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Home > Molecular Genetics of Autosomal Recessive Retinitis Pigmentosa in Consanguineous Pakistani Families

Molecular Genetics of Autosomal Recessive Retinitis Pigmentosa in Consanguineous Pakistani Families

Thesis Info

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Author

Sultan, Neelam

Program

PhD

Institute

University of Agriculture

City

Faisalabad

Province

Punjab

Country

Pakistan

Thesis Completing Year

2013

Thesis Completion Status

Completed

Subject

Chemistry

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/2602/1/2617S.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726709291

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It is an established fact that genetic disorders are one of the most important threats to human health. Several genetic disorders have been described clinically but their etiology is still unidentified and mysterious. The molecular basis for most of them is also unknown. With the advancement in the field of molecular biology different powerful techniques have been developed to understand the molecular basis of hereditary disorders. This would help in the subsequent identification of causative genes and mutations. Blindness and visual impairment due to genetic disorders are more common in developing countries like Pakistan than in developed countries. Retinitis pigmentosa (RP) is a major form of incurable blindness affecting one out of 4000 people worldwide. This highly heterogeneous disease has numerous inheritance patterns with the end result of partial to complete irreversible blindness. Another ocular disorder called fundus albipunctatus (FAP) also has some symptoms similar to RP like night blindness. In FAP this night blindness occurs in childhood but it remains stationary and day vision is not affected as in the case of RP where constriction of day vision occurs gradually. The present study was aimed to analyze families with ocular disorder. Families with autosomal recessive hereditary retinitis pigmentosa were used for mapping the disease genes and mutations. Seven consanguineous unrelated families (RP8, RP9, RP11, RP12, RP13, RP14 and RP16) with inherited RP were ascertained from different regions of Pakistan. The mode of inheritance in all families was inferred as autosomal recessive. The strategy used for this study was candidate gene approach. Linkage analysis was performed by PCR using STR (short tandem repeats) microsatellite markers for the known loci/genes. Direct sequencing (next generation sequencing) of the PCR products was carried out for identification of pathogenic mutations. In the present study linkage to crumbs homolog 1 (CRB1) gene on chromosome 1q31.3 was confirmed in family RP12. A novel missense mutation in human CRB1 gene has been found after sequence analysis of exon 6 of the CRB1 gene at nucleotide position xx 1459 (c.1459T>C). At protein level this mutation resulted in a substitution of proline for serine at amino acid 487 (p.Ser487Pro). It was inferred that mutation in this gene is strong enough to cause autosomal recessive retinitis pigmentosa. After the initial screening of autosomal recessive retinitis pigmentosa loci for family RP13, it was evident that there was no involvement of retinitis pigmentosal loci in the disease phenotype and it was a rare case of fundus albipunctatus, with RDH5 gene defect as the underlying cause. The family RP13 showed linkage to retinol dehydrogenase 5 (11-cis/9-cis) RDH5 gene after homozygosity mapping. A novel missense mutation at nucleotide position 602 (c.602 C>T) was identified after next generation sequencing of exon 4 of the RDH5 gene .This mutation resulted in substitution of phenylealanine for serine at amino acid 201 (p.Ser201Phe) of the RDH5 gene. The mutations in RDH5 gene are related to fundus albipunctatus (FAP). This is an exceptional form of stationary night blindness, it was deduced that mutation in this gene was responsible for autosomal recessive FAP in this family. The family RP14 showed exclusion to all the known genes and loci of RP. It was inferred that a novel locus/gene is responsible for causing RP in this family. The strongest candidate gene was RY2R which was earlier involved in cardiac disorder. Fine mapping in future would confirm the involvement of this gene in RP. Four families (RP8, RP9, RP11 and RP16) with some of the common selected loci/gene showed heterozygosity for the different combinations of the parental alleles in both affected and normal individuals after the linitial linkage. This heterozygosity confirmed exclusion to five selected known loci or genes on different chromosomes associated with autosomal recessive RP. Since many genes and loci are involved in this disease and genotyping using vertical polyacrylamide gel electrophoresis (PAGE) is a time taking and laborious method so commonly found genes in RP were initially selected which showed exclusion.On the basis of these exclusions it was inferred that a novel locus/gene or mutation is involved in these families which could be identified by SNP affymetrix array technique and sequencing. Many loci/genes/mutations are yet to be identified for this phenotype. It would be helpful in future to understand the disease prognosis. This research will also provide a smooth way for carrier screening, genetic counseling and prenatal diagnosis. This study may help gaining insight into the genetic causes underlying these disorders, to improve the clinical management and prevention.
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جیہڑا حسن ازل مہتاباں وچ

جیہڑا حسن ازل مہتاباں وچ
اوہو چمکے نور آفتاباں وچ
جیہڑی ہووے بھل چک بھل جانا
اساں لکھیا خط شتاباں وچ
جہیڑا وڑیا عشق قبیلے نوں
اوہ آگیا سدا بے تاباں وچ
سانوں مان نہ مال و دولت دا
روٹی اوہو جیہڑی رکاباں وچ
جس کان پنجاب دا ناں بنیا
پانی لبھدا نہیں چناباں وچ
نہیں شوق عمل دی داد کوئی
علم رہ گیا صرف کتاباں وچ

توں یار میرے دی پچھنا ایں
جیویں سوہنا پھل گلاباں وچ
کدی عشق دے قیدی نہیں چھٹ دے
اینویں گزری عمر عذاباں وچ
اینویں دکھاں درداں ماریا اے
جگر جیوں کر سیخ کباباں وچ
کسے دکھی دل دی کر خدمت
رب لبھدا نہیں محراباں وچ
ہو عقل حیران کھلوندی اے
کیا لذت عشق دے باباں وچ
جیہڑے مال خزانے ونڈ دے سن
اوہ صفتاں کدوں نواباں وچ
جہدی خاطر جگ جہان بنیا
پڑھاں لکھ سلام جناباں وچ
کدی پچھ حنیف نوں جا کے تے
کی لبھیا عشق نصاباں وچ

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Molecular Characterization of Resistant and Susceptible Sugarcane Saccharum Hybrids L. Cultivars to Smut Disease

Sugarcane (Saccharum hybrids L.) is a highly treasured perennial crop and happens to be the economic backbone of many countries including Pakistan. Apart from abiotic factors, diseases inflicted by fungal, bacterial or viral pathogens have the most damaging effect over the growth of sugarcane. Whip smut of sugarcane is one such disease caused by fungus Sporisorium scitamineum which posses a major threat to cane yield. The most effectual remedy to tackle the problem is to develop resistant cultivars that stand a far greater chance of surviving the disease outbreak.The advent of molecular marker techniques has massively enhanced the process of selection for disease resistance in sugarcane employed in breeding programs. The current work was a small contribution towards the same goal and exploited the potential of molecular markers to distinguish between smut resistant and susceptible cultivars of sugarcane. Moreover, identification of Resistance Gene Analogues (RGAs) was another strategy to understand the defense mechanism utilized by the crop. The initial screening experiments to differentiate between two completely resistant and two completely susceptible Pakistani cultivars involved detection of DNA polymorphism among the respective samples using 200 RAPD primers. Forty four of these primers turned out to be highly polymorphic, 20 of which produced trait specific loci in the four sugarcane genotypes. Furthermore, it was discovered that decamers A-20, E-05 and OPAV-10 produced 4 loci linked with resistant cultivars, while 4 loci were generated by primers B-17, OPAD-01, OPAD-13 and OPAX-14 specific to susceptible cultivars. However, primer A-09 amplified 2 markers of 1200 bp and 500 bp from resistant and susceptible cultivars, respectively. The disparity between resistant and susceptible cultivars was further highlighted when cluster analysis separated the two genotypes into two discrete groups. In order to detect RAPD markers associated with smut resistance phenotype in sugarcane, six pooled bulks of DNA from Pakistani cultivars (i.e. comprising 2 completely resistant, 2 completely susceptible, 4 moderately resistant and 4 moderately susceptible genotypes) and USA cultivar (i.e. containing 5 resistant and 5 susceptible clones of LCP85-84 F2 mapping population) were prepared. The screening of the six DNA bulks with 500 arbitrary decamers eventually revealed two RAPD markers (B-17 and I-20) linked with smut responses in Pakistani and USA cultivars, respectively. The marker B-17 produced a reproducible polymorphic fragment which appeared to cosegregate in repulsion with sugarcane smut resistance in Pakistani cultivars. On the other hand, RAPD decamer I-20 was tightly linked with resistance in smut resistant clones of USA cultivar LCP85-384 F2 population. Two Sequence Characterized Amplified Region (SCAR) markers were designed from the sequences of B-17 and I-20 products and were found to be specific to resistant cultivars of Pakistan and resistant clones of LCP85-384 F2 population, respectively. The SCAR marker developed from B-17 sequence was used to screen seven additional sugarcane cultivars of Pakistan with SCAR marker, verified the earlier findings by showing essentially similar results.In order to conduct further study, ten sets of oligonucleotides were designed to tag the nucleotide-binding site attached to leucine-rich repeat (NBS-LRR) domain of RGAs (resistance gene analogues) and other related sequences reported in the members of family Poaceae (maize, rice, sorghum and foxtail millet). The PCR amplifications of Pakistani and USA cultivars using these 10 primers resulted in the identification of three RGAs (MRGA3, MRGA5 and MRGA2) showing discriminating products with respect to smut resistance trait in sugarcane. The sequences of three isolated RGAs were analyzed and compared with that of documented R genes. The results of NCBI blast, multiple sequence alignment and phylogenetic analysis showed sequence homology of the three RGAs with reported R genes and RGA-like sequences. The final study was based on targeting sequences in sugarcane genome which may have a part to play in the resistance mechanism of plants against fungal attack. These sequences included a reported SCAR marker linked with covered smut resistance in barley and a canecystatin partial mRNA sequence. In a nut-shell, our study provided molecular basis to distinguish between smut resistant and smut susceptible sugarcane cultivars of both Pakistan and USA.