Comparison and integration of four barley genetic maps

Barley (Hordeum vulgare L.) is one of the most extensively studied food crops in recent molecular research. More than 1000 molecular markers have been located on the barley genome by using five independent populations. For the present study, four segregation data sets, 'Proctor' x 'Nudinka', 'Igri' x 'Franka', 'Steptoe' x 'Morex', and 'Harrington' x TR306, were downloaded from the publicly available GrainGenes databank. Since 22% of the markers are common to at least two of the independent data sets, we were able to establish an integrated map using the computer package JOINMAP v2.0. The integrated map contains 898 markers, covers 1060 cM, and removes many large gaps present in the individual maps. Comparison of the integrated map with the individual maps revealed that the overall linear order of markers is in good agreement and that the integrated map is consistent with the component maps. No significant reordering of markers was found. This conservative property of the barley genome makes the integrated map reliable and successful. Except for chromosome 7 (5H), marker clustering was observed in the centromeric regions, probably owing to the centromeric suppression of recombination. Based on this integrated map, geneticists and breeders can choose their favourite markers in any region of interest of the barley genome. Key words : Hordeum vulgare, RFLP, integrated map.     

Alignment of molecular and classical linkage maps of rice,Oryza sativa

Application of genetic linkage maps in plant genetics and breeding can be greatly facilitated by integrating the available classical and molecular genetic linkage maps. In rice, Oryza sativa L., the classical linkage map includes about 300 genes which correspond to various important morphological, physiological, biochemical and agronomic characteristics. The molecular maps consist of more than 500 DNA markers which cover most of the genome within relatively short intervals. Little effort has been made to integrate these two genetic maps. In this paper we report preliminary results of an ongoing research project aimed at the complete integration and alignment of the two linkage maps of rice. Six different F₂ populations segregating for various phenotypic and RFLP markers were used and a total of 12 morphological and physiological markers (Table 1) were mapped onto our recently constructed molecular map. Six linkage groups (i.e., chr. 1, 3, 7, 9, 11 and 12) on our RFLP map were aligned with the corresponding linkage groups on the classical map, and the previous alignment for chromosome 6 was further confirmed by RFLP mapping of an additional physiological marker on this chromosome. Results from this study, combined with our previous results, indicate that, for most chromosomes in rice, the RFLP map encompasses the classical map. The usefulness of an integrated genetic linkage map for rice genetics and breeding is discussed.Abbreviations RFLP restriction fragment length polymorphism - chr chromosome - cM centiMorgan     

An integrated genetic linkage map of pepper (Capsicum spp.)

An integrated genetic map of pepper including 6 distinct progenies and consisting of 2262 markers covering 1832 cM was constructed using pooled data from six individual maps by the Keygene proprietary software package INTMAP. The map included: 1528 AFLP, 440 RFLP, 288 RAPD and several known gene sequences, isozymes and morphological markers. In total, 320 anchor markers (common markers in at least two individual maps) were used for map integration. Most anchor markers (265) were common to two maps, while 27, 26 and 5 markers were common to three, four and five maps, respectively. Map integration improved the average marker density in the genome to 1 marker per 0.8 cM compared to 1 marker per 2.1 cM in the most dense individual map. In addition, the number of gaps of at least 10 cM between adjacent markers was reduced in the integrated map. Although marker density and genome coverage were improved in the integrated map, several small linkage groups remained, indicating that further marker saturation will be needed in order to obtain a full coverage of the pepper genome. The integrated map can be used as a reference for future mapping studies in Capsicum and to improve the utilization of molecular markers for pepper breeding.These authors contributed equally to the work described in this paper(e-mail:     

Single nucleotide polymorphisms for integrative mapping in the Turkey (Meleagris gallopavo)

When multiple genetic maps exist for a species, integration of these maps requires a set of common markers be genotyped across the individual mapping populations. In the turkey, three genetic maps based on separate mapping populations are available. In this study, SNP-based markers were developed for integrating the cDNA/RFLP-based map (1) with microsatellite markers of the second-generation turkey genome map (2). Forty-eight primer sets were designed and tested and 33 (69%) correctly amplified turkey genomic DNA by PCR. Putative SNPs were detected in 20 (61%) of the amplified gene fragments, and 10 SNP markers were subsequently genotyped by PCR/RFLP for segregation analysis. Eight SNP markers were incorporated into the turkey genetic map.     

An integrated restriction fragment length polymorphism--amplified fragment length polymorphism linkage map for cultivated sunflower.

Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 x HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 x HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 x HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.     

Construction of an integrated pepper map using RFLP,SSR, CAPS,AFLP, WRKY,rRAMP, and BAC end sequences

Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum ‘TF68’ and C. chinense ‘Habanero’) and two intraspecific (C. annuum ‘CM334’ and C. annuum ‘Chilsungcho’) populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum ‘CM334’. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.     

Restriction Fragment Length Polymorphism Linkage Map of Arabidopsis thaliana

We have constructed a restriction fragment length polymorphism (RFLP) linkage map of the nuclear genome of the small flowering plant Arabidopsis thaliana. The map is based on the meiotic segregation of both RFLP and morphological genetic markers from five independent crosses. The morphological markers on each of the five chromosomes were included in the crosses to allow alignment of the RFLP map with the established genetic map. The map contains 94 new randomly distributed molecular markers (nine identified cloned Arabidopsis genes and 85 genomic cosmid clones) that detect polymorphisms between the Landsberg erecta and Columbia races. In addition, 17 markers from an independently constructed RFLP map of the Arabidopsis genome [Chang, C., Bowman, J.L., DeJohn, A.W., Lander, E.S., and Meyerowitz, E.M. (1988). Proc. Natl. Acad. Sci. USA 85, 6856-6860] have been included to permit integration of the two RFLP maps.     

Integration of the classical and RFLP linkage maps of the short arm of tomato chromosome 1

The classical map of the short arm of chromosome 1 of tomato (Lycopersicon esculentum) has been shown to contain inaccuracies while the RFLP map of this region is known to be generally accurate. Molecular analysis of populations derived from crosses between L. esculentum lines carrying chromosome 1 classical markers and L. pennellii has enabled us to produce an integrated classical and RFLP marker map of this region. New data concerning the linkage relationships between classical markers have also been combined with previous data to produce a new classical map of the short arm of chromosome 1. The orders of the classical markers on these two new maps are in almost complete agreement and are very different to that shown on the previous classical map.     

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background  

Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers.     

An integrated SSR map of grapevine based on five mapping populations

A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Re-orientation and integration of the classical and interspecific linkage maps of the long arm of tomato chromosome 7

To obtain reliable classical and integrated interspecies maps of the long arm of chromosome 7 of tomato, detailed mapping work was undertaken and several phenotypic and molecular markers were assigned loci on both maps to provide reliable cross-reference points. To maximise the value of the new maps, pair-wise segregation data for classical genetic markers from the literature were included, based on large segregating populations with readily scorable phenotypes. In addition, to increase confidence in these maps, introgression lines were used to confirm important map locations. The revised classical map is based on two- and three-point test-cross data from a number of F₂ and BC₁ mapping populations. The integrated interspecies map is based on F₂ mapping populations derived from crosses of Lycopersicon esculentum with Lycopersicon pennellii (LA716). The genetic analyses for both maps were performed using the computer package JoinMap. The revised composite classical map indicates that some of the map positions reported in the literature are incorrect. The linear order of the classical markers common to both the revised classical and integrated interspecies maps are in complete agreement. Production of the integrated interspecies map resulted in re-orientation of the existing molecular map. Received: 13 September 2000 / Accepted: 20 December 2000     

Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers

A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Seven linkage groups, putatively corresponding to the seven haploid rose chromosomes, were identified for each parent, spanning 487 cM and 490 cM, respectively. The average length of 70 cM may cover more than 90% of the rose genome. An integrated map was constructed by incorporating the homologous parental linkage groups, resulting in seven linkage groups with a total length of 545 cM. The present linkage map is currently the most advanced map in rose with regard to marker density, genome coverage and with robust markers, giving good perspectives for QTL mapping and marker-assisted breeding in rose. The SSR markers, together with RFLP markers, provide good anchor points for future map alignment studies in rose and related species. Codominantly scored AFLP markers were helpful in the integration of the parental maps.     

A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees.

A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males (1983.7 cM [Kosambi mapping function (K)]) and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes n = 12 of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers approximately 1300 cM(K).     

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

Background

The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.

Results

We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa.

Conclusions

Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.     

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.     

Tomato chromosome 6: a high resolution map of the long arm and construction of a composite integrated marker-order map

Integration of molecular and classical genetic maps is an essential requirement for marker-assisted breeding, quantitative trait locus mapping and map-based cloning. With respects to tomato, such maps are only available for the top part of chromosome 1, for chromosome 3 and for the short arm and the centromere proximal part of the long arm of chromosome 6. Employing an L. esculentum line carrying an L. hirsutum introgression we constructed an integrated linkage map for the telomere proximal part of the long arm of tomato chromosome 6, thereby completing the integrated map published previously. With an average map distance of only 0.6 cM the map provides detailed information on the relative position of molecular markers and several traits of economical importance, such as the fruit color marker B. Furthermore, two additional crosses using lines containing L. pennellii introgressions were performed to address the question as to how the recombination frequency in a marked interval on the long arm of chromosome 6 is affected by introgressed segments from different origins. It is concluded that recombination is not merely affected by the local level of homology but also by surrounding sequences. Combination of all the linkage data generated in various crosses described in this and other studies enabled the construction of the first integrated map of an entire tomato chromosome. This map carries 42 loci and shows the position of 15 classical genes relative to 59 molecular markers.     

HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers

We present two Web interfaces that generate genetic maps for given sets of human or mouse microsatellite markers. The genetic maps are generated from available databases using linear interpolation of physical map distances to infer genetic map positions for missing markers in these databases.     

Index, Comprehensive Microsatellite, and Unified Linkage Maps of Human Chromosome 14 with Cytogenetic Tie Points and a Telomere Microsatellite Marker

Three sets of linkage maps (index, comprehensive microsatellite, and unified) have been constructed for human chromosome 14 based on genotypes from the CEPH reference pedigrees. The index maps consist of 18 microsatellite markers, with heterozygosities of at least 68% and intermarker spacing no greater than 11 cM. The sex-average comprehensive microsatellite map is 125 cM in length and includes 115 markers with 54 loci uniquely placed with odds for marker order of at least 1000:1. The sex-average index map length is 121 cM, and the female- and male-specific maps are 143 and 101 cM, respectively. A unified map was also constructed from 147 loci (162 marker systems), which includes 32 RFLP markers in addition to the 115 microsatellites. The sex-average length of the unified map is 128 cM with 69 loci uniquely placed. Our maps are anchored by a microsatellite telomere marker sCAW1 (D14S826), developed from a telomere YAC clone TYAC196, which extends the linkage map to the physical terminus of the long arm of chromosome 14. Furthermore, we have also physically mapped seven of the loci by fluorescencein situhybridization of cosmid clones orAlu-PCR products amplified from YACs containing the marker sequences. Together with previously established cytogenetic map designations for other loci, our maps display links between genetic markers for 10 of 13 cytogenetic bands of chromosome 14 at the 550 genome band resolution.