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PubMed1998

An integrated genetic linkage map of the laboratory rat.

The laboratory rat, Rattus novegicus, is a major model system for physiological and pathophysiological studies, and since 1966 more than 422,000 publications describe biological studies on the rat (NCBI/Medline). The rat is becoming an increasingly important genetic model for the study of specific diseases, as well as retaining its role as a major preclinical model system for pharmaceutical development. The initial genetic linkage map of the rat contained 432 genetic markers (Jacob et al. 1995) out of 1171 developed due to the relatively low polymorphism rate of the mapping cross used (SHR x BN) when compared to the interspecific crosses in the mouse. While the rat genome project continues to localize additional markers on the linkage map, and as of 11/97 more than 3,200 loci have been mapped. Current map construction is using two different crosses (SHRSP x BN and FHH x ACI) rather than the initial mapping cross. Consequently there is a need to provide integration among the different maps. We set out to develop an integrated map, as well as increase the number of markers on the rat genetic map. The crosses available for this analysis included the original mapping cross SHR x BN reciprocal F2 intercross (448 markers), a GH x BN intercross (205 markers), a SS/Mcw x BN intercross (235 markers), and a FHH/Eur x ACI/Hsd intercross (276 markers), which is also one of the new mapping crosses. Forty-six animals from each cross were genotyped with markers polymorphic for that cross. The maps appear to cover the vast majority of the rat genome. The availability of these additional markers should facilitate more complete whole genome scans in a greater number of strains and provide additional markers in specific genomic regions of interest.

Animals↗
PubMed2002

Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana.

Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.

Arabidopsis↗
PubMed2004

A microsatellite genetic linkage map for Xiphophorus.

Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between "male" and "female" maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.

Animals↗
PubMed2006

A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal.

Animals↗
PubMed2002

Development of a mungbean ( Vigna radiata) RFLP linkage map and its comparison with lablab ( Lablab purpureus) reveals a high level of colinearity between the two genomes.

A genetic linkage map of mungbean ( Vigna radiata, 2n = 2 x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an inter-subspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' ( V. radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab ( Lablab purpureus, 2n = 2 x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

Journal Article↗
PubMed2003

Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes.

A new linkage map of Cucumis melo, derived from the F2 progeny of a cross between PI 414723 and C. melo 'TopMark' is presented. The map spans a total of 1421 cM and includes 179 points consisting of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSRs), simple sequence repeats (SSRs), and restriction fragment length polymorphism (RFLP) markers. The map also includes an aphid resistance trait (Vat) and the sex type gene, andromonoecious (a), the two of which are important in resistance breeding and the control of hybrid seed production, as well as a seed-color gene, Wt-2. Most RFLPs represent sequence-characterized cDNA probes from C. melo and Cucumis sativus. These include resistance gene homologues and genes involved in various aspects of plant development and metabolism. A sub-set of our SSR and RFLP markers were also mapped, as part of this study, on additional mapping populations that were published for this species. This provides important reference points ("anchors"), enabling us to identify several linkage groups with respect to other melon maps.

Chromosome Mapping↗
PubMed1991

Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8.

Linkage mapping in a large, seven-generation family with type 2 autosomal dominant retinitis pigmentosa (ADRP) demonstrates linkage between the disease locus (RP1) and DNA markers on the short arm of human chromosome 8. Five markers were most informative for mapping ADRP in this family using two-point linkage analysis. The markers, their maximum lod scores, and recombination distances were ANK1 (ankyrin)--2.0 at 16%; D8S5 (TL11)--5.3 at 17%; D8S87 [a(CA)n repeat]--7.2 at 14%; LPL (lipoprotein lipase)--1.5 at 26%; and PLAT (plasminigen activator, tissue)--10.6 at 7%. Multipoint linkage analysis, using a simplified pedigree structure for the family (which contains 192 individuals and two inbreeding loops), gave a maximum lod score of 12.2 for RP1 at a distance 8.1 cM proximal to PLAT in the pericentric region of the chromosome. Based on linkage data from the CEPH (Paris) reference families and physical mapping information from a somatic cell hybrid panel of chromosome 8 fragments, the most likely order for four of these five loci and the diseases locus is 8pter-LPL-D8S5-D8S87-PLAT-RP1. (The precise location of ANK1 relative to PLAT in this map is not established). The most likely location for RP1 is in the pericentric region of the chromosome. Recently, several families with ADRP with tight linkage to the rhodopsin locus at 3q21-q24 were reported and a number of specific rhodopsin mutations in families with ADRP have since been reported. In other ADRP families, including the one in this study, linkage to rhodopsin has been excluded. Thus mutations at two different loci, at least, have been shown to cause ADRP. There is no remarkable clinical disparity in the expression of disease caused by these different loci.

Base Sequence↗
PubMed1990

An interspecific backcross linkage map of the proximal half of mouse chromosome 14.

We have generated a 30-cM molecular genetic linkage map of the proximal half of mouse chromosome 14 by interspecific backcross analysis. Loci that were mapped in this study include Bmp-1, Ctla-1, Hap, hr, Plau, Psp-2, Rib-1, and Tcra. A region of homology between mouse chromosome 14 and human chromosome 10 was identified by the localization of Plau to chromosome 14. This interspecific backcross map will be valuable for establishing linkage relationships of additional loci to mouse chromosome 14.

Animals↗
PubMed2006

A microsatellite linkage map of Barramundi, Lates calcarifer.

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its compact genome (approximately 700 Mb) is among the smallest genomes of food fish species. We established a first-generation genetic linkage map of Barramundi with a mapping panel containing three parents (two males and one female) and 93 progeny. A total of 240 microsatellite markers were mapped into 24 linkage groups. Among these markers, 10 were located in ESTs and known genes. The total lengths of the female and male maps were 873.8 and 414.5 cM with an average marker spacing of 6.20 and 4.70 cM, respectively. Comparing the flanking sequences of the 240 Barramundi microsatellites with the assembled whole-genome sequences of Tetraodon nigrovidiris revealed 55 homologous sequences located in 19 of the 21 chromosomes of T. nigrovidiris. The map will not only enable the mapping of quantitative trait loci, but also provide new resources for understanding the evolution of fish genomes.

Animals↗
PubMed1992

The CEPH consortium linkage map of human chromosome 2.

This paper describes the Centre d'Etude du Polymorphisme Humain (CEPH) consortium linkage map of chromosome 2. The map contains 36 loci defined by genotyping generated from the CEPH family DNAs. A total of 73 different markers were typed by 14 contributing laboratories; of these, 36 loci are ordered on the map with likelihood support of at least 1000:1. Markers are placed along the length of the chromosome but no markers were available to anchor the map at either telomere or the centromere. Multilocus linkage analysis has produced male, female, and sex-averaged maps extending for 261, 430, and 328 cM, respectively. The sex-averaged map contains five intervals greater than 15 cM and the mean genetic distance between the 36 uniquely placed loci is 9.1 cM.

Chromosome Mapping↗
PubMedDate not supplied

The mouse linkage map. A computer program.

Computer programs have been developed to serve as a method for storing, retrieving, and sorting mouse linkage data. The programs accept and store raw data and reference information for gene linkage; calculate recombination values for each data set and for combined data sets; retrieve, sort, and print-out raw data, references, and recombination values; and generate linkage maps.

Animals↗
PubMed2001

[A new method for constructing linkage maps of molecular markers: three-point selfcross method].

The method for constructing linkage maps has almost been so far the three-point testcross in higher organisms. This method is, however, considerably limited to a requirement of a parent or line with three recessive genes that can be obtained by only cross breeding. In this paper, the three-point selfcross method for mapping was proposed. This method can also provide us with informations of mapping as the same as the three-point testcross method. However, the three-point selfcross method does not have any limitation of requiring a parent with three recessive genes. It was theoretically proved that this method could be used to map molecular marker loci in small sample of F2 population. Exactly to test both the methods for mapping, Fisher information content was applied to prove that the three-point selfcross method is powerful for mapping. Further to test this method, data of the first 6 loci were chosen from 12 RFLP loci detected in 333 F2 individuals in SAMPLE. RAW file in MAPMAKER/EXP version 3.0 that Lander et al. (1987) provided. The result showed that, like MAPMAKER program, the three-point selfcross method is powerful to detect linkage relationship among loci, to order them on linkage groups and to calculate distances between nearest neighbor loci. Besides, this method could provide us with the other information of map such as the positive or negative interference and couple or repulsion configuration.

Chromosome Mapping↗
PubMed1989

Twenty-five loci form a continuous linkage map of markers for human chromosome 7.

We have constructed a primary genetic linkage map from DNA markers that define 25 loci on chromosome 7. The markers form a continuous linkage group of 141 cM in males and 340 cM in females; female genetic distances were on average more than twofold higher than those in males throughout the chromosome. The average heterozygosity of the loci was 45%. A subset of the markers can be used for efficient application of this map to studies of human genetic disease.

Alleles↗
PubMed2003

Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin.

Amplified fragment length polymorphisms (AFLPs), along with some microsatellite and Type I markers, were used for linkage analysis in Crassostrea virginica Gmelin, the eastern oyster. Seventeen AFLP primer combinations were selected for linkage analysis with two parents and their 81 progeny. The 17 primer combinations produced 396 polymorphic markers, and 282 of them were segregating in the two parents. Chi-square analysis indicated that 259 (91.8%) markers segregated in Mendelian ratio, while the other 23 (8.2%) showed significant (P < 0.05) segregation distortion, primarily for homozygote deficiency and probably due to deleterious recessive genes. Moderately dense linkage maps were constructed using 158 and 133 segregating markers (including a few microsatellite and Type I markers) from male and female parents, respectively. The male framework map consisted of 114 markers in 12 linkage groups, covering 647 cM. The female map had 84 markers in 12 linkage groups with a length of 904 cM. The estimated genome length was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and female map when all linked markers were considered. Genetic maps observed in this study are longer than the cytogenetic map, possibly because of low marker density.

Animals↗
PubMed2002

Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears.

Genetic linkage maps of the European pear ( Pyrus communis L.) cultivar 'Bartlett' and the Japanese pear ( Pyrus pyrifolia Nakai) cultivar 'Housui' were constructed based on AFLPs, SSRs from pear, apple and Prunus, isozymes and phenotypic traits by using their F(1) progenies. The map of the female parent Bartlett consisted of 226 loci including 175 AFLPs, 49 SSRs, one isozyme and one S locus on 18 linkage groups over a total length of 949 cM, while that for 'Housui' contained 154 loci including 106 AFLPs, 42 SSRs, two phenotypic traits and the other four markers on 17 linkage groups encompassing a genetic distance of 926 cM. These maps were partially aligned using 20 codominant markers which showed segregating alleles in both parents. Compared with the reports of apple genetic maps, these pear maps were not saturated but were near saturation. Distorted segregation was observed in two and one regions of the genome of Bartlett and Housui, respectively. The position of 14 SSRs originating from apple could be successfully determined in pear maps, which enabled us to compare the two maps. Some SSRs developed from Prunus (peach, cherry) were also mapped. The relationships between pear and the other species belonging to the Rosaceae were discussed based on the position of SSRs.

Chromosome Mapping↗
PubMed2001

[Construction and analysis of a genetic linkage map of soybean].

A high-density genetic map was constructed with a RILs population (NJRIKY) from a cross of two cultivated soybean Kefeng 1 and Nannong 1138-2, using RFLP, SSR, RAPD and AFLP markers. The map consists of 24 linkage groups, which include 792 genetic markers, and covers 2,320.7 cM with an average genetic distance of 2.9 cM. The higher polymorphsims between two parents were identified with SSR markers. Due to its simplicity and stability, they could be used as anchored marker to integrate different maps constructed with different genetic markers. AFLP marker system is efficient for map construction while it easily form clusters to cause big gaps in the map. A total of 21.7% of markers was found with distorted segregation in the RILs population. The high-density molecular linkage map is fundamental for gene localization, comparative genomics, and QTL mapping of important agronomic traits.

Genetic Linkage↗
PubMed2003

Genetic linkage maps of the West African clawed frog Xenopus tropicalis.

Amphibians, and particularly the African clawed frog Xenopus laevis, have been used for more than a century as models of vertebrate embryonic development. However, in many cases, elucidation of developmental functions of specific gene sequences could be severely impeded, because X. laevis is a tetraploid species, with multiple functional copies of many genes of interest. Recent studies have shifted focus to the West African or tropical clawed frog, X. tropicalis, the only known diploid species of the genus Xenopus. Here, we present two preliminary linkage maps, constructed by analysis of joint segregation of amplified fragment length polymorphism (AFLP) markers in a X. tropicalis interstrain hybrid. A total of 53 markers, including 51 AFLP markers and 2 isozyme markers, are presently assigned to 13 multipoint linkage groups on a map of the maternal strain, whereas 9 AFLP markers from the paternal strain are assigned to 3 linkage groups on a separate map. A dense genetic linkage map is essential in mapping new developmental mutants and determining their sequences by positional cloning.

Africa↗
PubMed1990

The CEPH consortium primary linkage map of human chromosome 10.

The first CEPH consortium map, that of chromosome 10, is presented. This primary linkage map contains 28 continuously linked loci defined by genotypes generated from CEPH family DNAs with 37 probe and enzyme combinations. Cytogenetic localization of some of the genetic markers indicates that the consortium map extends, at least, from 10p13 to 10q26. The order of loci on the consortium map agrees with the physical localization data. The female map spans 309 cM (206 cM if an approximation of interference is included in the mapping function used to construct the map), and the mean genetic distance of intervals is 11 cM (7 cM). Also presented are maps of chromosome 10 from each of five CEPH collaborating laboratories, based on genotypes for all relevant markers in the CEPH database. The CEPH consortium map of chromosome 10 should be useful for localization of any gene of interest falling within the span covered. The genotypes in the chromosome 10 consortium map database are now available to the scientific community.

Chromosome Mapping↗