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At least 595 records · Page 33Linked to original sources
PubMed2001

Construction of a reference linkage map for melon.

A map of melon (Cucumis melo L.) with 411 markers (234 RFLPs, 94 AFLPs, 47 RAPDs, 29 SSRs, five inter-SSRs, and two isozymes) and one morphological trait (carpel number) was constructed using the F2 progeny of a cross between the Korean accession P1161375 and the Spanish melon type 'Pinyonet Piel de Sapo'. RFLPs were obtained using 212 probes from different genomic and cDNA melon libraries, including 16 Arabidopsis ESTs, 13 Cucumis known genes, and three resistant gene homologues. Most loci (391) mapped to 12 major linkage groups, spanning a total genetic distance of 1197 cM, with an average map interval of 3 cM/marker. The remaining 21 loci (six RAPDs and 15 AFLPs) were not linked. A majority (66%) of the markers were codominant (RFLPs, SSRs, and isozymes), making them easily transferable to other melon crosses. Such markers can be used as a reference, to merge other melon and cucumber maps already constructed. Indeed, some of them (23 SSRs, 14 RFLPs, one isozyme, and one morphological trait) could act as anchor points with other published cucurbit maps.

Chromosome Mapping↗
PubMed1998

A second-generation linkage map of the sheep genome.

A genetic map of Ovis aries (haploid n = 27) was developed with 519 markers (504 microsatellites) spanning approximately 3063 cM in 26 autosomal linkage groups and 127 cM (female specific) of the X Chromosome (Chr). Genotypic data were merged from the IMF flock (Crawford et al., Genetics 140, 703, 1995) and the USDA mapping flock. Seventy-three percent (370/504) of the microsatellite markers on the map are common to the USDA-ARS MARC cattle linkage map, with 27 of the common markers derived from sheep. The number of common markers per homologous linkage group ranges from 5 to 22 and spans a total of 2866 cM (sex average) in sheep and 2817 cM in cattle. Marker order within a linkage group was consistent between the two species with limited exceptions. The reported translocation between the telomeric end of bovine Chr 9 (BTA 9) and BTA 14 to form ovine Chr 9 is represented by a 15-cM region containing 5 common markers. The significant genomic conservation of marker order will allow use of linkage maps in both species to facilitate the search for quantitative trait loci (QTLs) in cattle and sheep.

Animals↗
PubMed1986

Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes by using chromosome-specific alpha satellite DNA probes: implications for development of centromere-based genetic linkage maps.

We describe a general strategy for the detection of high-frequency restriction fragment length polymorphisms in the centromeric regions of human chromosomes by molecular analysis of alpha satellite DNA, a diverse family of tandemly repeated DNA located near the centromeres of all human chromosomes. To illustrate this strategy, cloned alpha satellite repeats isolated from two human chromosomes, 17 and X, have been used under high-stringency conditions that take advantage of the chromosome-specific organization of this divergent repeated DNA family. Multiple high-frequency restriction fragment length polymorphisms are described for the centromeric region of both chromosome 17 and X chromosome. Mendelian inheritance of the variants is demonstrated. The X-linked alpha satellite polymorphisms in particular are highly informative and constitute a virtually unique centromeric DNA marker for each X chromosome examined. Since the strategy we describe is a general one, the alpha satellite family of DNA should provide a rich source of molecular variation in the human genome and should contribute to the development of centromere-based genetic linkage maps of human chromosomes.

Centromere↗
PubMed1986

Conjugational fertility and location of chloramphenicol biosynthesis genes on the chromosomal linkage map of Streptomyces venezuelae.

In Streptomyces venezuelae fertility, defined as chromosomal gene recombination, was enhanced over 1000-fold when one parent in a biparental conjugational cross lacked the physically-undetected plasmid SVP1, as compared with crosses in which both parents carried SVP1. The existence of SVP1 and at least two other fertility plasmids, SVP2 and SVP3, was detected in S. venezuelae by 'lethal zygosis' elicited by a plasmid-plus mycelium in contact with a plasmid-minus mycelium. Conjugational crosses were used to construct a linkage map of S. venezuelae which was highly consistent with the map of analogous loci in S. coelicolor A3(2). A cluster of genes governing chloramphenicol biosynthesis was located near arg, cys and pdxB genes at a position roughly equivalent to the 1-2 o'clock region of the S. coelicolor A3(2) map.

Chloramphenicol↗
PubMed2004

Ovine alpha-amylase genes: isolation, linkage mapping and association analysis with milk traits.

On the basis of comparisons between cattle and sheep genome mapping information the ovine alpha-amylase gene was examined as a possible genetic marker for milk traits in sheep. The objective of the present study was to isolate, map and determine whether this gene is a candidate gene for milk traits. DNA fragments (832 and 2360 bp) corresponding to two different AMY genes were isolated, and one SNP in intron 3 and one GTG deletion in exon 3 of the 2360 bp DNA fragment were found. The 2360 bp ovine AMY DNA fragment was located on chromosome 1 by linkage mapping using the International Mapping Flock. No association was found between estimated breeding values for milk yield, protein and fat contents and AMY genotypes in a daughter design comprising 13 Manchega families with an average of 29 daughters (12-62) per sire.

Animals↗
PubMed2002

[Construction the RFLP linkage map and location the NCBL QTL of maize].

There exists the race differential phenomenon in Exserohilum turcicum (namely NCBL). At present, there are 5 identified races of NCBL and some un-known races in China. For improvement of maize resistance to NCBL, a basic method is to improve maize quantitative resistance. To identify the numbers and effects of the quantitative resistant loci to NCBL in maize, we constructed F2:3 population from resistant line P138 as male parent cross with sensitive line Z3 as female parent. Using RFLP marker technique, the RFLP linkage map of maize was cons cracted covering 1999. 8 cM, and the average distance between markers was 16.5 cM. Identified QTL of NCBL lesion length, width, and area were 3, 3, 2, respectively. The combined contribution ratios of these QTL were 58.1%, 71.5%, 27.5%, respectively. No QTL was identified NCBL lesion number per leaf, it was a trait that might be controlled by one- or oligo-genes. Finally, authors discussed and prospected the maize NCBL research in future.

Ascomycota↗
PubMed1992

Linkage mapping of the carbonyl reductase (CBR) gene on human chromosome 21 using a DNA polymorphism in the 3' untranslated region.

A DNA polymorphism has been found in the 3' untranslated region of the carbonyl reductase gene (CBR). Genotypes of the members of the CEPH pedigrees have been obtained and used in linkage analysis to map the CBR gene in the linkage map of human chromosome 21. The gene maps between the interferon-alpha receptor (IFNAR) and the D21S55 loci.

Alcohol Oxidoreductases↗
PubMed1998

A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf.

Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.

Chromosome Mapping↗
PubMed2001

The assignment by linkage mapping of four genes from human chromosome 22 to bovine chromosome 5 and 17.

Polymerase chain reaction oligonucleotides were designed to amplify bovine specific sequences for four genes that are located on human chromosome 22 (HSA22): crystallin beta A4 (CRY B A4), parvalbumin (PVALB), tissue inhibitor of metalloproteinase 3 (TIMP3) and matrix metalloproteinase 11 (MMP11). Single strand conformation analysis of these bovine gene fragments defined polymorphisms within a population of three large half-sib families of three F1 Charolais x Brahman sires and a composite herd comprising an equal proportion of Africander, Brahman, Hereford and Shorthorn breeds (CSIRO pedigree). The DNA marker genotypes were used to define linkage associations to other DNA markers already placed on the CSIRO linkage map. The genes TIMP3 and PVALB were assigned to BTA5 and CRYbetaA4 and MMP11 to BTA17.

Animals↗
PubMed2003

Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits.

The bovine CSN1S1 5' flanking region (CSN1S1-5') was screened for polymorphisms in different cattle breeds. Single-strand conformation polymorphisms (SSCP) and sequence analyses revealed four alleles (1-4), two of them being new allelic forms (3 and 4). Sequences were deposited in GenBank with accession numbers AF549499-502. In alleles 1 and 4, potential transcription factor binding sites are altered by the mutations. Using SSCP analysis, all four alleles were identified in German Holsteins. Six intragenic haplo-types comprising CSN1S1-5' (alleles 1, 2, 3, 4) and exon 17 (CSN1S1*B and C) genotypes were found. Linkage mapping using half-sib families from the German QTL project positioned CSN1S1 between the markers FBN14 and CSN3, with 5.6 cM distance between CSN1S1 and CSN3. Variance analysis, using family and CSN1S1 promoter genotypes as fixed effects, of breeding values and deregressed proofs for milk production traits (milk, fat, and protein yield and also fat and protein percentage) revealed significant effects on protein percentage when all families and genotypes were considered. Contrast calculations assigned a highly significant effect to genotype 24, which was associated with highest LS-means for protein percentage breeding values. As CSN1S1 is one of the main caseins in milk, this could be an effect of mutations in regulatory elements in the promoter region. An effect on milk yield breeding values was indicated for genotype 12, but is probably caused by a linked locus.

Alleles↗
PubMed1993

Abundant (A)n.(T)n mononucleotide repeats in the pig genome: linkage mapping of the porcine APOB, FSA, ALOX12, PEPN and RLN loci.

A computer analysis revealed that the mononucleotide repeat (A)n.(T)n is about five times as common as (CA)n.(GT)n repeats in the porcine genome, with frequency estimates of one every 7kb and 30kb, respectively. Seven mononucleotide repeats with n = 12-25 located close to coding sequences were analysed for polymorphism using polymerase chain reaction (PCR) amplification and polyacrylamide gel electrophoresis. All loci were variable with 3-6 alleles and heterozygosities of 0.26-0.69 based on investigation of 10 unrelated pigs (two wild boars and eight domestic sows). Repeat length correlated with degree of polymorphism. A comparison with (CA)n.(GT)n polymorphisms suggested that the number of repeat units rather than the total length of the repeat region is the common denominator that governs polymorphism at both mono- and dinucleotide repeat loci. (A)n.(T)n polymorphisms allowed linkage mapping of relaxin to chromosome 1, apolipoprotein B to chromosome 3, aminopeptidase N to chromosome 7, arachidonate 12-lipoxygenase to chromosome 12, and follistatin to chromosome 16. The rich abundance of potentially informative (A)n.(T)n repeats will increase the chances of finding a PCR-based marker near any DNA sequence of interest.

Aminopeptidases↗
PubMed1995

A linkage map with microsatellites isolated from swine flow-sorted chromosome 11.

We have developed a simple and efficient method to construct partial libraries of swine Chromosome (Chr) 11, starting with only 300 flow-sorted copies. DNA is amplified by PARM-PCR with primer containing at the 5'-end the sequence AGCU-. After amplification, digestion of PCR products with uracil DNA glycosylase generates cohesive ends corresponding to the SstI site. The amplified fragments can then be ligated in vector linearized with the SstI enzyme. Using five different primers, we PARM-PCR amplified and cloned swine Chr 11 DNA. These chromosome-specific libraries have been used to develop 14 different (TG)n microsatellites. Ten of these markers were assigned to Chr 11 by PCR analysis of a panel of Pig-Rodent somatic hybrids and by linkage analysis of the 171 individuals of the PiGMaP reference families. A complete linkage map of 147 cM of this chromosome was then realized by integrating existing markers.

Animals↗
PubMed2005

QTL analysis of Fusarium head blight resistance using a high-density linkage map in barley.

Fusarium head blight (FHB) resistance was evaluated in a set of recombinant inbred (RI) lines from a cross between Russia 6 (resistant) and H.E.S. 4 (susceptible), which had one of the widest differences of FHB resistance reactions among ca. 5,000 barley germplasm accessions in Okayama University. Field-grown spikes were sampled and inoculated by the 'cut-spike test'. Resistance reactions on the parents and RI lines were scored by eleven grades, from resistant (0) to susceptible (10). Quantitative trait loci (QTL) analysis detected three QTL: two located on the long arm of chromosome 2H, and another on the short arm of chromosome 5H. A QTL located on chromosome 2H was coincident with the vrs1 locus, which governs inflorescence row type. The other QTL on chromosome 2H was positioned in the vicinity of cleistogamy locus (cly1 or Cly2) that determines inflorescence opening/closing. Resistant gene analog (RGA) and expressed sequence tag (EST) markers with homology for disease resistance genes were integrated into the high-density linkage map. Most of these markers were not localized near the identified resistance QTL, except for one RGA marker (FXLRRfor_XLRRrev170) localized in the vicinity of the cly1/Cly2 locus. Five AFLP markers localized in the vicinity of the identified QTL were sequenced to convert them into sequence tagged site (STS) markers. Genotyping of each RI line using two AFLP-STS markers and the vrs1 locus indicated that the RI lines with three Russia 6 QTL alleles exhibited the same level of high FHB resistance reactions as Russia 6. In contrast, RI lines with three susceptible alleles showed reactions close to H.E.S. 4. Therefore, the markers closely linked to the QTL can be efficiently used for the selection of resistance.

Chromosome Mapping↗
PubMed2004

Joining genetic linkage maps using a joint likelihood function.

We present an efficient method to join genetic maps derived from different crosses, which is especially appropriate for dominant markers. In contrast to the "JoinMap" algorithm, which estimates information about recombination in a given cross from the LOD values and then combines estimates among crosses assuming a binomial sampling distribution, we construct a joint likelihood function that combines information across all crosses, to obtain a joint estimate of recombination. Simulations indicated that the difference between these two approaches is small when codominant markers are used, but that the joint likelihood approach shows substantially improved estimates when dominant or a mixture of dominant and codominant markers are used. This is because the joint likelihood implicitly finds the optimal weights among different classes of data, while the former method does not accurately predict the information from crosses involving dominant markers. Application of our method is illustrated by the construction of a linkage map for Linanthus using both backcrosses and the F2 of a cross between Linanthus jepsonii and L. bicolor, assayed with amplified fragment length polymorphisms (AFLP).

Chromosome Mapping↗
PubMed1995

Linkage mapping in Papio baboons: conservation of a syntenic group of six markers on human chromosome 1.

We have established multipoint genetic linkage among six loci in baboons (Papio hamadryas). Published PCR primers designed to amplify five human microsatellite loci were used to amplify homologous loci in 229 pedigreed baboons. Southern blotting was used to type two RFLPs in a functional gene (anti-thrombin III) in a subset of those animals. All six loci are known to map to human chromosome 1q, a region of the genome predicted by karyotype studies to be conserved in baboons. Pairwise recombination frequencies and lod scores indicate that the six loci are also linked in baboons. Recombination distances among the loci are similar to those reported for humans. Like humans, the baboons exhibit higher rates of recombination in females than in males. This study demonstrates that (1) microsatellite loci first described and characterized in the human genome can be effectively used for genetic linkage mapping in non-human primates, (2) a group of genetic loci known to be linked on human chromosome 1q are also linked in the baboon genome, and (3) sex differences in recombination frequencies among loci on human chromosome 1q are also observed in the genome of this Old World monkey. This constitutes the first reported multipoint linkage map in any nonhuman primate.

Animals↗
PubMed2003

Efficient construction of high-density linkage map and its application to QTL analysis in barley.

Using a High Efficiency Genome Scanning (HEGS) system and recombinant inbred (RI) lines derived from the cross of Russia 6 and H.E.S. 4, a high-density genetic map was constructed in barley. The resulting 1,595.7-cM map encompassed 1,172 loci distributed on the seven linkage groups comprising 1,134 AFLP, 34 SSR, three STS and vrs1 (kernel row type) loci. Including PCR reactions, gel electrophoresis and data processing, 6 months of work by a single person was sufficient for the whole mapping procedure under a reasonable cost. To make an appraisal of the resolution of genetic analysis for the 95 RI lines based on the constructed linkage map, we measured three agronomic traits: plant height, spike exsertion length and 1,000-kernel weight, and the analyzed quantitative trait loci (QTLs) associated with these traits. The results were compared on the number of detected QTLs and their effects between a high-density map and a skeleton map constructed by selected AFLP and anchor markers. The composite interval mapping on the high-density map detected more QTLs than the other analyses. Closely linked markers with QTLs on the high-density map could be powerful tools for marker-assisted selection in barley breeding programs and further genetic analyses including an advanced backcross analysis or a map-based cloning of QTL.

Chromosome Mapping↗
PubMed1994

A linkage map of microsatellite markers on the human X chromosome.

The efficiency of mapping and diagnosis of X-linked disorders by linkage depends upon the existence of a high-density genetic map of polymerase chain reaction (PCR)-based markers. DXS1120, DXS1122, DXS1123, DXS1124, DXS1125, DXS1126, and DXS1153 were randomly isolated from a flow-sorted lambda bacteriophage library of the human X chromosome. The CCN (N = A or G) repeat within the androgen receptor was also found to be polymorphic and primers were designed for genotyping the CCN polymorphism in addition to the AGC polymorphism. The above markers, together with microsatellite polymorphisms at DXS237 (GMGX9), 5'DYS-II and 3'DYS MS (within the dystrophin locus), DXS538 (XL27B), PGK1P1, DXS300 (VK29AC), DXS294 (VK17AC), and DXS102 (cX38.1AC), were genotyped in the 40 CEPH reference families. One marker, DXS1153, was found to include cryptic alleles that amplify only in homozygotes and hemizygotes but not heterozygotes. A PCR-based linkage map was constructed using all of the above markers plus PCR-based markers from the CEPH database and those PCR-based markers previously typed in our laboratory: ALAS2, DXS292 (VK14AC), DXS297 (VK23AC), FRAXAC1, and FRAXAC2. The genetic map of the X chromosome incorporates 62 PCR-based marker loci, integrates the Weissenbach markers, and extends from XG near Xpter to DXS52 near Xqter, a distance of 236 cM.

Alleles↗
PubMed1999

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).

Chromosome Mapping↗