MaizeDB - a functional genomics perspective

MaizeDB (http://www.agron.missouri.edu/) has existed since the early 90's as a genomespecific database that is grounded in genetic maps, their documentation and annotation. The database management system is robust and has continuously been Sybase. In this brief review we provide an introduction to the database as a functional genomics tool and new accesses to the data: 1) probe tables by bin location 2) BLAST access to map data 3) cMap, a comparative map graphical tool.     

Development of an integrated laboratory information management system for the maize mapping project

MOTIVATION: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons. RESULTS: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available. AVAILABILITY: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.     

EST derived SSR markers for comparative mapping in wheat and rice

Structural and functional relationships between the genomes of hexaploid wheat (Triticum aestivum L.) (2n=6x=42) and rice (Oryza sativa L.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (SSR) loci obtained from publicly available expressed sequence tags (ESTs). EST-SSR markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer design. Amplification was more consistent using the species-specific primer design for each gene. Forty-four percent of the primers designed specifically for wheat sequences were successful in amplifying DNA from both species. Existing genetic linkage maps were enhanced for the wheat and rice genomes using orthologous loci amplified with 58 EST-SSR markers obtained from both wheat and rice ESTs. The PCR-based anchor loci identified by these EST-SSR markers support previous patterns of conservation between wheat and rice genomes; however, there was a high frequency of interrupted colinearity. In addition, multiple loci amplified by these primers made the comparative analysis more difficult. Enhanced comparative maps of wheat and rice provide a useful tool for interpreting and transferring molecular, genetic, and breeding information between these two important species. These EST-SSR markers are particularly useful for constructing comparative framework maps for different species, because they amplify closely related genes to provide anchor points across species.Communicated by R. Hagemann     

R/qtl: QTL mapping in experimental crosses

SUMMARY: R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates. AVAILABILITY: The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.     

InterStoreDB:A Generic Integration Resource for Genetic and Genomic Data

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http://www.interstoredb.org     

A direct comparison between the genetic maps of sorghum and rice

A direct comparison of the genetic linkage maps of sorghum and rice is proposed. It is based on the mapping of a common set of 123 RFLP probes scattered on the genomes of both species. For each species a composite map was established by merging two individual maps comprising many common loci. This enabled us to confirm the global correspondence scheme that had previously been established between the chromosomes of sorghum and rice. It also provided a more detailed insight into the conservation of synteny and colinearity: 69% of the loci mapped on a given rice chromosome mapped to the corresponding homoeologous chromosome in sorghum; among them, 84% formed a colinear arrangement between the two species. Local inversions and translocations were detected. Received: 27 April 2000 / Accepted: 26 May 2000     

The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.)

Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of recombination and gene distribution in the 2L1.0 region of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Both wheat and barley belong to tribe Triticeae and are closely related. High-density detailed comparison of physical and genetic linkage maps revealed that wheat genes are present in physically small gene-rich regions (GRRs). One of the largest GRRs is located around fraction length 1.0 of the long arm of wheat homoeologous group 2 chromosomes termed the "2L1.0 region." The main objective of this study was to analyze the structural and functional organization of the 2L1.0 region in barley in comparison to wheat. Using the 29 physically mapped RFLP markers for the region, wheat and barley consensus genetic linkage maps of the 2L1.0 region were generated by combining information from 18 wheat and 7 barley genetic linkage maps. Comparative analysis using these consensus maps and other available wheat and barley mapping resources identified 227 DNA markers and ESTs for the region. The region accounted for 58% of the genes and 68% of the arm's recombination in wheat. However, the corresponding region in barley accounted for about 42% of the genes and 81% of the recombination. The kb/cM ratio for the region was 122 in barley compared to 244 in wheat. Distribution of genes and recombination varied between the two species even though the gene order and density were similar.     

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control

rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps. AVAILABILITY: rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm     

RAPD-based genetic linkage maps of yellow passion fruit (Passiflora edulis Sims. f. flavicarpa Deg.).

A single cross between two clones of passion fruit (Passiflora edulis Sims. f. flavicarpa Deg., 2n = 18) was selected for genetic mapping. The mapping population was composed of 90 F1 plants derived from a cross between 'IAPAR 123' (female parent) and 'IAPAR 06' (male parent). A total of 380 RAPD primers were analyzed according to two-way pseudo-testcross mapping design. The linkage analysis was performed using Mapmaker version 3.0 with LOD 4.0 and a maximum recombination fraction (theta) of 0.30. Map distances were estimated using the Kosambi mapping function. Linkage maps were constructed with 269 loci (2.38 markers/primer), of which 255 segregated 1:1, corresponding to a heterozygous state in one parent and null in the other. The linkage map for 'IAPAR123' consisted of 135 markers. A total of nine linkage groups were assembled covering 727.7 cM, with an average distance of 11.20 cM between framework loci. The sizes of the linkage groups ranged from 56 to 144.6 cM. The linkage map for 'IAPAR 06' consisted of 96 markers, covering 783.5 cM. The average distance between framework loci was 12.2 cM. The length of the nine linkage groups ranged from 20.6 to 144.2 cM. On average, both maps provided 61% genome coverage. Twenty-four loci (8.9%) remained unlinked. Among their many applications, these maps are a starting point for the identification of quantitative trait loci for resistance to the main bacterial disease affecting passion fruit orchards in Brazil, caused by Xanthomonas campestris pv. passiflorae, because parental genotypes exhibit diverse responses to bacterial inoculation.     

Characterization of 215 simple sequence repeat markers in creeping bentgrass (Agrostis stolonifera L.)

Creeping bentgrass (Agrostis stolonifera L.) is a versatile, cross-pollinated, temperate and perennial turfgrass species. It occurs naturally in a wide variety of habitats and is also cultivated on golf courses, bowling greens and tennis courts worldwide. Isozymes and amplified fragment length polymorphisms (AFLPs) have been used to determine genetic diversity, and restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA (RAPDs) were used to construct a genetic linkage map of this species. In the current report, we developed and characterized 215 unique genomic simple sequence repeat (SSR) markers in creeping bentgrass. The SSRs reported here are the first available markers in creeping bentgrass to date. Eight hundred and eighteen alleles were amplified by 215 SSR loci, an average of 3.72 alleles per locus. Fifty-nine per cent of those alleles segregated in a 1:1 Mendelian fashion (P > 0.05). Twenty-two per cent had a distorted segregation ratio (P ≤ 0.05). These SSR markers will be useful for assessing genetic diversity in creeping bentgrass and will be important for the development of genetic linkage maps and identifying quantitative trait loci. These markers could enhance breeding programmes by improving the efficiency of selection techniques.     

Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE

MOTIVATION: Sex-specific marker maps have become increasingly available. We have implemented the usage of sex-specific recombination frequencies in the GENEHUNTER-MODSCORE program that performs multipoint linkage analysis. Furthermore, we have devised a consistent method to choose the combinations of male and female genetic positions at which linkage scores should be calculated. Marker coordinates can be read automatically from publicly available genetic maps. RESULTS: In a MOD-score analysis of the COGA dataset provided for Genetic Analysis Workshop 14, the highest linkage peak on chromosome 1 further increases when using sex-specific maps, while some smaller peaks are decreased. Simulations confirm that the MOD score can be biased when a sex-averaged instead of the correct sex-specific map is employed. This shows that an adequate modeling of the female:male ratio of genetic distances is important, especially for complex traits. AVAILABILITY: The new version of GENEHUNTER-MODSCORE can be downloaded from the following website: http://www.staff.uni-marburg.de/~strauchk/software.html     

Cytologically based physical maps of the group-2 chromosomes of wheat

We have constructed cytologically based physical maps (CBPMs), depicting the chromosomal distribution of RFLP markers, of the group-2 chromosomes of common wheat (Triticum aestivum L. em Thell). Twenty-one homozygous deletion lines for 2A, 2B, and 2D were used to allocate RFLP loci to 19 deletion-interval regions. A consensus CBPM was colinearily aligned with a consensus genetic map of group-2 chromosomes. The comparison revealed greater frequency of recombination in the distal regions. Several molecularly tagged chromosome regions were identified which may be within the resolving power of pulsed-field gel electrophoresis. The CBPMs show that the available probes completely mark the group-2 chromosomes, and landmark loci for sub-arm regions were identified for targeted-mapping.     

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.     

Comparative mapping in loblolly and radiata pine using RFLP and microsatellite markers

Genetic linkage maps were constructed for loblolly pine (Pinus taeda L.) and radiata pine (P. radiata D. Don) using a common set of RFLP and microsatellite markers. The map for loblolly pine combined data from two full-sib families and consisted of 20 linkage groups covering 1281 cM. The map for radiata pine had 14 linkage groups and covered 1223 cM. All of the RFLP probes readily hybridise between loblolly and radiata pine often producing similar hybridisation patterns. There were in total 60 homologous RFLP loci mapped in both species which could be used for comparative purposes. A set of 20 microsatellite markers derived from radiata pine were also assayed; however, only 9 amplified and revealed polymorphic loci in both species. Single-locus RFLP and microsatellite markers were used to match up linkage groups and compare order between species. Twelve syntenic groups were obtained each consisting of from 3 to 9 homologous loci. The order of homologous loci was colinear in most cases, suggesting no major chromosomal rearrangements in the evolution of these species. Comparative mapping between loblolly and radiata pine should facilitate genetic research in both species and provide a framework for mapping in other pine species. Received: 25 November 1998 / /Accepted: 19 December 1998     

An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations

Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750?kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59-140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6?cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059?cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24?%. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.     

Combined genome scans for body stature in 6,602 European twins: evidence for common Caucasian loci

Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were combined and related to the sequence positions using software developed by us, which is publicly available (https://apps.bioinfo.helsinki.fi/software/cartographer.aspx). Variance component linkage analysis was performed with age, sex, and country of origin as covariates. The covariate adjusted heritability was 81% for stature in the pooled dataset. We found evidence for a major QTL for human stature on 8q21.3 (multipoint logarithm of the odds 3.28), and suggestive evidence for loci on Chromosomes X, 7, and 20. Some evidence of sex heterogeneity was found, however, no obvious female-specific QTLs emerged. Several cohorts contributed to the identified loci, suggesting an evolutionarily old genetic variant having effects on stature in European-based populations. To facilitate the genetic studies of stature we have also set up a website that lists all stature genome scans published and their most significant loci (http://www.genomeutwin.org/stature_gene_map.htm).     

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     

Correlation between genetic and cytogenetic maps of the rat

To correlate rat genetic linkage maps with cytogenetic maps, we localized 25 new cosmid-derived simple sequence length polymorphism (SSLP) markers and 14 existing genetic markers on cytogenetic bands of chromosomes, using fluorescence in situ hybridization (FISH). Next, a total of 58 anchor loci, consisting of the 39 new and 19 previously reported ones, were integrated into the genetic linkage maps. Since most of the new anchor loci were developed to be localized near the terminals of the genetic or cytogenetic maps for each chromosome, the orientation and coverage of the whole genetic linkage maps were determined or confirmed with respect to the cytogenetic maps. Thus, we provide here a new base for rat genetic maps. Received: 9 September 1997 / Accepted: 11 November 1997     

Heterogeneity in Rates of Recombination across the Mouse Genome

If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.