National Institute for Genomics and Advanced Biotechnology

Islamabad, Pakistan

National Institute for Genomics and Advanced Biotechnology

Islamabad, Pakistan
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Spielman D.J.,International Food Policy Research Institute | Zaidi F.,International Food Policy Research Institute | Zambrano P.,International Food Policy Research Institute | Khan A.A.,Muhammad Nawaz Shareef University of Agriculture | And 8 more authors.
PLoS ONE | Year: 2017

Genetically modified, insect-resistant Bacillus thuringiensis (Bt) cotton is cultivated extensively in Pakistan. Past studies, however, have raised concerns about the prevalence of Bt cotton varieties possessing weak or nonperforming insect-resistance traits conferred by the cry gene. We examine this issue using data drawn from a representative sample of cotton- growing households that were surveyed in six agroclimatic zones spanning 28 districts in Pakistan in 2013, as well as measurements of Cry protein levels in cotton tissue samples collected from the sampled households' main fields. The resultant dataset combines information from 593 sampled households with corresponding plant tissue diagnostics from 70 days after sowing, as well as information from 589 sampled households with corresponding diagnostics from 120 days after sowing. Our analysis indicates that 11 percent of farmers believed they were cultivating Bt cotton when, in fact, the Cry toxin was not present in the tested tissue at 70 days after sowing (i.e., a Type I error). The analysis further indicates that 5 percent of farmers believed they were cultivating non-Bt cotton when, in fact, the Cry toxin was present in the tested tissue (i.e., a Type II error). In addition, 17 percent of all sampled farmers were uncertain whether or not they were cultivating Bt cotton. Overall, 33 percent of farmers either did not know or were mistaken in their beliefs about the presence of the cry gene in the cotton they cultivated. Results also indicate that toxic protein levels in the plant tissue samples occurred below threshold levels for lethality in a significant percentage of cases, although these measurements may also be affected by factors related to tissue sample collection, handling, storage, and testing procedures. Nonetheless, results strongly suggest wide variability both in farmers' beliefs and in gene expression. Such variability has implications for policy and regulation in Pakistan's transgenic cotton seed market. © 2017 Spielman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Ijaz A.,The Water Council | Ijaz A.,University of Gujrat | Anwar Z.,University of Gujrat | Irshad M.,University of Gujrat | And 6 more authors.
Romanian Biotechnological Letters | Year: 2014

Bio-conversion of cellulosic based biomass materials for cellulase production is one among the major increasing demands for various biotechnological applications. Aspergillus niger was cultured in corn cobs based fermentation medium under some pre-optimized growth conditions. After four days of still culture incubation a large magnitude of cellulase (28.3±0.24U/mL) was achieved when the SSF medium containing 10 g corn cobs inoculated with 5 mL of inoculum at 30°C. The effects of different minerals were optimized through Response Surface Methodology (RSM) by adopting a Central Composite Design (CCD). The crude cellulase was purified 5.71 fold with specific activity of 232.5U/mg using ammonium sulfate precipitation, and Sephadex-G-100 gel filtration column chromatography. Enzyme was found to be a monomeric protein as evident by single band corresponding to 43 kDa on SDS-PAGE. Characterization revealed that the purified cellulase was optimally active and thermally more stable at pH 7 and 70oC, respectively. Using carboxymethyl cellulose as substrate, the enzyme showed maximum activity (Vmax) of 45.5U/mL with its corresponding Km value of 25μM. Among activators/inhibitors, different metal ions (EDTA, Hg2+ and Zn+2) showed inhibitory effect up to different extents as different concentrations, whereas, the enzyme was activated by Co2+ and Mg2+ at the concentration of 5mM. © 2014 University of Bucharest.


Asif M.,University of Alberta | Yang R.-C.,University of Alberta | Navabi A.,Agriculture and Agri Food Canada | Iqbal M.,University of Alberta | And 7 more authors.
Crop Science | Year: 2015

A randomly derived recombinant inbred line (RIL) population (n = 163) from a cross between CIMMYT spring wheat ‘Attila’ and the Canadian ‘CDC Go’ was used to map quantitative trait loci (QTL) affecting various agronomic and qual­ity traits. The experiment was also designed to investigate the feasibility of organic wheat breeding by determining selection differentials and the effect of Rht-B1 in paired organic and conventional management systems. Heritabil­ity estimates differed between systems for five of nine traits measured; including grain yield, number of tillers, plant height, kernel weight, and grain protein content. Direct selection in each management system resulted in 50% or fewer selected individuals in common between the two systems, for eight of the nine (except for flower­ing time) studied traits. Most QTL were specific to either the organic or the conventional man­agement system. However, consistent QTL for grain yield, grain volume weight, kernel weight, and days to flowering were mapped in both systems on chromosomes 6A, 1B, 3A, and 5B, respectively. The effect of Rht-B1 was more pro­nounced in organic systems, where RILs carrying the wild-type allele were taller, produced more grain yield with higher grain protein content, and suppressed weed biomass to a greater extent than those carrying dwarfing alleles. Results of the present study suggest that differences exist between the two management systems for QTL effects. Indirect selection of superior genotypes from one system to another will not result in the advancement of the best possible genotypes. Therefore, selection of spring wheat cultivars for organic systems should be conducted on organ­ically managed lands. © Crop Science Society of America


Iqbal M.M.,National Institute for Genomics and Advanced Biotechnology | Nazir F.,National Institute for Genomics and Advanced Biotechnology | Ali S.,National Institute for Genomics and Advanced Biotechnology | Asif M.A.,National Institute for Genomics and Advanced Biotechnology | And 3 more authors.
Molecular Biotechnology | Year: 2012

A Rice chitinase-3 under enhance version of CaMV 35S was introduced into peanut (Arachis hypogaea L.) through Agrobacterium mediation. Agrobacterium tumefaciens strain LB4404 was used harboring the binary vector (pB1333-EN4-RCG3) containing the chitinase (chit) and hygromycin resistance (hpt) gene as selectable marker. Putative transgenic shoots were regenerated and grown on MS medium supplemented with 5 mg/l BAP, 1 mg/l kinetin, and 30 mg/l hygromycin. Elongated shoots were examined for the presence of the integrated rice chitinase gene along with hygromycin gene as selectable. The integration pattern of transgene in the nuclear genome of the putative transformed plants (T 0) was confirmed through Southern hybridization analysis of the genomic DNA. Survival rate of the in vitro regenerated plantlets was over 60% while healthy putatively transgenic (T 0) plants with over 42% transformation frequency were produced through Agrobacterium mediated gene transfer of the rice chitinase gene and all the plants flowered and set seed normally. T1 plants were tested for resistance against Cercospora arachidicola by infection with the microspores. Transgenic strains exhibited a higher resistance than the control (non-transgenic plants). chitinase gene expression in highly resistant transgenic strains was compared to that of a susceptible control. A good correlation was observed between chitinase activity and fungal pathogen resistance. © 2011 Springer Science+Business Media, LLC.


Khalid A.,Pmas Arid Agriculture University | Kausar F.,Pmas Arid Agriculture University | Arshad M.,University of Agriculture at Faisalabad | Mahmood T.,Pmas Arid Agriculture University | Ahmed I.,National Institute for Genomics and Advanced Biotechnology
Applied Microbiology and Biotechnology | Year: 2012

Presence of huge amount of salts in the wastewater of textile dyeing industry is one of the major limiting factors in the development of an effective biotreatment system for the removal of azo dyes from textile effluents. Bacterial spp. capable of thriving under high salt conditions could be employed for the treatment of saline dyecontaminated textile wastewaters. The present study was aimed at isolating the most efficient bacterial strains capable of decolorizing azo dyes under high saline conditions. Fiftyeight bacterial strains were isolated from seawater, seawater sediment, and saline soil, using mineral salt medium enriched with 100 mg l-1 Reactive Black-5 azo dye and 50 g NaCl l-1 salt concentration. Bacterial strains KS23 (Psychrobacter alimentarius) and KS26 (Staphylococcus equorum) isolated from seawater sediment were able to decolorize three reactive dyes including Reactive Black 5, Reactive Golden Ovifix, and Reactive Blue BRS very efficiently in liquid medium over a wide range of salt concentration (0-100 g NaCl l-1). Time required for complete decolorization of 100 mg dye l-1 varied with the type of dye and salt concentration. In general, there was an inverse linear relationship between the velocity of the decolorization reaction (V) and salt concentration. This study suggested that bacteria isolated from saline conditions such as seawater sediment could be used in designing a bioreactor for the treatment of textile effluent containing high concentration of salts. © Springer-Verlag Berlin Heidelberg 2012.


Mahmood I.A.,Land Resources Research Institute | Ali A.,Land Resources Research Institute | Shahzad A.,National Institute for Genomics and Advanced Biotechnology | Sultan T.,Land Resources Research Institute
Pakistan Journal of Scientific and Industrial Research Series B: Biological Sciences | Year: 2016

A two years field study according to split plot design was conducted to investigate the impact of crop residue (CR) incorporation and P application (0, 40, 80, 120 kg P2O5/ha) on P use efficiency and yield of direct seeded rice (DSR) and wheat grown under saline soil (ECe = 4.59 dS/m; pHs = 8.38; SAR = 6.57 (mmolc/L)1/2; extractable P = 4.07 mg/kg; texture = sandy clay loam), during the years 2011 and 2012. Planting of DSR (with and without crop residue incorporation @ 2 tonnes/ha) were placed in main plots and P application was in sub plots. Data on tillering, plant height, panicle length, 1000 grain weight, paddy and straw yields were collected. On an average of two years, maximum tillers (18), panicle length (33), grain/panicle (121) and paddy yield (3.26 t/ha) were produced with P application @ 80 kg P2O5/ha along with CR incorporation. Similarly in case of wheat grown after DSR, maximum tillers (17), spike length (17), grains/panicle (66) and grain yield (3.56 t/ha) were produced with P application @ 80 kg P2O5/ha along with CR incorporation. Although, the growth and yield contributing parameters with this treatment (80 kg P2O5/ha + CR) performed statistically equal to 120 kg P2O5/ha without CR incorporation during both the years, but on an average of two years, grain yield of DSR and wheat was significantly superior (22 and 24%, respectively) than that of higher P rate (120 kg/ha) without CR. Overall, continuous two years CR incorporation further increased (17%) paddy yields during the follow up year of crop harvest. Higher P use efficiency and concentrations of P, K+ and Ca2+ in both DSR and wheat plant tissues was found where 80 kg P2O5/ha was applied along with CR incorporation or 120 kg P2O5/ha alone while Na+ and Mg2+ concentration decreased with CR incorporation and increasing P rate. An increasing trend in DSR paddy and wheat grain yields was observed with increasing the rate of P application without CR incorporation, however, it was not as much as that of 80 kg P2O5/ha application with CR incorporation and found to be superior than rest of the treatments during both study years. © 2016, Oriental Scientific Publishing Company. All rights reserved.


Gurcan K.,Erciyes University | Onal N.,Erciyes University | Yilmaz K.U.,Erciyes University | Ullah S.,National Institute for Genomics and Advanced Biotechnology | And 2 more authors.
Scientia Horticulturae | Year: 2015

Apricot (Prunus armeniaca L.) is an important fruit crop in Turkey, where a rich diversity of apricot cultivars and seedlings is prevalent. The genetic diversity of the Turkish apricot germplasm was investigated. The profiles of 18 simple sequence repeat (SSR) loci of 239 accessions in the genetic source collection of the country as well as those of European and Pakistani accessions were obtained. Eleven SSRs were selected from the apricot molecular linkage group 1 (LG1), and these are located close to the major Plum pox virus (PPV) resistance locus. The remaining seven SSRs represent the other six linkage groups. A high level of genetic diversity (He. =. 0.74, Ho. =. 0.63) was observed. Stark Early Orange (SEO)/Harlayne-type resistance alleles of three SSR loci (PGS1.21-240, PGS1.23-161 and PGS1.24-119) were found to be rare in the Turkish accessions (1.7%) but were abundantly found in the Pakistani accessions (41.7%). The genetic clustering analyses, the neighbor-joining tree constructed from the genetic distances of the proportions of shared alleles and the population genetic structure did not distinguish the European accessions from the Turkish accessions. However, 'Harlayne', 'SEO' and the putative resistant apricot accessions were grouped together, indicating a common heritage for the resistant accessions. SSR profiles of the accessions will improve the management of apricot gene banks, and information on the genetic variation in Turkish apricots will assist the international research community. © 2015 Elsevier B.V.


Zafar A.Y.,National Institute for Genomics and Advanced Biotechnology | Zafar A.Y.,Pakistan Atomic Energy Commission PAEC | Iqbal J.,National Institute for Genomics and Advanced Biotechnology | Iqbal M.M.,National Institute for Genomics and Advanced Biotechnology | And 4 more authors.
Molecular Biotechnology | Year: 2011

Salinity and drought are main threat to agriculture productivity, to avoid further losses it is necessary to improve the genetic material of crops against these stresses In this present study, AtNHX1, a vacuolar type Na +/H + antiporter gene driven by 35S promoter was introduced into groundnut using Agrobacterium tumefaciens transformation system. The stable integration of the AtNHX1 gene was confirmed by polymerase chain reaction (PCR) and southern blot analysis. It was found that transgenic plants having AtNHX1 gene are more resistant to high concentration of salt and water deprivation than the wild type plants. Salt and proline level in the leaves of the transgenic plants were also much higher than that of wild type plants. The results showed that overexpression of AtNHX1 gene not only improved salt tolerance but also drought tolerance in transgenic groundnut. Our results suggest that these plants could be cultivated in salt and drought-affected soils. © Springer Science+Business Media, LLC 2011.


ul Hassan M.,Pmas Arid Agriculture University | Akram Z.,Pmas Arid Agriculture University | Ali S.,National Institute for Genomics and Advanced Biotechnology | Ali G.M.,National Institute for Genomics and Advanced Biotechnology | And 4 more authors.
Crop Breeding and Applied Biotechnology | Year: 2016

Peanut (Arachis hypogaea) is an important legume and oilseed crop, native to South America and grown in all tropical and temperate regions of the world. A simplified and rapid direct gene delivery system in peanut was developed by vortexing silicon carbide whiskers with callus and with plasmid harboring chitinase and hygromcin genes. The effects of callus age and whisker quantity on transformation efficiency were evaluated. Transformation efficiency (6.88%) was highest when 200 mg of whiskers were used with 5 µg plasmid for 2 g of 20-day-old callus. Hygromcin-resistant calli were regenerated to complete plants which produced seeds normally. Transgene insertion and number of transgene copieswere confirmed by PCR and southern blot analyses, respectively. Transgene expression was evaluated by a pathogenecity test and RT-PCR analysis. In transgenic events, the resistance level to leaf spot disease was far higher than in control plants. © 2016, Brazilian Society of Plant Breeding. All rights reserved.


PubMed | National Institute for Genomics and Advanced Biotechnology
Type: Journal Article | Journal: Molecular biotechnology | Year: 2012

A Rice chitinase-3 under enhance version of CaMV 35S was introduced into peanut (Arachis hypogaea L.) through Agrobacterium mediation. Agrobacterium tumefaciens strain LB4404 was used harboring the binary vector (pB1333-EN4-RCG3) containing the chitinase (chit) and hygromycin resistance (hpt) gene as selectable marker. Putative transgenic shoots were regenerated and grown on MS medium supplemented with 5 mg/l BAP, 1 mg/l kinetin, and 30 mg/l hygromycin. Elongated shoots were examined for the presence of the integrated rice chitinase gene along with hygromycin gene as selectable. The integration pattern of transgene in the nuclear genome of the putative transformed plants (T(0)) was confirmed through Southern hybridization analysis of the genomic DNA. Survival rate of the in vitro regenerated plantlets was over 60% while healthy putatively transgenic (T(0)) plants with over 42% transformation frequency were produced through Agrobacterium mediated gene transfer of the rice chitinase gene and all the plants flowered and set seed normally. T1 plants were tested for resistance against Cercospora arachidicola by infection with the microspores. Transgenic strains exhibited a higher resistance than the control (non-transgenic plants). chitinase gene expression in highly resistant transgenic strains was compared to that of a susceptible control. A good correlation was observed between chitinase activity and fungal pathogen resistance.

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