a map in a more efficient way using a core set of RILs.