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Comparative Mapping (comparative + mapping)
Selected AbstractsGenetic Analysis of ele Mutants and Comparative Mapping of ele1 Locus in the Control of Organ Internal Asymmetry in Garden PeaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2010Xin Li Previous study has shown that during zygomorphic development in garden pea (Pisum sativum L.), the organ internal (IN) asymmetry of lateral and ventral petals was regulated by a genetic locus, SYMMETRIC PETAL 1 (SYP1), while the dorsoventral (DV) asymmetry was determined by two CYC - like TCP genes or the PsCYC genes, KEELED WINGS (K) and LOBED STANDARD 1 (LST1). In this study, two novel loci, ELEPHANT EAR-LIKE LEAF 1 (ELE1) and ELE2 were characterized. These mutants exhibit a similar defect of IN asymmetry as syp1 in lateral and ventral petals, but also display pleiotropic effects of enlarged organ size. Genetic analysis showed that ELE1 and ELE2 were involved in same genetic pathway and the enlarged size of petals but not compound leaves in ele2 was suppressed by introducing k and lst1, indicating that the enlargement of dorsal petal in ele2 requires the activities of K and LST1. An experimental framework of comparative genomic mapping approach was set up to map and clone LjELE1 locus in Lotus japonicus. Cloning the ELE1 gene will shed light on the underlying molecular mechanism during zygomorphic development and further provide the molecular basis for genetic improvement on legume crops. [source] Introgression of crown rust (Puccinia coronata) resistance from meadow fescue (Festuca pratensis) into Italian ryegrass (Lolium multiflorum): genetic mapping and identification of associated molecular markersPLANT PATHOLOGY, Issue 1 2006I. P. Armstead Crown rust (Puccinia coronata) resistance (CRres), which had been introgressed from meadow fescue (Festuca pratensis) into the Italian ryegrass (Lolium multiflorum) background, was genetically mapped with amplified fragment length polymorphism (AFLP) and sequence tagged site (STS) markers to a terminal segment of chromosome 5. Comparative mapping had previously shown that this region of the Lolium/Festuca genome has a degree of conserved genetic synteny with chromosomes 11 and 12 of rice. Sequences from rice chromosome 12 were used as templates for identifying further STS markers that cosegregated with CRres. The relative genomic positions of molecular markers associated with CRres in L. multiflorum, L. perenne, F. pratensis and oats is discussed, along with their relationships to physical positions on rice chromosomes C11 and C12. [source] A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannameiANIMAL GENETICS, Issue 3 2010Z.-Q. Du Summary Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r2), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r2 increased with decreasing inter-marker distance from ,80 cm, and increased more rapidly from ,30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits. [source] Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9ANIMAL GENETICS, Issue 1 2001S. P. Suchyta Comparative mapping of chicken and human genomes is described, primarily of regions corresponding to human chromosomes 1, 4 and 9. Segments of chicken orthologues of selected human genes were amplified from parental DNA of the East Lansing backcross reference mapping population, and the two parental alleles were sequenced. In about 80% of the genes tested, sequence polymorphism was identified between reference population parental DNAs. The polymorphism was used to design allele-specific primers with which to genotype the backcross panel and place genes on the chicken linkage map. Thirty-seven genes were mapped which confirmed the surprisingly high level of conserved synteny between orthologous chicken and human genes. In several cases the order of genes in conserved syntenic groups differs between the two genomes, suggesting that there may have been more frequent intrachromosomal inversions as compared with interchromosomal translocations during the separate evolution of avian and mammalian genomes. [source] Mapping of 443 porcine EST improves the comparative maps for SSC1 and SSC7 with the human genomeANIMAL GENETICS, Issue 5 2005O. Demeure Summary Numerous mapping studies of complex traits in the pig have resulted in quantitative trait loci (QTL) intervals of 10,20 cM. To improve the chances to identify the genes located in such intervals, increased expressed sequence tags (EST)-based marker density, coupled with comparative mapping with species whose genomes have been sequenced such as human and mouse, is the most efficient tool. In this study, we mapped 443 porcine EST with a radiation hybrid (RH) panel (384 had LOD > 6.0) and a somatic cell hybrid panel. Requiring no discrepancy between two-point and multipoint RH data allowed robust assignment of 309 EST, of which most were located on porcine chromosomes (SSC) 1, 4, 7, 8 and X. Moreover, we built framework maps for two chromosomes, SSC1 and SSC7, with mapped QTL in regions with known rearrangement between pig and human genomes. Using the Blast tool, we found orthologies between 407 of the 443 pig cDNA sequences and human genes, or to existing pig genes. Our porcine/human comparative mapping results reveal possible new homologies for SSC1, SSC3, SSC5, SSC6, SSC12 and SSC14 and add markers in synteny breakpoints for chromosome 7. [source] Radiation hybrid and comparative mapping of 83 canine brain ESTsANIMAL GENETICS, Issue 5 2004J. A. Hendrickson First page of article [source] FISH mapping and sequence analysis of 87 porcine BAC clonesANIMAL GENETICS, Issue 1 2004R. Anistoroaei Summary Ninety-one bacterial artificial chromosomes (BAC) clones, selected effectively at random from our library, were used as probes for fluorescence in situ hybridization. Of these, 87 clones gave a specific signal in one, two or three different pair(s) of swine metaphase chromosomes. The ends of 35 BAC clones were sequenced in order to obtain information for comparative mapping. Fifteen of them gave useful comparative mapping information. [source] Chromosomal assignments for porcine genes encoding enzymes in hepatic metabolic pathwaysANIMAL GENETICS, Issue 4 2002K. Wimmers Increasing the number of mapped genes will facilitate (1) the identification of potential candidate genes for a trait of interest within quantitative trait loci regions and (2) comparative mapping. The metabolic activities of the liver are essential for providing fuel to peripheral organs, for regulation of amino acid, carbohydrate and lipid metabolism and for homoeostasis of vitamins, minerals and electrolytes. We aimed to identify and map genes coding for enzymes active in the liver by somatic cell genetics in order to contribute to the improvement of the porcine gene map. We mapped 28 genes of hepatic metabolic pathways including six genes whose locations could be confirmed and 22 new assignments. Localization information in human was available for all but one gene. In total 24 genes were assigned to in the expected chromosomal regions on the basis of the currently available information on the comparative human and pig map while for four genes our results suggest a new correspondence or extended regions of conservation between porcine and human chromosomes. [source] Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6 and 9ANIMAL GENETICS, Issue 2 2002H. S. Sun Previous comparative mapping suggested that at least five pig chromosomes (Sscr4, 6, 9, 10 and 14) share homology with human chromosome 1 (Hsap1). A significant quantitative trait loci (QTL) for fat deposition has been identified on Sscr4 that appears to be near the junction region between Sscr4 and Sscr9 relative to Hsap1. It is of interest to define the boundaries of conserved synteny between pig chromosomes and Hsap1 to use human map information to identify putative comparative positional candidates for this QTL. Eleven genes, including Janus kinase 1 (JAK1), Prostaglandin E receptor3 (PTGER3), urate oxidase (UOX), coagulation factor 3 (F3), vascular cell adhesion molecule 1 (VCAM1), ribosomal protein L5 (RPL5), POU domain, class 2, transcription factor 1 (POU2F1), coagulation factor 5 (F5), Prostaglandin endoperoxide synthase-2 (PTGS2), myosin binding protein H (MYBPH) and Antithrombin III (SERPINC1), were selected to refine the boundaries of the blocks of conserved synteny between Hsap1 and pig chromosomes. Pig sequence tagged sites (STSs) were developed and used to physically map these 11 genes using a somatic cell hybrid panel. Eight loci have been mapped by using fluorescent in situ hybridization (FISH) to improve map resolution. Heterologous FISH was used to refine the location of VCAM1 on human chromosomes. In addition, human yeast artificial chromosomes (YACs) were mapped by heterologous FISH on pig metaphases to refine the boundaries of the regions of homology between Sscr4 and Sscr9 on Hsap1. Results from this study suggest the precise break in conserved synteny on Hsap1 corresponding to the Sscr4/6 and Sscr4/9 transitions are most likely on the Hsap1p22 and Hsap1q24,25 regions, respectively. Further, our data predict that Hsap1q21,24 is a candidate region for the backfat QTL localized to Sscr4. [source] Chicken microsatellite primers are not efficient markers for Japanese quailANIMAL GENETICS, Issue 1 2001M. Inoue-Murayama Domestic fowl or chicken (Gallus gallus) and Japanese quail (Coturnix japonica) belong to the family Phasianidae. The exchange of marker information between chicken and quail is an important step towards the construction of a high-resolution comparative genetic map in Phasianidae, which includes several poultry species of agricultural importance. We tested chicken microsatellite markers to see if they would be suitable as genetic linkage markers in Japanese quail. Twenty-six per cent (31/120) of chicken primers amplified individual loci in Japanese quail and 65% (20/31) of the amplified loci were found to be polymorphic. Eleven of the polymorphic loci were excluded as uninformative because of the lack of amplification in some individuals or high frequency of nonspecific amplification. The sequence information of the remaining nine loci revealed six of them to contain microsatellites that were nearly identical with those of the orthologous regions in chicken. For these six loci, allele frequencies were estimated in 50 unrelated quails. Although the very few chicken markers that do work well in quail could be used as anchor points for a comparative mapping, most chicken markers are not useful for studies in quail. Therefore, more effort should be committed to developing quail-specific markers rather than attempting to adapt chicken markers for work in quail. [source] Human Chromosome 17 in Essential HypertensionANNALS OF HUMAN GENETICS, Issue 2 2003J. Knight Summary Hypertension affects up to 30% of the adult population in Western societies and is a major risk factor for kidney disease, stroke and coronary heart disease. It is a complex trait thought to be influenced by a number of genes and environmental factors, although the precise aetiology remains unknown at this time. A number of methods have been successfully used to identify mutations that cause Mendelian traits and these are now being applied to the investigation of complex diseases. This review summarises the data gathered, using such approaches, that suggest there is a gene or genes on chromosome 17 causing human essential hypertension. Studies in rodent models are discussed first, followed by studies of human hypertension that include the investigation of pseudohypoaldosteronism type II, a monogenic trait that manifests with hypertension alongside other phenotypic variables. In addition, candidate gene studies, genome screens and linkage studies based on comparative mapping are outlined. To date no gene has been identified on human chromosome 17 that influences blood pressure and causes human essential hypertension. However, results of ongoing fine mapping and candidate gene studies in both rodents and man are eagerly awaited. [source] | ||||||||||