Assignment of canine MSS1 microsatellite markers to chromosomes by linkage data.

Recent advances in mapping the canine genome have led to an increase in the number of linkage studies aimed at dissecting the genetic causes of many hereditary diseases that affect the domestic dog. The first step in developing molecular tools for a whole genome scan was the characterization of a set of microsatellite markers, termed minimal screening set 1 (MSS1), that provided an estimated coverage of 10 cM. A limiting factor in use of the MSS1 is not all of the 172 MSS1 markers have been localized to specific chromosomes. Seventy-five of the markers were positioned on a total of 15 chromosomes with the original publication of the MSS1. The localization based on linkage data of 14 additional MSS1 markers to chromosomes using CRIMAP v. 2.4 to build a linkage map of 113 MSS1 markers that were polymorphic in a kindred of Dalmatians is reported here.     

Chromosomal assignment of 11 loci in the rat by mouse-rat somatic hybrids and linkage

Eleven rat genes have been assigned to rat chromosomes by use of mouse × rat somatic hybrids and/or use of linkage to known chromosome markers. Among them, the genes for the inducible nitric oxide synthase (Nos2) and for a vasoactive intestinal peptide receptor (Vipr) are potential candidates for genetic regulation of blood pressure and were localized to rat Chromosomes (Chrs) 10 and 8 respectively. Genes for gastric H,K-ATPase alpha subunit (Atp4a). Class I alcohol dehydrogenase (Adh), and aldolase C (Aldoc) were localized to Chrs 1, 2, and 10 respectively, and thus provide more DNA markers for genetic mapping of quantitative trait loci for blood pressure on those chromosomes. Genes for alkaline phosphatase (Alp1) and cardiac AE-3 Cl^-/HCO₃ ^- exchanger (Ae3) were both localized to Chr 9. Genes for glutamate dehydrogenase (Glud) and gastric H,K-ATPase beta subunit (Atp4b) were localized to Chr 16. The ornithine decarboxylase (Odc) gene and ornithine decarboxylase pseudogene (Odcp) were localized to Chrs 6 and 11 respectively.     

Chromosomal assignment of microsatellite loci in cotton

Microsatellite markers or simple sequence repeats (SSRs) represent a new class of genetic markers for cotton (Gossypium sp.). Sixty-five SSR primer pairs were used to amplify 71 marker loci and genotype 13 monosomic and 27 monotelodisomic cotton cytogenetic stocks. Forty-two SSR loci were assigned to cotton chromosomes or chromosome arms. Thirty SSRs were not located to specific chromosomes in this study. Nineteen marker loci were shown to occur on the A subgenome and 11 on the D subgenome by screening accessions of G. herbaceum (2n = 2x = 26 = 2A1) and G. raimondii (2n = 2x = 26 = 2D5). The aneuploid stocks proved to be very powerful tools for localizing SSR markers to individual cotton chromosomes. Multiplex PCR bins of the SSR primers and semiautomated detection of the amplified products were optimized in this experiment. Thirteen multiplex PCR bins were optimized to contain an average of 4 SSR primer pairs per bin. This provides a protocol for high-throughput genotyping of cotton SSRs that improves the efficiency of genetic mapping and marker-assisted programs utilizing SSR markers.     

Chromosomal localization of six bovine microsatellite markers

Six lambda genomic clones containing polymorphic microsatellite (MS) markers were assigned to bovine chromosomes 1, 3, 5, 7, 13 and 24 by fluorescence in situ hybridization (FISH). Linkage data for four MS markers were presented earlier and linkage data for the remaining two on chromosome 7 and 24 are presented here. All assignments either orient or confirm the orientation of linkage groups relative to the centromere. A comparison of physical assignments and linkage intervals was possible on chromosome 5 (three loci, 38 cM) and 13 (two loci, 6 cM).     

Chromosomal assignment of porcine EAD, EAO, LPR and P3 genes by linkage analysis

A two-point linkage analysis was performed between blood group (14), allotype (8), polymorphic protein (11), DNA type I (2), and microsatellite (2) loci in Wild Boar x Pietrain and Meishan x Pietrain three-generation families. The following new pairwise linkages were detected: LPR-EAN (Z_max= 60.68, Ø= 0.055), EAD-GH1 (Z_max= 17.43, Ø= 0.246), EAO—P3 (Z_max= 15.81, Ø= 0.239), and P3—S0003 (Z_max= 5.43, Ø= 0.312). This study and published mapping data enabled the localization of LPR (LPR allotype) to chromosome 9, EAD (erythrocyte antigen D) to chromosome 12, and EAO (erythrocyte antigen O) and P3 (P3 allotype) to the q arm of chromosome 6 with gene order SOOO3—P3—EAO, EAO being the most distal.     

Chromosomal assignment of chicken clone contigs by extending the consensus linkage map

The bacterial artificial clone-based physical map for chicken plays an important role in the integration of the consensus linkage map and the whole-genome shotgun sequence. It also provides a valuable resource for clone selection within applications such as fluorescent in situ hybridization and positional cloning. However, a substantial number of clone contigs have not yet been assigned to a chromosomal location or have an ambiguous chromosome assignment. In this study, 86 single nucleotide polymorphism markers derived from 86 clones were mapped on the genetic map. These markers added anchoring information for 56 clone contigs and 13 individual clones, covering a total of 57,145 clones.     

Improved linkage map and thirty new microsatellite markers for rat Chromosome 10

An improved linkage map for rat Chromosome (Chr) 10 with two F₂ populations was constructed. Thirty new microsatellite markers were generated from a Chr 10-specific, small-insert genomic library and mapped to rat Chr 10. Among them were the rat homologs for the mouse gene for light and heavy chains of myeloperoxidase and human neurofibromatosis 1. Eight newly generated markers (D10Mco62, D10Mco63, D10Mco64, D10Mco65, D10Mco67, D10Mco68, D10Mco70, and D10Mco74) were mapped to the region of the rat Chr 10 blood pressure QTL. The availability of such markers may be instrumental in the search for genes responsible for the hypertension. Received: 13 July 1998 / Accepted: 9 September 1998     

Chromosomal assignment of seven genes on canine chromosomes by fluorescence in situ hybridization

Our group has developed more than 600 DNA markers to build a map of the canine genome. Of these markers, 125 correspond to genes (anchor loci). Here we report the first six autosomal genes assigned to canine chromosomes by fluorescence in situ hybridization (FISH), using cosmid DNA: adenine phosphoribosyl transferase on Chromosome (Chr) 3; creatine kinase muscle type on Chr 4; pyruvate kinase liver and red blood cell type on Chr 2; and colony-stimulating factor-1 receptor, glucose transporter protein-2, and tumor protein p53 on Chr 5. These assignments are based on the karytotype proposed by Stone and associates (Genome 34, 407, 1991) using high-resolution techniques. In addition, we have assigned the Menkes gene to the X Chr of the dog. Received: 18 August 1995 / Accepted: 17 November 1995     

Chromosomal assignment and deletion mapping of barley EST markers

From about 10000 PCR-based EST markers of barley we chose 1421 EST markers that were demonstrated to be amplified differently by PCR between wheat (Triticum aestivum cv. Chinese Spring) and barley (Hordeum vulgare cv. Betzes). We assigned them to the seven barley chromosomes (1H to 7H) by PCR analysis using a set of wheat-barley chromosome addition lines. We successfully assigned 701 (49.3%) EST markers to the barley chromosomes: 75 to 1H, 127 to 2H, 119 to 3H, 94 to 4H, 108 to 5H, 81 to 6H and 97 to 7H. By using a set of Betzes barley telosomic addition lines of Chinese Spring, we could successfully determine the chromosome-arm (S or L) location of at least 90% of the EST markers assigned to each barley chromosome. We conducted a trial mapping using 90 EST markers assigned to 7HS (49) or 7HL (41) and 19 wheat lines carrying 7H structural changes. More EST markers were found in the distal region than in the proximal region.     

常染色体显性遗传小眼球病与12个微卫星多态标志的初步连锁分析

本文报道了一个常染色体显性遗传小眼球的大家系,初步排除了此家系致病基因在目前已知位点(CHXl0、MITF、RX、MCOP、NN01、NN02)的可能,并探讨了与11号染色体上的微卫星DNA标志的连锁关系。采用聚合酶链(PCR)扩增微卫星DNA片段,扩增产物进行聚丙烯酰胺凝胶电泳,用银染显示结果;用MLINK连锁分析软件计算LOD值。结果显示,本家系小眼球致病基因与6个已知位点及ll号染色体上的微卫星DNA标志之间不存在连锁,提示此家系的致病位点目前尚未被定位。     

Towards linkage analysis with markers in linkage disequilibrium by graphical modelling

We review recent developments of MCMC integration methods for computations on graphical models for two applications in statistical genetics: modelling allelic association and pedigree based linkage analysis. We discuss and illustrate estimation of graphical models from haploid and diploid genotypes, and the importance of MCMC updating schemes beyond what is strictly necessary for irreducibility. We then outline an approach combining these methods to compute linkage statistics when alleles at the marker loci are in linkage disequilibrium. Other extensions suitable for analysis of SNP genotype data in pedigrees are also discussed and programs that implement these methods, and which are available from the author's web site, are described. We conclude with a discussion of how this still experimental approach might be further developed.     

AFLP linkage group assignment to the chromosomes of Allium cepa L. via monosomic addition lines

Two complete sets of Allium fistulosum L.– A. cepa monosomic addition lines (2n=2x+1=17) together with an AFLP linkage map based on a cross between A. cepa and A. roylei Stearn were used to re-evaluate the eight A. cepa linkage groups identified in the mapping study. The linkage groups could be assigned to individual, physical chromosomes. The low level of molecular homology between A. cepa and A. fistulosum enabled the identification of 186 amplified fragment length polymorphisms (AFLP™ markers) present in A. cepa and not in A. fistulosum with ten different primer combinations. With the monosomic addition lines the distribution of the markers over the eight chromosomes of A. cepa could be determined. Of these 186 AFLP markers 51 were absent in A. roylei and consequently used as markers in the mapping study (A. cepa ×A. roylei cross). Therefore, these 51 AFLP markers could be used to assign the eight A. cepa linkage groups identified in the mapping study to physical chromosomes. Seven isozyme and three CAPS markers were also included. Two of the linkage groups had to be split because they included two sets of markers corresponding to different chromosomes. A total of 20 (approx. 10%) of the A. cepa-specific AFLP markers were amplified in more than one type of the monosomic addition lines, suggesting unlinked duplications. The co-dominant isozyme and CAPS markers were used to identify the correspondence of linkage groupsoriginating from A. cepa or from A. roylei. Received: 16 April 1999 / Accepted: 13 August 1999     

Model-free linkage analysis with covariates confirms linkage of prostate cancer to chromosomes 1 and 4

As with many complex genetic diseases, genome scans for prostate cancer have given conflicting results, often failing to provide replication of previous findings. One factor contributing to the lack of consistency across studies is locus heterogeneity, which can weaken or even eliminate evidence for linkage that is present only in a subset of families. Currently, most analyses either fail to account for locus heterogeneity or attempt to account for it only by partitioning data sets into smaller and smaller portions. In the present study, we model locus heterogeneity among affected sib pairs with prostate cancer by including covariates in the linkage analysis that serve as surrogate measures of between-family linkage differences. The model is a modification of the Olson conditional logistic model for affected relative pairs. By including Gleason score, age at onset, male-to-male transmission, and/or number of affected first-degree family members as covariates, we detected linkage near three locations that were previously identified by linkage (1q24-25 [HPC1; LOD score 3.25, P=.00012], 1q42.2-43 [PCAP; LOD score 2.84, P=.0030], and 4q [LOD score 2.80, P=.00038]), near the androgen-receptor locus on Xq12-13 (AR; LOD score 3.06, P=.00053), and at five new locations (LOD score > 2.5). Without covariates, only a few weak-to-moderate linkage signals were found, none of which replicate findings of previous genome scans. We conclude that covariate-based linkage analysis greatly improves the likelihood that linked regions will be found by incorporation of information about heterogeneity within the sample.     

Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better.     

Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions

We mapped two loci for ADP-ribosylation factor homologues (ARF1, ARF2) and two loci for cysteine proteinase inhibitors (oryzacystatin-I and -II: OCI, OCII) by linkage analysis of restriction fragment length polymorphism loci in rice (Oryza sativa L.) genomic DNAs using their cDNAs as probes.Oc-1 andArf-2 were found to be closely located to each other on chromosome 1, whileOc-2 andArf-1,both found on chromosome 5, were also located close to each other. The map distances are about 2 cM in both pairs. In each chromosome, theArf locus was located about 27 cM from that of the aldolase gene (Ald-2 in chromosome 1 andAld-1 in chromosome 5). These three genes are in the same order,Ald-Arf-Oc, but in opposite orientations relative to the distal ends of the linkage group. The presence of two sets of three linked genes on chromosomes 1 and 5 strongly suggests a structural similarity of the blocks of the two chromosomes, which probably reflects duplication of the segment. A recent investigation by other workers has shown that these rice blocks correspond to two regions in maize chromosomes 8 and 6, that have previously been shown to share many duplicated nucleotide sequences. It is therefore very likely that the duplication of the region occurred before the divergence of rice and maize during the evolution of the subfamilies of the grasses (Gramineae). In view of a recently discovered possible structural similarity between the small GTP-binding protein superfamily, which includesArf andras proteins, and the cystatin family, the close linkage ofOc andArf loci found in the present study suggests a possible cluster of genes related to the small GTP-binding proteins.     

PCR multiplexed microsatellite panels to expedite canine genetic disease linkage analysis

Modern dog breeds possess large numbers of genetic diseases for which there are currently few candidate genes or diagnostic tests. Linkage of a microsatellite marker to a disease phenotype is often the only available tool to aid in the development of screening tests for disease carriers. Detection of linkage to a specific disease phenotype requires screening of large numbers of markers across known affected and unaffected animals. To establish high throughput genome scanning this study placed 100 canine microsatellite markers, arranged by fragment size and fluorescent dye label, into 12 PCR multiplexed panels. The highest degree of multiplexing was 11 markers per panel while the lowest was five markers per panel; each panel was run in one gel lane on automated DNA sequencers. Selection of the markers was based upon chromosomal or linkage group locations, degree of polymorphism, PCR multiplex compatibility and ease of interpretation. The marker set has an average spacing of 22.25 centiMorgan (cM). Marker polymorphism was evaluated across 28 American Kennel Club (AKC) recognized breeds. The utility of buccal swab vs. blood samples was also validated in this study as all template DNA was derived from swabs obtained and submitted by participating dog breeders and owners. The PCR multiplexed microsatellite panels and sampling method described in this report will provide investigators with a cost effective and expedient means of pursuing linkage studies of specific canine genetic diseases.     

Linkage mapping of fifty-eight new rat microsatellite markers

Fifty-eight new anonymous simple sequence repeats (SSR) were generated and mapped to various rat chromosomes. Among them two genes (rat homologs for human cadherin-14 and mouse fibroblast growth factor-related protein) were mapped on Chromosomes (Chrs) 2 and 11 respectively. The majority of markers were generated from a small insert genomic library specific to Chr 11, 13, 14, and 15. Twenty new markers were mapped to Chr 13, which is known to contain a blood pressure quantitative trait locus (QTL). Several approaches to obtain microsatellite markers are described. The protocols and newly generated markers should be useful for ongoing rat genome project. Received: 24 April 1998 / Accepted: 23 June 1998