Betaine-homocysteine methyltransferase expression in porcine and human tissues and chromosomal localization of the human gene.

We have prepared antibodies against porcine liver betaine-homocysteine methyltransferase (BHMT; EC 2.1.1.5) and recently cloned cDNAs encoding the porcine and human liver enzymes. Porcine tissues were evaluated for BHMT expression by measuring catalytic activity and Western analysis. Liver and kidney were the only organs tested that had immunodetectable levels of BHMT, and these organs expressed high levels of enzyme activity. BHMT was expressed in the kidney cortex and not the medulla. Porcine pancreas, brain, heart, lung, and spleen were devoid of BHMT activity and immunodetectable protein. Human tissues were tested for BHMT expression by Northern analysis. Human liver and kidney were the only organs tested that expressed BHMT mRNA. Human pancreas, brain, heart, skeletal muscle, spleen, and placenta were devoid of BHMT mRNA. The human BHMT gene has been mapped to chromosome 5q13.1-q15.

Identification of a gene that causes primary open angle glaucoma.

Glaucoma is a major cause of blindness and is characterized by progressive degeneration of the optic nerve and is usually associated with elevated intraocular pressure. Analyses of sequence tagged site (STS) content and haplotype sharing between families affected with chromosome 1q-linked open angle glaucoma (GLC1A) were used to prioritize candidate genes for mutation screening. A gene encoding a trabecular meshwork protein (TIGR) mapped to the narrowest disease interval by STS content and radiation hybrid mapping. Thirteen glaucoma patients were found to have one of three mutations in this gene (3.9 percent of the population studied). One of these mutations was also found in a control individual (0.2 percent). Identification of these mutations will aid in early diagnosis, which is essential for optimal application of existing therapies.

Fine mapping of the autosomal dominant juvenile open angle glaucoma (GLC1A) region and evaluation of candidate genes.

Juvenile Open Angle Glaucoma (GLC1A) is an autosomal optic neuropathy that has been localized previously to chromosome 1q. Here we report the fine mapping of the disease region using YACs and a high density of polymorphic microsatellite markers. This study utilized two large JOAG pedigrees genotyped at 36 loci from chromosome 1q21-q31 to refine the GLC1A locus to a approximately 3-cM region flanked by YAC-derived microsatellite markers D1S3665 and D1S3664. The candidate genes LAMC1, NPR1, and CNR2 were excluded from the region by linkage. Four other genes, SELE, SELL, TXGP1, and APT1LG1, were determined to lie within the critical region through YAC content and linkage mapping. The YAC-STS content map of the critical region provides the groundwork for the construction of a transcription map and the identification of the disease-causing gene.

Chromosomal assignment of 2900 tri- and tetranucleotide repeat markers using NIGMS somatic cell hybrid panel 2.

Two thousand nine hundred and thirty-one tri- and tetranucleotide short tandem repeat polymorphisms (STRPs) developed by the Cooperative Human Linkage Center were assigned to chromosomes using the NIGMS somatic cell hybrid mapping panel 2 and an efficient pooling strategy. Approximately 82% of all STRPs tested were assigned by this method, with 96.7% accuracy. Many of the single chromosome cell lines contained portions of additional chromosomes, confirming previous reports. The cell lines for chromosomes 6, 14, and 20 contained extensive portions of other chromosomes. Five previously unreported chromosomal contaminants were identified and are reported. A new pooling strategy was designed to minimize ambiguous assignments.

A collection of tri- and tetranucleotide repeat markers used to generate high quality, high resolution human genome-wide linkage maps.

We report a collection of tri- and tetranucleotide repeat sequence polymorphic markers used to construct genome-wide human linkage maps. Using a strategy of marker selection to create libraries highly enriched for the presence of specific tandem repeat elements, we have developed over 2000 high heterozygosity, easy-to-use tri- and tetranucleotide short tandem repeat polymorphisms (STRPs). To date, over 1300 of these markers have been genotyped on the CEPH reference families. Additional STRPs were assigned to chromosomes using human monochromosomal somatic cell hybrids. The linkage maps constructed with these markers have been integrated with other CEPH genotypes into a comprehensive high density linkage map. These STRPs have been shown to be robust for genotyping in a variety of laboratories using a variety of methods. The high quality of these STRPs makes them ideal candidates for use in genome-wide linkage searches. The integration of these markers with physical mapping reagents and other genetic markers will create a resource for moving from genome-wide linkage searches to rapid sublocalization of disease loci.

Linkage of autosomal dominant iris hypoplasia to the region of the Rieger syndrome locus (4q25).

Iris hypoplasia is an autosomal dominant disorder which is frequently associated with glaucoma. This glaucoma is usually resistant to medical therapy and can lead to blindness. A large family of Scandinavian descent with a five generation history of iris hypoplasia was studied. Fifteen individuals were found to have iris hypoplasia, nine of whom had associated glaucoma. In an attempt to identify the chromosomal location of the disease-causing gene, this family was genotyped with short tandem repeat polymorphisms (STRPs) known to map to loci previously associated with glaucoma. The juvenile glaucoma locus at 1q25 and a congenital glaucoma locus on 6p were both statistically excluded. However, significant linkage was demonstrated at the Rieger syndrome locus at 4q25. The highest observed LOD score was 3.70 (theta = 0) and was obtained with marker D4S1616. Three recombination events were observed in affected individuals that together demonstrate that the disease-causing gene lies between markers ACT3E03 and D4S1611, an interval of approximately 7 cM. These results suggest that autosomal dominant iris hypoplasia and Rieger syndrome are allelic.

Linkage of posterior polymorphous corneal dystrophy to 20q11.

Posterior polymorphous dystrophy (PPMD) is an autosomal dominant disorder of the cornea that is clinically recognized by the presence of vesicles on the endothelial surface of the cornea. The corneal endothelium is normally a single layer of cells that lose their mitotic potential after development is complete. In PPMD, the endothelium is often multi-layered and has several other characteristics of an epithelium including the presence of desmosomes, tonofilaments, and microvilli. These abnormal cells retain their ability to divide and extend onto the trabecular meshwork to cause glaucoma in up to 40% of cases. A large family with 21 members affected with PPMD was genotyped with short tandem repeat polymorphisms distributed across the autosomal genome. Linkage was established with markers on the long arm of chromosome 20. The highest observed LOD score was 5.54 (theta = 0) with marker D20S45. Analysis of recombination events in four affected individuals revealed that the disease gene lies within a 30cM interval between markers D20S98 and D20S108.

Identification of a Bardet-Biedl syndrome locus on chromosome 3 and evaluation of an efficient approach to homozygosity mapping.

Bardet-Biedl syndrome is an autosomal recessive disorder characterized by mental retardation, obesity, retinitis pigmentosa, polydactyly and hypogonadism. Individuals with this disorder also have an increased incidence of hypertension, diabetes mellitus, and renal and cardiac anomalies. We previously identified a locus on chromosome 16 causing this disorder, and provided evidence that Bardet-Biedl syndrome is heterogeneous. In this study, we identify another Bardet-Biedl syndrome locus on chromosome 3 and confirm the non-allelic heterogeneity of this disorder in Bedouin populations. In addition, we demonstrate the feasibility of using pooled DNA samples from members of large kindreds as an efficient approach to homozygosity mapping.

The Booroola fecundity (FecB) gene maps to sheep chromosome 6.

The Booroola (FecB) mutation in sheep is linked to markers from a region of syntenic homology to human chromosome HSA4q, but the chromosomal location in sheep has not been determined. Analysis of linkage in Booroola half-sib pedigrees and 17 full-sib families identified genetic linkage between platelet-derived growth factor receptor-alpha (PDGFRA) and alpha s1-casein (CSN1S1) at 12 cM (Zmax = 9.14) and between PDGFRA and the microsatellite markers BM143 and OarHH55 (Zmax = 6.28 and 3.83, respectively). The microsatellite markers OarAE101 and BM143 and genes from the linkage group (PDGFRA, SPP1, and EGF) were mapped in a partial sheep x hamster somatic cell hybrid panel. All markers identified bands specific to somatic cell hybrids containing the sheep chromosome t1 (rob6;24) or t1q (chromosome 6). In sheep the casein genes alpha s1 (CSN1S1), alpha s2 (CSN1S2), beta (CSN2), and kappa (CSN3) are tightly linked, and CSN2 has been mapped to sheep chromosome 6q23-q31. We conclude that the Booroola mutation is located within a conserved syntenic group that maps to sheep chromosome 6.

Sheep linkage mapping: nineteen linkage groups derived from the analysis of paternal half-sib families.

Nineteen linkage groups containing a total of 52 markers have been identified in the sheep genome after typing large paternal half-sib families. The linkage groups range in size from 2 markers showing no recombination to a group containing 6 markers covering approximately 30 cM of the sheep genome. Thirteen of the groups have been assigned to a sheep chromosome. Three groups contain markers from bovine syntenic groups U2, U7 and U29, and one other group contains a marker that has been mapped only in humans. The remaining three groups are unassigned. This information will provide a useful foundation for a genetic linkage map of sheep.

Linkage of bovine erythrocyte antigen loci B, C, L, S, Z, R' and T' and the serum protein loci post-transferrin 2 (PTF 2), vitamin D binding protein (GC) and albumin (ALB) to DNA microsatellite markers.

Seven bovine erythrocyte antigen loci and three serum protein loci were tentatively assigned to chromosomes or synteny groups by linkage analysis to previously assigned microsatellite DNA markers. The erythrocyte antigen locus EAB was mapped to synteny group U27; EAC to chromosome 18, synteny group U9; EAL to chromosome 3, synteny group U6; EAS to chromosome 21, synteny group U4; EAZ to chromosome 10, synteny group U5; EAR' to chromosome 16, synteny group U1; and EAT' to chromosome 19, synteny group U21. The vitamin D binding protein (GC) and albumin (ALB) loci were assigned to chromosome 6, synteny group U15 and post-transferrin 2 (PTF 2) to chromosome 19, synteny group U21.

A genetic linkage map for cattle.

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).

A conceptual database model for genomic research.

We describe a conceptual model for genome databases that facilitates the process of building, maintaining, and disseminating physically anchored genetic linkage maps. The model has been implemented as a relational database at the Roman L. Hruska U.S. Meat Animal Research Center (MARC). Development of consensus maps using disparate data from different reference pedigrees or laboratories is supported. The model is of use to quantitative and population geneticists interested in loci that affect phenotypes and marker-assisted selection, and it is sufficiently flexible for centralized, species genome databases facilitating comparative mapping. The MARC genome database is used to assemble, maintain, and disseminate physically anchored genetic linkage maps for cattle, swine, and sheep currently based on more than 100,000 genotypes from 1,000 markers. Integrated with linkage analysis software, this database permits frequent updates of physically anchored genetic linkage maps.