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Linkage Mapping (linkage + mapping)
Selected AbstractsApproaches to the identification of susceptibility genesPARASITE IMMUNOLOGY, Issue 5 2009A. COLLINS SUMMARY Although previous studies have revealed a great deal about the genetic basis of susceptibility and resistance to parasite infection, there is now an opportunity to considerably enhance understanding through genome-wide association mapping. The application of association mapping to complex inheritance has recently become achievable given reduced costs, sophisticated genotyping platforms and powerful statistical methods which build upon increased knowledge of the linkage disequilibrium structure of the human genome. Linkage mapping and related approaches remain useful for the localization of the rarer genetic variants and candidate region association studies can be a very cost-effective route to progress. However, genome-wide association offers the greatest promise, despite the challenges posed by phenotype complexity, ensuring genotype coverage/quality and robust statistical analysis. The available approaches for mapping genes underlying susceptibility are reviewed here, emphasizing their relative merits and drawbacks and highlighting specific software tools and resources that enable successful mapping. [source] Mutations in the first MyTH4 domain of MYO15A are a common cause of DFNB3 hearing lossTHE LARYNGOSCOPE, Issue 4 2009A. Eliot Shearer BSc Abstract Objectives. To use clinical and genetic analyses to determine the mutation causing autosomal recessive nonsyndromic hearing loss (ARNSHL) segregating in two consanguineous Iranian families. Study Design. Family study. Methods. Members of each family received otologic and audiometric examination for the type and extent of hearing loss. Linkage mapping using Affymetrix 50K GeneChips and short tandem repeat (STRP) analysis localized the hearing loss in both families to the DFNB3 locus. Direct sequencing of the MYO15A gene was completed on affected members of both families. Results. Family L-3165 segregated a novel homozygous missense mutation (c.6371G>A) that results in a p.R2124Q amino acid substitution in the myosin XVa protein, while family L-896 segregated a novel homozygous missense (c.6555C>T) mutation resulting in a p.P2073S amino acid change. Conclusions. These are the first MYO15A mutations reported to cause DFNB3 sensorineural hearing loss in the Iranian population. Like other mutations located in the myosin tail homology 4 (MyTH4) domain, the p.R2124Q and p.P2073S mutations are predicted to disrupt the function of the myosin XVa protein, which is integral to the mechanosensory activity of hair cells in the inner ear. Laryngoscope, 2009 [source] Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traitsANIMAL GENETICS, Issue 3 2009X. L. Xu Summary To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST (BI596262) was further identified as the porcine cardiomyopathy associated 1 (CMYA1) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5,-untranslated region and a 630-bp 3,-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire × Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance = 2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses (P < 0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms. [source] Linkage mapping of gene-associated SNPs to pig chromosome 11ANIMAL GENETICS, Issue 3 2006M. Sawera Summary Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino,Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig. [source] Linkage mapping of the MC3R gene to porcine chromosome 17ANIMAL GENETICS, Issue 6 2004K. Civá No abstract is available for this article. [source] Linkage mapping of chicken ovoinhibitor and ovomucoid genes to chromosome 13ANIMAL GENETICS, Issue 4 2004K. Kinoshita No abstract is available for this article. [source] Linkage mapping of Microphthalmia-associated transcription factor to cattle chromosome 22ANIMAL GENETICS, Issue 3 2004S. A. Strom No abstract is available for this article. [source] Linkage mapping of the porcine cathepsin F (CTSF) gene close to the QTL regions for meat and fat deposition traits on pig chromosome 2ANIMAL GENETICS, Issue 2 2004V. Russo No abstract is available for this article. [source] Linkage mapping of the porcine hairless gene (HR,) to chromosome 14ANIMAL GENETICS, Issue 4 2003A. Fernández No abstract is available for this article. [source] Linkage mapping of the mitochondrial aconitase (ACO2) gene to chicken chromosome 1ANIMAL GENETICS, Issue 4 2002T Shimogiri No abstract is available for this article. [source] Linkage mapping of the ovine ANLN gene using an insertion/deletion polymorphismANIMAL GENETICS, Issue 3 2002C. Diez-Tascón No abstract is available for this article. [source] Linkage mapping of four genes (OTC, SERPINA7, SLC25A5 and FMR1) on porcine chromosome XANIMAL GENETICS, Issue 2 2001epica First page of article [source] Linkage mapping and comparative analysis of bovine expressed sequence tags (ESTs)ANIMAL GENETICS, Issue 3 2000W M Grosse Summary Bovine expressed sequence tags (ESTs) containing microsatellites are suitable markers for both linkage and comparative maps. We isolated clones from a bovine fetal thigh skeletal muscle cDNA library that were positive for a (CA)10 probe. Thirty individual clones were isolated and characterised by sequencing. Sequences from the 5, and 3, ends of a clone were considered as separate ESTs until a contiguous sequence was identified. A total of 47 ESTs were sequenced from the 5, and/or 3, ends and full sequence was obtained for the 30 clones. BLAST nucleotide analysis identified significant homology to known mammalian coding regions for 31 of the bovine ESTs, 30 of which also matched human ESTs or sequence-tagged sites (STS). The remaining 16 bovine ESTs represented novel transcripts. Microsatellites were isolated in 27 of the ESTs, 11 of which were developed into markers and placed on the MARC bovine linkage map. Human cytogenetic map positions were available for 20 of the 30 human EST orthologs, and a putative bovine map position for 17 of the sequences could be inferred using comparative mapping data. These results demonstrated that mapping bovine ESTs containing microsatellites is a plausible strategy to increase the density of gene markers on the bovine linkage and comparative maps. [source] CARD15 mutations in familial granulomatosis syndromes: A study of the original Blau syndrome kindred and other families with large-vessel arteritis and cranial neuropathyARTHRITIS & RHEUMATISM, Issue 11 2002Xiaoju Wang Objective To analyze the CARD15 gene in families with heritable multi-organ granulomatoses, including the original Blau syndrome kindred as well as other families with related granulomatous conditions. Methods Linkage mapping was performed in 10 families. Observed recombination events were used to exclude regions centromeric or telomeric to 16q12.1, and the Blau gene critical region was refined to <3 cM, corresponding to a physical distance of 3.5 megabasepairs. Based on its known biochemical function, CARD15 was analyzed as a positional candidate for the Blau syndrome susceptibility gene, by direct DNA sequencing. Results These studies resulted in the identification, in 5 of the families, of 2 sequence variants at position 334 of the gene product (R334W and R334Q). Affected family members from the original Blau syndrome kindred were heterozygous for the R334W missense mutation; mutations at the same position were also observed in several unrelated Blau syndrome families, some of whose phenotypes included large-vessel arteritis and cranial neuropathy. The missense mutations segregated with the disease phenotype in the families, and were not seen in 208 control alleles. Conclusion These findings demonstrate that CARD15 is an important susceptibility gene for Blau syndrome and for other familial granulomatoses that display phenotypic traits beyond those of classic Blau syndrome. [source] Prostate cancer aggressiveness locus on chromosome segment 19q12,q13.1 identified by linkage and allelic imbalance studiesGENES, CHROMOSOMES AND CANCER, Issue 4 2003Phillippa J. Neville Whole-genome scan studies recently identified a locus on chromosome segments 19q12,q13.11 linked to prostate tumor aggressiveness by use of the Gleason score as a quantitative trait. We have now completed finer-scale linkage mapping across this region that confirmed and narrowed the candidate region to 2 cM, with a peak between markers D19S875 and D19S433. We also performed allelic imbalance (AI) studies across this region in primary prostate tumors from 52 patients unselected for family history or disease status. A high level of AI was observed, with the highest rates at markers D19S875 (56%) and D19S433 (60%). Furthermore, these two markers defined a smallest common region of AI of 0.8 Mb, with 15 (29%) prostate tumors displaying interstitial AI involving one or both markers. In addition, we noted a positive association between AI at marker D19S875 and extension of tumor beyond the margin (P = 0.02) as well as a higher Gleason score (P = 0.06). These data provide strong evidence that we have mapped a prostate tumor aggressiveness locus to chromosome segments 19q12,q13.11 that may play a role in both familial and non-familial forms of prostate cancer. © 2003 Wiley-Liss, Inc. [source] Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locusMOLECULAR ECOLOGY, Issue 2010LAURA FERGUSON Abstract The mimetic wing patterns of Heliconius butterflies are an excellent example of both adaptive radiation and convergent evolution. Alleles at the HmYb and HmSb loci control the presence/absence of hindwing bar and hindwing margin phenotypes respectively between divergent races of Heliconius melpomene, and also between sister species. Here, we used fine-scale linkage mapping to identify and sequence a BAC tilepath across the HmYb/Sb loci. We also generated transcriptome sequence data for two wing pattern forms of H. melpomene that differed in HmYb/Sb alleles using 454 sequencing technology. Custom scripts were used to process the sequence traces and generate transcriptome assemblies. Genomic sequence for the HmYb/Sb candidate region was annotated both using the MAKER pipeline and manually using transcriptome sequence reads. In total, 28 genes were identified in the HmYb/Sb candidate region, six of which have alternative splice forms. None of these are orthologues of genes previously identified as being expressed in butterfly wing pattern development, implying previously undescribed molecular mechanisms of pattern determination on Heliconius wings. The use of next-generation sequencing has therefore facilitated DNA annotation of a poorly characterized genome, and generated hypotheses regarding the identity of wing pattern at the HmYb/Sb loci. [source] Sequence polymorphisms in porcine homologs of murine coat colour-related genesANIMAL GENETICS, Issue 2 2010N. Okumura Summary Herein, we report the variability among 57 porcine homologs of murine coat colour-related genes. We identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within 44 expressed gene sequences by aligning eight pig complementary DNA (cDNA) samples. The sequence alignment revealed a total of 485 SNPs and 15 InDels. The polymorphisms were then validated by performing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with reference DNA samples obtained from 384 porcine individuals. Of the 384 individuals, three parents of the experimental F2 family were included to detect polymorphisms between them for linkage mapping. We also genotyped previously reported polymorphisms of 12 genes, and one SNP each in three genes that were detected by performing a BLAST search of the Trace database. A total of 211 SNPs and three InDels were successfully genotyped from our porcine DNA panel. We detected SNPs in 33 of the 44 genes among the parents of an experimental F2 family and then constructed a linkage map of the 33 genes for this family. The linkage assignment of each gene to the porcine chromosomes was consistent with the location of the BAC clone in the porcine genome and the corresponding gene sequence. We confirmed complete substitutions of EDNRB and MLPH in the Jinhua and Clawn miniature breeds, respectively. Furthermore, we identified polymorphic alleles exclusive to each pig group: 13 for Jinhua, two for Duroc, three for Meishan, four for the Japanese wild boar, one for the Clawn miniature pig and four for the Potbelly pig. [source] Genetic mapping of the belt pattern in Brown Swiss cattle to BTA3ANIMAL GENETICS, Issue 2 2009C. Drögemüller Summary The white belt pattern of Brown Swiss cattle is characterized by a lack of melanocytes in a stretch of skin around the midsection. This pattern is of variable width and sometimes the belt does not fully circle the body. To identify the gene responsible for this colour variation, we performed linkage mapping of the belted locus using six segregating half-sib families including 104 informative meioses for the belted character. The pedigree confirmed a monogenic autosomal dominant inheritance of the belted phenotype in Brown Swiss cattle. We performed a genome scan using 186 microsatellite markers in a subset of 88 animals of the six families. Linkage with the belt phenotype was detected at the telomeric region of BTA3. Fine-mapping and haplotype analysis using 19 additional markers in this region refined the critical region of the belted locus to a 922-kb interval on BTA3. As the corresponding human and mouse chromosome segments contain no obvious candidate gene for this coat colour trait, the mutation causing the belt pattern in the Brown Swiss cattle might help to identify an unknown gene influencing skin pigmentation. [source] Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon)ANIMAL GENETICS, Issue 4 2006C. Maneeruttanarungroj Summary In this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT-rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35,48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon-primed intron-crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non-EST-associated microsatellites and two EST-associated microsatellites) were analysed across the international P. monodon mapping family. A total of 144 new markers were added to the P. monodon maps, including 36 of the microsatellite-containing ESTs. The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome. [source] Ovine alpha-amylase genes: isolation, linkage mapping and association analysis with milk traitsANIMAL GENETICS, Issue 4 2004J. H. Calvo Summary On the basis of comparisons between cattle and sheep genome mapping information the ovine , - 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. [source] Differences in recombination rates on chromosome 23 between German Angus and German Simmental and breed specific linkage mappingANIMAL GENETICS, Issue 3 2003C. Weimann Summary Five paternal half sib families of German Angus (GA) (n = 428) and six of German Simmental (GS) (n = 378) including dams were genotyped with 11 microsatellites (INRA132, RM033, BM1815, BM1258, BOLA-DRB1, BM1818, BM1905, BM1443, CYP21, CSSM5 and DYMS1) derived from chromosome 23. Differences in heterozygosity between the breeds were observed. Significant differences in recombination rates between GA and GS could be demonstrated for the marker intervals INRA132 - CSSM5, CYP21 - BOLA - DRB1 and BOLA - DRB1 - BM1818. The length of the map of GA was 90.5 cM in contrast to 117.8 cM for GS. The breed specific linkage maps show differences in length but confirmation of the order of the markers. [source] Polymorphisms in the equine WNT1 gene allow linkage mapping to ECA6qANIMAL GENETICS, Issue 2 2003C. Mau No abstract is available for this article. [source] Partial cloning, cytogenetic and linkage mapping of the porcine resistin (RSTN) geneANIMAL GENETICS, Issue 5 2002S. Cepica No abstract is available for this article. [source] SNP detection and linkage mapping of the porcine ferritin heavy-chain geneANIMAL GENETICS, Issue 4 2002S. Ponsuksili No abstract is available for this article. [source] Comparative porcine gene mapping relative to human chromosomes 9, 10, 20 and 22ANIMAL GENETICS, Issue 5 2001J. H. Lee Comparative anchor tagged sequence (CATS) consensus primers from loci mapped to human chromosomes 9, 10, 20, and 22 have been used to amplify homologous loci in pigs. Of 53, CATS primers tested in pigs, only 23 yielded products homologous to the human locus (42% success). Ten loci were physically mapped (43% success rate for verified products, but only 19% for primers tested). Due to lack of polymorphism, linkage mapping was possible only for AMBP. Map locations were consistent with human/pig ZOO-FISH, except for ADRA1A, whose position is still equivocal in humans. These CATS primers have made very limited contributions to pig/human comparative gene mapping because of low efficiency of amplification of orthologous porcine product, frequent amplification from rodent template in a somatic hybrid panel and low level of polymorphism. [source] The porcine sarcolipin (SLN) gene: identification of an SNP and linkage mapping to chromosome 9ANIMAL GENETICS, Issue 2 2001L. Fontanesi No abstract is available for this article. [source] Physical and linkage mapping of the bovine acidic ,-glucosidase gene to chromosome 19ANIMAL GENETICS, Issue 4 2000I Tammen No abstract is available for this article. [source] | |||||||||||||