Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L. ) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Background: An adaptive mechanism in plant roots is initiated in the event of nitrogen and potassium deficiency, and it facilitates the active uptake of these elements in order to ensure plant growth and survival in stress conditions. Signaling and transduction of signals in response to changing nitrogen and potassium concentrations is a complex process, affected by interactions between various gene expression products, and often subjected to modifications. Results: In order to identify genotypic differences between phenotypes of two populations of recombinant inbred rye lines (153/79-1 x Ot1-3 and Ot0-6 x Ot1-3) in response to nutrition stress caused by nitrogen and potassium deficiency at the seedling stage, bulk segregant analysis was utilized. Identification of genotypic differences between and within pooled DNA samples involved 424 RAPD, 120 ISSR primers and 50 combinations of R-ISSR. Identified markers were sequenced and converted to SCAR, attributing to them unique ESTs annotations, and chromosomal ones to selected localizations. Significant relationships with the examined trait were described for nine and eight RAPD markers, four and five ISSR, one and three R-ISSR markers for population 153/79-1 x Ot1-3 and Ot0-6 x Ot1-3, respectively. Sequences identified for the rye genome were characterized by a uniqueness and a similarity to the sequence of aquaporin PIP1, a gene encoding protein related to the function of the transcription factor in plant response to iron deficiency and the putative ethylene-responsive transcription factor, cytosolic acetyl-CoA carboxylase, HvHKT1 transporter, as well as HCBT proteins. Conclusion: Identified molecular markers differentiating rye genotypes of extreme response of root system on nitrogen and potassium deficiency play a significant role in systemic plant response to stress, including stress caused by nitrogen and potassium deficiency. They may constitute a system facilitating selection, and together with the material they are described in, they may be a starting point for research on mechanisms of sensing and transduction of signal across the plant.

Glaucoma in Costa Rica. Initial approaches: [minireview]

Glaucoma is the second most frequent cause of irreversible blindness worldwide. Genetic factors have been implicated in the development of the disease. So far six loci (GLC1A-GLC1F) and two genes (TIGR/MYOC and OPTN) are involved in the development of juvenile (JOAG) and adult onset or chronic primary open angle glaucoma (COAG), while two loci (GLC3A,GLC3B) and one gene (CYP1B1) are known for primary congenital glaucoma (PCG). Here we summarize the results of the first genetic studies of glaucoma in Costa Rica. Nine families: 1 with JOAG, 1 with PCG and 7 with COAG were screened for mutations at the known genes. A 10 bp duplication, 1546-1555dupTCATGCCACC, at the CYP1B1 gene, causes, in homozygous state, glaucoma in the consanguineous PCG family. This mutation has been found in different countries and generates an early stop codon that termitates protein synthesis 140 amino acids earlier than the normal allele. In exon 1 of the T1GR/MYOC the innocuous Arg76Lys variant was found in two of the COAG families. In the OPTN gene two variants in the coding region (Thr34Thr, Met 98Lys) and 7 intronic changes were found in other Costa Rican glaucoma patients. One of the COAG families was chosen for a genome scan with 379 microsatellite markers and linkage analysis. LOD scores [quot ]suggestive[quot ] of linkage were obtained for several chromosomal regions. Evidence indicates that hereditary glaucoma in Costa Rica is highly heterogeneous and that further studies in the country will probably disclose some up to now unknown genes responsible for the disease.

Association of Polymorphic Regulatory Region of TIGR Gene with Glaucoma

PURPOSE: To identify the polymorphism in the regulatory region of trabecular meshwork inducible glucocorticoid response(TIGR) gene and evaluate the association of it with glaucoma. METHODS: 5'regulatory region of TIGR gene of 101 normal persons and 91 unrelated glaucoma patients were analyzed by DNA sequencing and restriction enzyme digestion. To know the possible effects of the polymorphism on the transcription rate of TIGR gene, electrophoretic mobility shift assay and luciferase reporter gene assay were performed with cultured cells, and their extracts of trabecular meshwork and ciliary body in which the gene was expressed. RESULTS: Of the 480 bp examined, G to A transition(G-241A) located at 241 bp upstream from transcription start site was identified and its frequency of occurrence was proved to be higher in steroid induced glaucoma patients(18.9%) compared with that in normal population(8.9%), POAG(8.3%) and normal tension glaucoma patients(6.7%, P<0.05). In mobility shift assay, the G-241A probe was proved to have affinity to some DNA-binding proteins and its affinity was revealed to be two times stronger than that of normal sequence. The luciferase activities, however, were observed to be similar in cells transfected with vectors having normal promoter sequence or G-241A containing one. CONCLUSION: The result suggest that G-241A itself is not a cause of steroid-induced glaucoma but is in linkage disequilibrium with the actual causes of the disease.

Association of(G-T)n Dinucleotide Repeat Polymorphism of 5'-Flanking Region of TIGR/MYOC with Normal-Tension Glaucoma and Steroid-Induced Glaucoma

PURPOSE: We investigated whether TIGR/MYOC, a candidate gene for the primary open angle glaucoma(POAG) is also involved in the pathogenesis of normal tension glaucoma(NTG) and steroid-induced glau-coma(SIG). METHODS: Genomic DNA was extracted from the peripheral blood samples collected from 72 normal volunteers and 60 POAG, 47 NTG, 61 SIG patients. The genotype distribution of dinucleotide repeat polymorphism, (G-T)n microsatellite located 249 bp upstream of transcription start site was determined by direct sequencing of the Polymerase Chain Reaction(PCR) product. RESULTS: We found 6 alleles in the (G-T)n microsatellite of TIGR/MYOC ranging from 12 to 17, which differ slightly from that of previous reports. There was no obvious difference in the genotype distribution and allele frequency between the POAG group and the control group. However, a significant association of the microsatellite marker with SIG and, to a lesser extent, with NTG was observed. A significant increase in the frequency of (G-T)13/(G-T)13 genotype and a concomitant decrease in the frequency of (G-T)13/(G-T)14 genotype was seen in both the NTG and SIG group compared to that of the control group. In the SIG group, a significant decrease in the frequency of (G-T)14 allele was also observed compared to the control group, although the decrease did not contribute to the increase in the frequency of the allele. CONCLUSIONS: These findings suggest that a polymorphism in the 5 flanking region of the TIGR/MYOC is associated with patients with NTG and SIG.

Analysis of TIGR Gene Mutation in Glaucoma

In the present study, we have evaluated the mutations of the TIGR[Trabecular meshwork Inducible Glucocorticoid Response] gene, which has been reported to be associated with the glaucoma, in primary open angle glaucoma[POAG], normal tension glaucoma[NTG], and steroid-induced glaucoma[SIG]. We have analyzed the TIGR gene in 18 members of 3 families affected with POAG, 28 familially unrelated patients with POAG, 32 patients with NTG, 30 patients with SIG, and 45 normal subjects.DNA was extracted from the blood samples of each patient, exon 2 and exon 3 of the TIGR gene were amplified by PCR and DNA sequencing was performed.No mutation was found in familially unrelated patients with POAG.Two kinds of mutation[Ser341Pro, Gly367Arg]were found in 3 families affected with POAG.Another mutations, located in exon 3, were detected in one NTG patient and in one SIG patient, but they were silent substitution.Identification of TIGR gene mutation will provide early diagnosis of POAG before irreversible visual impairment develops in cases of positive family history of glaucoma.