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Khan M.R.,Pakistan National Agricultural Research Center | Khan M.R.,Max Planck Institute for Plant Breeding Research | Ali G.M.,Pakistan National Agricultural Research Center
Plant Molecular Biology | Year: 2013

Evolution of phenotypic morphologies is closely associated with modular organization of cis-regulatory elements underlying expression divergence. The MADS-box gene family is the subject of extensive studies that try to unscramble the structural complexity of flowering plants. This study is envisaged to explore the potential of CRMs in highly constrained non-coding elements of STMADS11superclade MADS-box genes in expression divergence. Phylogenetic reconstruction differentiated the STMADS11 genes into SVP-like, ZMM19-like, MPF1-like and MPF2-like clades. Differential gene expression in vegetative and floral organs was evident within the clades as well as at inter-clade level. The genomic DNA search for clusters of short motifs and sequence conservation of the -2 kb promoter region of particularly, MPF2-like clade permitted to establish three well defined CRMs where transcription factors bind, being CRM1 the activator, CRM2 the repressor, and CRM3 the enhancer element. Similar clusters were also mapped in the large 1st introns in the coding region. Within these CRMs many transcription factor-binding sites, particularly the hotspots for MADS-domain TF binding elements-CArG-boxes, directing sepal specific expression in Arabidopsis-were accrued in the CRM1 of MPF2-like promoters. Site-directed mutagenesis and motif swapping through reporter assays allude towards their implication as functionally active elements. In terms of directional evolution of MPF2-like promoters, CRMs are significantly more conserved than flanking regions, hence, bearing the signatures for purifying selection. Thus, CRMs are the pervasive feature of STMADS11 genes and mutations and/or appearance of new transcription factor binding sites and position of the CRMs are responsible for the divergence in expression patterns in this clade. These results have implications in understanding functional evolution of cis-regulatory modules in plants. © 2013 Springer Science+Business Media Dordrecht.


Khan M.R.,Pakistan National Agricultural Research Center | Hu J.,Max Planck Institute for Plant Breeding Research | Ali G.M.,Pakistan National Agricultural Research Center
PLoS ONE | Year: 2012

Expression divergence is thought to be a hallmark of functional diversification between homologs post duplication. Modification in regulatory elements has been invoked to explain expression divergence after duplication for several MADS-box genes, however, verification of reciprocal loss of cis-regulatory elements is lacking in plants. Here, we report that the evolution of MPF2-like genes has entailed degenerative mutations in a core promoter CArG-box and an auxin response factor (ARF) binding element in the large 1st intron in the coding region. Previously, MPF2-like genes were duplicated into MPF2-like-A and -B through genome duplication in Withania and Tubocapsicum (Withaninae). The calyx of Withania grows exorbitantly after pollination unlike Tubocapsicum, where it degenerates. Besides inflated calyx syndrome formation, MPF2-like transcription factors are implicated in functions both during the vegetative and reproductive development as well as in phase transition. MPF2-like-A of Withania (WSA206) is strongly expressed in sepals, while MPF2-like-B (WSB206) is not. Interestingly, their combined expression patterns seem to replicate the pattern of their closely related hypothetical progenitors from Vassobia and Physalis. Using phylogenetic shadowing, site-directed mutagenesis and motif swapping, we could show that the loss of a conserved CArG-box in MPF2-like-B of Withania is responsible for impeding its expression in sepals. Conversely, loss of an ARE in MPF2-like-A relaxed the constraint on expression in sepals. Thus, the ARE is an active suppressor of MPF2-like gene expression in sepals, which in contrast is activated via the CArG-box. The observed expression divergence in MPF2-like genes due to reciprocal loss of cis-regulatory elements has added to genetic and phenotypic variations in the Withaninae and enhanced the potential of natural selection for the adaptive evolution of ICS. Moreover, these results provide insight into the interplay of floral developmental and hormonal pathways during ICS development and add to the understanding of the importance of polyploidy in plants. © 2012 Khan et al.


Rashid A.,Quaid-i-Azam University | Nawaz S.,UK Environment Agency | Barker H.,UK Environment Agency | Ahmad I.,Pakistan National Agricultural Research Center | Ashraf M.,National University of Sciences and Technology
Journal of Chromatography A | Year: 2010

A procedure based on QuEChERS extraction and a simultaneous liquid-liquid partition clean-up was developed. The procedure involved extraction of hydrated soil samples using acetonitrile and clean-up by liquid-liquid partition into n-hexane. The hexane extracts produced were clean and suitable for determination using gas chromatography-tandem mass spectrometry (GC-MS/MS). The method was validated by analysis of soil samples, spiked at five levels between 1 and 200 μgkg-1. The recovery values were generally between 70 and 100% and the relative standard deviation values (%RSDs) were at or below 20%. The procedure was validated for determination of 19 organochlorine (OC) pesticides. These were hexachlorobenzene (HCB), α-HCH, β-HCH, γ-HCH, heptachlor, heptachlor epoxide (trans), aldrin, dieldrin, chlordane (trans), chlordane (cis), oxychlordane, α-endosulfan, β-endosulfan, endosulfan sul-fate, endrin, p,p′-DDT, o,p′-DDT, p,p′-DDD and p,p′-DDE. The method achieved low limits of detection (LOD; typically 0.3 μgkg-1) and low limits of quantification (LOQ; typically 1.0 μgkg-1). The method performance was also assessed using five fortified soil samples with different physico-chemical proper-ties and the method performance was consistent for the different types of soil samples. The proposed method was compared with an established procedure based on Soxtec extraction. This comparison was carried out using six soil samples collected from regions of Pakistan with a history of intensive pesticide use. The results of this comparison showed that the two procedures produced results with good agree-ment. The proposed method produced cleaner extracts and therefore led to lower limits of quantification. The proposed method was less time consuming and safer to use. The six samples tested during this com-parison showed that soils from cotton growing regions contained a number of persistent OC residues at relatively low levels (<10 μgkg-1). These residues were α-HCH, γ-HCH, heptachlor, chlordane (trans), p,p′-DDT, o,p′-DDT, p,p′-DDD, p,p′-DDE, β-endosulfan and endosulfan sulfate. © 2010 Elsevier B.V.


Kamran A.,University of Alberta | Kamran A.,University of Punjab | Iqbal M.,University of Alberta | Iqbal M.,Pakistan National Agricultural Research Center | Spaner D.,University of Alberta
Euphytica | Year: 2014

Wheat is one of the most widely cultivated crops and, being the staple diet of more than 40 countries, it plays an imperative role in food security. Wheat has remarkable genetic potential to synchronize its flowering time with favourable environmental conditions. This ability to time its flowering is a key factor for its global adaptability and enables wheat plant to produce satisfactory grain yield under very diverse temperature and soil moisture conditions. Vernalization (Vrn), photoperiod (Ppd) and earliness per se (Eps) are the three genetic systems controlling flowering time in wheat. The objective of this review is to provide comprehensive information on the physiological, molecular and biological aspects of the three genetic constituents of flowering and maturity time in wheat. Reviews written in the past have covered either one of the aspects; and generally focused on one of the three genetic constituents of the flowering time. The current review provides (a) a detailed overview of all three gene systems (vernalization, photoperiod and earliness per se) controlling flowering time, (b) details of the primer sequences, their annealing temperatures and expected amplicon sizes for all known markers of detecting vernalization and photoperiod alleles, and (c) an up to date list of QTLs affecting flowering and/or maturity time in wheat. © 2014 Springer Science+Business Media Dordrecht.


Eqani S.A.-M.-A.-S.,Quaid-i-Azam University | Malik R.N.,Quaid-i-Azam University | Mohammad A.,Pakistan National Agricultural Research Center
Environmental Geochemistry and Health | Year: 2011

Organochlorine pesticides (OCPs), viz. β-hexachlorocyclohexane (β-HCH), γ-HCH, aldrin, dieldrin, endrin, heptachlor, endosulfan-I, endosulfan-II, heptachlor endoepoxide, heptachlor exoepoxide, mirex, dicofol, o,p′-dichlorodiphenyltrichloroethane (o,p′-DDT), p,p′-dichlorodiphenyltrichloroethane (p,p′-DDT), dichlorodiphenyldichloroethane (DDD), and dichlorodiphenyltrichloroethylene (DDE) and 12 other physicochemical parameters were measured in surface sediments from River Chenab during two sampling seasons (summer and winter, 2007) to evaluate spatial and temporal trends of sediment pollution. Hierarchical agglomerative cluster analysis identified three groups of sites based on spatial similarities in physicochemical parameters and OCP residual concentrations. Spatial discriminant function analysis (DFA) segregated 14 parameters, viz. dicofol, endosulfan-I, heptachlor endoepoxide, dieldrin, DDD, DDE, endosulfan-II, o,p′-DDT, p,p′-DDT, pH, electrical conductivity (EC), Cl-1, total P (%), and silt, which explained 96% of total variance between spatial groups. γ-HCH was the most frequently detected (63%) pesticide, followed by DDD (56%). The ratio of DDTs to their metabolites indicated current input and anaerobic biodegradation. Temporal DFA highlighted aldrin, heptachlor endoepoxide, Cl-1, total P, and EC as important variables which caused variations between summer and winter. DDTs were relatively more prevalent as compared to other OCPs in the sediments samples during both seasons. DDT metabolites were detected at greater frequencies and concentrations in winter, whereas DDT isomers were more prevalent in summer sediment samples. Factor analysis identified agricultural and industrial activities as major sources of sediment OCP contamination. Concentrations of γ-HCH, heptachlor endoepoxide, dieldrin, and DDTs (isomers and metabolites) in all sediment samples were well above interim sediment quality guidelines (ISQGs) and probable effect limits (PEL) given by Canadian Sediment Quality Guidelines (CSQGs). © 2010 Springer Science+Business Media B.V.


Suthar V.,Pakistan National Agricultural Research Center
Environmental monitoring and assessment | Year: 2014

Natural and chemically enhanced phytoextraction potentials of maize (Zea mays L.) and sesbania (Sesbania aculeata Willd.) were explored by growing them on two soils contaminated with heavy metals. The soils, Gujranwala (fine, loamy, mixed, hyperthermic Udic Haplustalf) and Pacca (fine, mixed, hyperthermic Ustollic Camborthid), were amended with varying amounts of ethylenediaminetetraacetic acid (EDTA) chelating agent, at 0, 1.25, 2.5, and 5.0 mM kg(-1) soil to enhance metal solubility. The EDTA was applied in two split applications at 46 and 60 days after sowing (DAS). The plants were harvested at 75 DAS. Addition of EDTA significantly increased the lead (Pb) and cadmium (Cd) concentrations in roots and shoots, uptake, bioconcentration factor, and phytoextraction rate over the control. Furthermore, addition of EDTA also significantly increased the soluble fractions of Pb and Cd in soil over the controls; the maximum increase of Pb and Cd was 13.1-fold and 3.1-fold, respectively, with addition of 5.0 mM EDTA kg(-1)soil. Similarly, the maximum Pb and Cd root and shoot concentrations, translocation, bioconcentration, and phytoextraction efficiency were observed at 5.0 mM EDTA kg(-1) soil. The results suggest that both crops can successfully be used for phytoremediation of metal-contaminated calcareous soils.


Akhtar S.,Pmas Arid Agriculture University | Khalid N.,University of Tokyo | Ahmed I.,Pakistan National Agricultural Research Center | Shahzad A.,Pakistan National Agricultural Research Center | Suleria H.A.R.,National University of Sciences and Technology
Critical Reviews in Food Science and Nutrition | Year: 2014

The legume Arachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and subtropics. Peanut is one of the most widely used legumes due to its nutrition and taste, and it occupies a rank of major oilseed crop in the world. It has been recognized as a functional food due to its role in a health promoting effect. Peanut oil contains a well-balanced fatty acid and antioxidant profile that provide protection against harmful substances especially free radicals. This paper gives an overview of scientific literature available on phytochemical and functional properties of peanut oil. Owing to its unique organoleptic properties associated with its cardioprotective and anti-inflammatory properties, peanut oil has found, recently, its place on the highly competitive international edible oil market. © 2014 Copyright Taylor & Francis Group, LLC.


Yunus A.W.,Pakistan National Agricultural Research Center | Bohm J.,University of Veterinary Medicine Vienna
Poultry Science | Year: 2013

The purpose of this study was to observe the effects of low doses of aflatoxin B1 (AFB1) on responses to common vaccines and levels of serum cations in broilers. Male broilers at 7 d of age were fed control (no AFB1), a 75 μg of AFB1/kg (75 ppb of AFB1) diet, or a 750 μg of AFB1/kg (750 ppb of AFB1) diet. The 750 ppb of AFB1 diet resulted in a temporary increase in ELISA titers against Newcastle disease virus (P = 0.014) and infectious bursal disease virus (P = 0.005) during wk 2 and 4 of exposure, respectively, compared with the control diet. Conversely, lower (P ≤ 0.01) serum protein concentrations were found in broilers under the 750 ppb AFB1 diet during wk 2 and 4. During wk 2 of exposure, lower serum levels of potassium were noted in birds under both the 75 (P = 0.037) and 750 ppb (P = 0.000) AFB1 diets compared with those under the control diet. During wk 5, higher serum magnesium (P = 0.004), and sodium (P = 0.000) under the 750 ppb AFB1 diet were found compared with the control diet. These data indicate that low dietary levels of AFB1 can temporarily increase or decrease the studied serological variables in broilers depending upon the stage of exposure. © 2013 Poultry Science Association Inc.


Ghafoor A.,Pakistan National Agricultural Research Center | McPhee K.,North Dakota State University
Euphytica | Year: 2012

In this contribution we review the state of the art for genetic resistance to powdery mildew, caused by Erysiphe pisi, in pea (Pisum sativum L.) and potential use of marker-assisted selection (MAS) for developing disease resistant cultivars. Powdery mildew is important in many production regions worldwide and reduces yield and crop quality when present in epidemic proportions. Although genetic resistance to powdery mildew is available (er1 and er2) and has been durable since its characterization in 1969, recently a new dominant gene (Er3) has been reported in Pisum fulvum, a wild relative of pea that is different from previously reported er1 and er2. The efficacy of these genes may be at risk from the point of view of new pathotypes and pathogens. Erysiphe trifolii has been reported that was not previously known as a pathogen of pea powdery mildew. A continued search for new and diverse resistant sources remains a priority in pea breeding and special emphasis should be paid to selection of resistance that will prolong durability of existing resistance genes. Marker assisted selection is a new emerging approach for target breeding that has been intensively employed especially in cereals and has recently got popularity among legume breeders. With the advancement of genomic research, especially related to quantitative traits loci, the MAS is potentially anticipated future technique for routine plant breeding that is scarce in legumes at present. In pea, various DNA markers have been reported linked to er1, er2 and Er3 at varying distances in different mapping populations that are currently being used in breeding programs. Currently MAS of single gene is the most powerful approach and successes have been witnessed. If single marker is not close enough to the gene of interest then two flanking markers are considerably utilized to improve the correct identification that is being successfully employed in MAS for powdery mildew resistance in pea. © 2011 Springer Science+Business Media B.V.


Due to similarity in seed texture, colour and size of vetch (Vicia sativa) with lentil (Lens culinaris), these two legumes are mixed when split as "dal" to fetch higher prices. The sole marketing as split seed of vetch cultivar "Blanche fleur" under the false name of "red dal" or its mixing with lentil created hue and cry during the last decade of previous millennium in most of the South Asian countries including Middle East. Identification of vetch from lentil was only possible through modern biochemical techniques involving sophisticated equipment and technical skill. One hundred and ten samples of split red dal along with reference sample for both the species collected from various grain markets were analyzed through SDSPAGE technique for three times, starting in 2001 with the interval of five years. The seed protein profiling was employed for distinguishing these two legumes belonging to different genera that were successfully utilized and the information was shared with researchers to create awareness among the consumers through print media. Varying degrees of mixing was observed that was gradually deceased during second and third sampling phase which was mainly due to robust information generated and dispersed. The electrophoretic pattern indicated a clear-cut differentiation of V. sativa from L. culinaris, hence this technique is very effective for species identification.

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