Publications by authors named "Shoaib Ur Rehman"

11 Publications

  • Page 1 of 1

Incredible Role of Osmotic Adjustment in Grain Yield Sustainability under Water Scarcity Conditions in Wheat ( L.).

Plants (Basel) 2020 Sep 15;9(9). Epub 2020 Sep 15.

Institute of Biological Sciences, University of Talca, Talca 3460000, Chile.

Interrogations of local germplasm and landraces can offer a foundation and genetic basis for drought tolerance in wheat. Potential of drought tolerance in a panel of 30 wheat genotypes including varieties, local landraces, and wild crosses were explored under drought stress (DS) and well-watered (WW) conditions. Considerable variation for an osmotic adjustment (OA) and yield components, coupled with genotype and environment interaction was observed, which indicates the differential potential of wheat genotypes under both conditions. Reduction in yield per plant (YP), thousand kernel weight (TKW), and induction of OA was detected. Correlation analysis revealed a strong positive association of YP with directly contributing yield components under both environments, indicating the impotence of these traits as a selection-criteria for the screening of drought-tolerant genotypes for drylands worldwide. Subsequently, the association of OA with TKW which contributes directly to YP, indicates that wheat attains OA to extract more water from the soil under low water-potential. Genotypes including WC-4, WC-8 and LLR-29 showed more TKW under both conditions, among them; LLR-29 also has maximum OA and batter yield comparatively. Result provides insight into the role of OA in plant yield sustainability under DS. In this study, we figure out the concept of OA and its incredible role in sustainable plant yield in wheat.
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http://dx.doi.org/10.3390/plants9091208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569908PMC
September 2020

Molecular Heterogeneity of β-Thalassemia in the Kohat Region, Khyber Pakhtunkhwa Province, Pakistan.

Hemoglobin 2020 Jan 21;44(1):37-41. Epub 2020 Feb 21.

Department of Forensic Medicine, Federal Medical and Dental College, Islamabad, Pakistan.

The present study was intended to report the incidence of the most frequently occurring β-thalassemia (β-thal) mutations in the Kohat region [Khyber Pakhtunkhwa (KP) Province, Pakistan], their inheritance pattern in patients, and consanguinity in the parents. Moreover, this study could provide valuable information regarding thalassemia diagnoses such as prenatal diagnosis (PND), genetic counseling and carrier screening for controlling the affected births in the population. During this study, 160 peripheral blood samples of affected patients, their parents and siblings were collected from 25 discrete families having at least one child needing regular blood transfusions from different areas of the Kohat region. β-Thalassemia mutations found in the population were screened the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). A total of 320 alleles was evaluated for the presence of six β-thal mutations. Of these six β-thal mutations, the frameshift codons (FSC) 8/9 (+G) (: c.27_28insG) was found to be the most frequent in the studied population, and more interestingly, followed by IVS-I-5 (G>C) (: c.92+5G>C) and FSC 5 (-CT) (: c.17_18delCT). The findings of the present study show differences with previous results from other regions of the Pashtun population, which demarcates the heterogeneity in mutations found in the Pashtun ethnicity. These observations may help in implementing parental meetings about disease recurrence in future, large scale mutation screening and PND for the population of the Kohat region and also the whole Pashtun ethnicity.
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http://dx.doi.org/10.1080/03630269.2019.1709206DOI Listing
January 2020

Fine mapping of MRT9 locus through genome wide homozygosity mapping in a consanguineous Pakistani family.

J Pak Med Assoc 2019 Dec;69(12):1903-1906

Department of Biotechnology, University of Science and Technology, Bannu.

Intellectual disability (ID) or Mental Retardation (MR) is a broad term, which occupies several medical directions. It is extremely heterogeneous and has about reported 25,000 genes of which half of the genes expression have been found in the brain. Intellectual disability causes severe disability and has a worldwide prevalence of around 2% while autosomal recessive form of ID causes almost 25% of all non syndromic (NS) ID cases. A consanguineous family (who will be referred as) MR7 with phenotype of ID was sampled in Swat region of Pakistan. All affected individuals in the family were observed having a low IQ and cognitive mutilation with no sign of biochemical, skeletal or neurological abnormalities. Their dc-ribonucleic acid (DNA) was extracted and subjected to STS (Single tagged sequence) marker analyses which showed exclusion of all known non syndromic autosomal recessive (NS-AR) ID genes. In the family MR7, autozygosity mapping was performed by microarray single-nucleotide polymorphism analysis in all the collected samples, for a close examination of the homozygous region in all the affected however no homozygosity was observed for the normal parent. In this consanguineous family of Pakistan, autozygosity mapping showed linkage interval (chr14: 30,294,526- 32,106,658) overlapping with already reported MRT9 locus (chr14:26,578,608-32,780,288) for NS- ARID.
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http://dx.doi.org/10.5455/JPMA.286929.DOI Listing
December 2019

The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli.

Plant Cell Physiol 2020 Feb;61(2):225-242

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China.

Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.
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http://dx.doi.org/10.1093/pcp/pcz230DOI Listing
February 2020

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits.

Theor Appl Genet 2019 Apr 5;132(4):907-919. Epub 2018 Dec 5.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Key Message: We developed breeder-friendly high-throughput and cost-effective KASP marker for marker-assisted selection for grain yield related traits in wheat. Plant-specific protein kinase, SnRK2s, is a major family of signaling genes associated with metabolic regulations, nutrient utilization and response to external stimuli. In the present study, three copies of TaSnRK2.9 were isolated from chromosomes 5A, 5B and 5D of wheat (Triticum aestivum L.). The coding regions of TaSnRK2.9-5A, TaSnRK2.9-5B and promoter region of TaSnRK2.9-5D were investigated for sequence polymorphism. Single nucleotide polymorphisms (SNPs) were identified for TaSnRK2.9-5A, while no polymorphism was identified in TaSnRK2.9-5B and TaSnRK2.9-5D. The nucleotide sequence of TaSnRK2.9-5A consisted of 2180 bp having eight introns and nine exons. Three SNPs were identified at 308 nt, 698 nt and 1700 nt. For high-throughput genotyping, two kompetitive allele-specific PCR (KASP) markers were developed. Four haplotypes Hap-5A-1, Hap-5A-2, Hap-5A-3 and Hap-5A-4 were detected in wheat populations collected from China, Europe and Pakistan. Association analysis was performed with mixed linear model in TASSEL (v 5.0). The results indicated that Hap-5A-1/2 of TaSnRK2.9-5A were significantly associated with high thousand kernel weight, while Hap-5A-4 with high grains per spike. Overexpressing transgenic rice also showed higher grains per spike which is in accordance with association analysis results. Geographic distribution and allelic frequency indicted that the favored haplotypes were positively selected in Chinese (Hap-5A-1/2), Pakistani (Hap-5A-1), east European (Hap-5A-1) and west European (Hap-5A-4) wheat breeding. The results suggest that the developed KASP markers can be utilized in yield improvement by marker-assisted selection in wheat breeding.
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http://dx.doi.org/10.1007/s00122-018-3247-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449320PMC
April 2019

Molecular Characterization of β-Thalassemia Mutations Via the Amplification Refractory Mutation System-Polymerase Chain Reaction Method at the North Waziristan Agency, Pakistan.

Hemoglobin 2018 Mar;42(2):91-95

a Department of Biotechnology , University of Science and Technology Bannu (USTB) , Bannu , Khyber Pakhtunkhwa Province , Pakistan.

β-Thalassemia (β-thal) is a monogenic disease characterized by mutations on the HBB gene, affecting the production of globin that results in hypochromic and microcytic anemia. The aim of this study was to determine the prevalence of six common β-thal mutations, and their frequency and inheritance pattern in affected populations of North Waziristan Agency, Pakistan. In this study, 130 blood samples from 37 unrelated β-thalassemic families having a minimum of one transfusion-dependent child with β-thal major (β-TM), were retrieved either from the Thalassaemia Centre for Women and Children Hospital Bannu or their home towns situated in Noth Waziristan Agency. All samples were analyzed by the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) using six allele-specific primers for the presence of the six β-thal mutations common in the Pakistani population. Of the six common mutations, our study demonstrated five HBB mutations comprising HBB: c.27_28insG, HBB: c.92+5G>C, HBB: c.126_129delCTTT, HBB: c.92+1G>T and HBB: c.17_18delCT from the families studied, while mutation HBB: c.47G>A [codon 15 (G>A)] was not detected in any of the studied families. Furthermore, the HBB: c.27_28insG and HBB: c.92+5G>C were noted to be the most common with frequencies of 42.85 and 31.42%, respectively. The findings of the present study may be useful in launching carrier screening and prenatal diagnosis (PND) programs by screening analyzed and other unanalyzed affected families for the possible presence of common mutations through the ARMS-PCR technique that will help to control the disease.
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http://dx.doi.org/10.1080/03630269.2018.1487308DOI Listing
March 2018

Investigation of molecular heterogeneity of β-thalassemia disorder in District Charsadda of Pakistan.

Pak J Med Sci 2016 Mar-Apr;32(2):491-4

Dr. Tabassum Yaseen, PhD (Pakistan). Department of Botany, Bacha Khan University Charsadda, Khyber Pakhtunkhwa, Pakistan.

Objective: Thalassemia is blood related disease which arises from the reduced level of hemoglobin in red blood cells (RBC), a protein responsible for carrying oxygen inside the body. Considering its widespread occurrence in developing countries like Pakistan, this study aims to investigate the common molecular anomalies of the beta thalassemia disease in district Charsadda, Khyber Pakhtunkhwa.

Methods: This work was done at Abdul Wali Khan University (AWKU) Mardan, Khyber Pakhtunkhwa, Pakistan. The work was performed on the blood samples collected from the patients and their families with beta thalassemia major (n = 13 families) belonged to District Charsadda. The collected blood samples were analyzed for presence of six known mutations with the help of polymerase cha in reaction technique i.e. amplification of refractory mutation system.

Results: Our Study reports six known mutations (IVS-1-5, FSC 8/9, CD 41/42, IVS-1-1, CD 15 and FSC-5) accounting for about 90% of total beta thalassemia genes in this country. Among the reported mutations, IVS 1-5 was the most prevalent beta thalassemia gene in patients belonging to District Charsadda.

Conclusion: The results and findings of the current study may help in accessing the frequency of these common mutations and in initiating pre-natal diagnosis programme in Pakistan.
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http://dx.doi.org/10.12669/pjms.322.9415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859051PMC
May 2016

GeneXpert assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens from a high TB endemic area of Pakistan.

Microb Pathog 2016 Jun 23;95:82-85. Epub 2016 Mar 23.

Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan. Electronic address:

Tuberculosis is a global health problem, and its early diagnosis is the ultimate strategy for prevention and control. The current study was undertaken to evaluate conventional and molecular diagnostic assays for the detection of mycobacteria in pulmonary tuberculosis (TB) patients from Khyber Pakhtunkhwa region of Pakistan. A total of 259 clinically suspected patients of TB were processed for Zeihl Neelsen (ZN) microscopy, BACTEC MGIT liquid culture and GeneXpert assay. Among 259 samples, 28 (10.81%) were positive for acid fast bacilli (AFB) on ZN microscopy. In liquid culture, the growth of mycobacterium species was obtained in 36 (13.89%) samples while the GeneXpert assay detected Mycobacterium tuberculosis (MTB) in 49 (18.91%) samples. Detection rate of MTB was significantly high (n = 49, p < 0.0095) on GeneXpert as compared to microscopy (n = 28); however no significant difference (p = 0.1230) was observed on GeneXpert (n = 49) and culture (n = 36) based detection of MTB. The strength of agreement between GeneXpert and microscopy was also poor (Kappa value < 0.114, 95% CI: -0.72 - 0.301) which support our results. MTB detection rate among female was high as compared to male TB patients while in age wise, the age group 55-64 years has almost high detection rate on microscopy, culture and GeneXpert assay. Findings of the present study highlighted that GeneXpert is more efficient tool for timely diagnosis and proper TB control in high TB endemic area.
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http://dx.doi.org/10.1016/j.micpath.2016.03.005DOI Listing
June 2016

Hypomorphic mutations in PGAP2, encoding a GPI-anchor-remodeling protein, cause autosomal-recessive intellectual disability.

Am J Hum Genet 2013 Apr;92(4):575-83

Wilhelm Johannsen Centre for Functional Genome Research, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark.

PGAP2 encodes a protein involved in remodeling the glycosylphosphatidylinositol (GPI) anchor in the Golgi apparatus. After synthesis in the endoplasmic reticulum (ER), GPI anchors are transferred to the proteins and are remodeled while transported through the Golgi to the cell membrane. Germline mutations in six genes (PIGA, PIGL, PIGM, PIGV, PIGN, and PIGO) in the ER-located part of the GPI-anchor-biosynthesis pathway have been reported, and all are associated with phenotypes extending from malformation and lethality to severe intellectual disability, epilepsy, minor dysmorphisms, and elevated alkaline phosphatase (ALP). We performed autozygosity mapping and ultra-deep sequencing followed by stringent filtering and identified two homozygous PGAP2 alterations, p.Tyr99Cys and p.Arg177Pro, in seven offspring with nonspecific autosomal-recessive intellectual disability from two consanguineous families. Rescue experiments with the altered proteins in PGAP2-deficient Chinese hamster ovary cell lines showed less expression of cell-surface GPI-anchored proteins DAF and CD59 than of the wild-type protein, substantiating the pathogenicity of the identified alterations. Furthermore, we observed a full rescue when we used strong promoters before the mutant cDNAs, suggesting a hypomorphic effect of the mutations. We report on alterations in the Golgi-located part of the GPI-anchor-biosynthesis pathway and extend the phenotypic spectrum of the GPI-anchor deficiencies to isolated intellectual disability with elevated ALP. GPI-anchor deficiencies can be interpreted within the concept of a disease family, and we propose that the severity of the phenotype is dependent on the location of the altered protein in the biosynthesis chain.
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http://dx.doi.org/10.1016/j.ajhg.2013.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617372PMC
April 2013

Autozygosity mapping of a large consanguineous Pakistani family reveals a novel non-syndromic autosomal recessive mental retardation locus on 11p15-tel.

Neurogenetics 2011 Aug 4;12(3):247-51. Epub 2011 Jun 4.

Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology & Genetic Engineering, Faisalabad, Pakistan.

Autosomal recessive inherited mental retardation is an extremely heterogeneous disease and accounts for approximately 25% of all non-syndromic mental retardation cases. Autozygosity mapping of a large consanguineous Pakistani family revealed a novel locus for non-syndromic autosomal recessive mental retardation (NS-ARMR). The affected individuals showed low IQ and cognitive impairment without any neurological, skeletal, and biochemical abnormalities. All known NS-ARMR genes were excluded by STS markers, so autozygosity mapping by microarray single-nucleotide polymorphism (SNP) analysis were done in all sampled individuals in the family. The nuclear central loop in the five generation family showed homozygosity for a 6-Mb telomeric region on 11p15, whereas all other linkage regions were excluded by calculation of logarithm of odds (LOD) for the SNP microarray data. A maximum LOD score of Z = 3.31 was calculated for the mapped region. These results suggest a novel genetic locus, MRT17, for NS-ARMR.
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http://dx.doi.org/10.1007/s10048-011-0286-5DOI Listing
August 2011

Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS.

Eur J Hum Genet 2010 Jun 13;18(6):733-6. Epub 2010 Jan 13.

Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan.

A cis-regulatory sequence also known as zone of polarizing activity (ZPA) regulatory sequence (ZRS) located in intron 5 of LMBR1 is essential for expression of sonic hedgehog (SHH) in the developing posterior limb bud mesenchyme. Even though many point mutations causing preaxial duplication defects have been reported in ZRS, the underlying regulatory mechanism is still unknown. In this study, we analyzed the effect on transcription factor binding of a novel ZRS point mutation (463T>G) in a Pakistani family with preaxial polydactyly and triphalangeal thumb. Electrophoretical mobility shift assay demonstrated a marked difference between wild-type and the mutant probe, which uniquely bound one or several transcription factors extracted from Caco-2 cells. This finding supports a model in which ectopic anterior SHH expression in the developing limb results from abnormal binding of one or more transcription factors to the mutant sequence.
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http://dx.doi.org/10.1038/ejhg.2009.225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987342PMC
June 2010