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Background Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad range of rice-growing environments results in a diverse array of local rice varieties. Many rice varieties have been lost as a result of biodiversity loss and are now grown in Pakistan. Methods and results To protect the biodiversity of rice varieties, an experiment was carried out to check the genetic and morphological variations between 8 exotic and 7 local rice genotypes, using 5 different SSR markers, i.e., RM3, RM259, RM341, RM520, and RM11943. The analysis of morphological and quality traits of rice observed significant variation across genotypes. The results revealed that genotype Irri-Pak attained the highest plant height and primary branch plant-1, while genotype Mushkan produced a higher number of productive tillers and obtained a higher fertility factor (%). Similarly, the highest value for panicle length was observed for genotype Faker-e-Malakand, 1000-grains weight in genotype Calmochi, and maximum days to maturity was noticed in genotype Swati-2014. Moreover, the genotype Brio attained the highest value of stem diameter, while maximum seed length was noted in the genotype Sug Dasi. The highest number of primary branches plant(-1) in genotype Ibge-I and secondary branches plant(-1) in genotype Calmochi were noticed. A higher concentration of sodium and potassium was observed for the genotype Marte, while the genotype Muskan attained the maximum content of copper. Moreover, the highest concentration of iron in genotype Originario, zinc in genotype JP-5, and cadmium content were noticed in genotype Ibge. Similarly, the dendrogram analysis for quantitative parameters showed three clusters at 74.13% similarities. Whereas all the genotypes of European origin formed a separate cluster. A set of 5 simple sequence repeat primers, covering four chromosomes, amplified a total of 14 alleles and showed 100% polymorphism with an average PIC value ranging from 0.39 to 0.91. The UPGMA cluster analysis separated the 15 rice genotypes into 3 main groups based on 32.5% similarities and the highest genetic distance (45.1%) was observed between two genotypes (Fakher-e-malakand and Musa), having different geographical origins. There was no genetic distance between the genotypes Marte and Brio, irrespective of having the same origin. Conclusions The maximum genetic distances were noted for genotype, Fakhre-e-Malakand and Musa having a different origin, while the minimum genetic distance was shown by genotypes, Marte and Onice, from the same origin.

Background: Broad base genetic diversity is essential for a sustainable crop yield to provide tolerance against biotic and abiotic stresses. In Pakistan, rice is ranked second as a staple food and cultivated under different climatic zones. However, very little is known in terms of rice genetic diversity.Methods and results: Present research were performed to evaluate the genetic diversity among 12 local rice varieties by using 5 SSR markers. Furthermore, agro-morphological parameters and seed characterization of these varieties were studied. The highest plant height (204.3 cm) and panicle length (40.1 cm) were observed for Hans-raj, the maximum number of panicles were recorded for dilrosh-97 (47.3). The maximum number of primary and secondary panicle branches were observed in Ratua-81 (51) and super basmati (62), respectively. Super basmati showed highest number of filled grains (264.3) and total number of grains per panicle (315). The minimum days to maturity was recorded for ratua-81 (140 days), and highest 1000 grains weight was recorded for Ksk-133 (27g). The highest concentration of elements, e.g. zinc (Zn) was observed in Ks-282 (44µg/g), Iron (Fe) in hansraj (190.3µg/g), manganese in bamla sufaid (111.3µg/g), copper (Cu) in hansraj (856.3µg/g), lead (Pb) in super basmati (3883.3µg/g), and nickel (Ni) was found in basmati-385 (314.6ug/g). For the genetic diversity analysis, five SSR markers were used and a total of 60 alleles were amplified with 20% polymorphism, RM28130 showed the highest PIC value (0.60). The maximum number (3) of alleles were produced by RM28089. Based on secondary panicle branches and total number of filled grains, Super basmati showed best panicle architecture and grain yield, which can be used in breeding program to develop high yielding aromatic rice genotypes.Conclusions: The highest number of filled grains and total number of grains per panicle were observed in super basmati, which indicated the potential adaptation. Basmati Hansraj, Ks-282, Super basmati and Basmati surkh-161 were found to be highly rich in micronutrients (iron, zinc, copper, lead and manganese). The maximum genetic distance was observed in basmati-2000 and basmati surkh 161 genotypes.

Water stress (WS) and heat stress (HS) have a negative effect on soybean plant growth and crop productivity. Changes in the physiological characteristics, proteome, and specific metabolites investigated on molecular and cellular functions were studied in two soybean cultivars exposed to different heat and water stress conditions independently and in combination. Leaf protein composition was studied using 2-DE and complemented with MALDI TOF mass spectrometry. While the two cultivars displayed genetic variation in response to water and heat stress, thirty-nine proteins were significantly altered in their relative abundance in response to WS, HS and combined WS+HS in both cultivars. A majority of these proteins were involved in metabolism, response to heat and photosynthesis showing significant cross-tolerance mechanisms. This study revealed that MED37C, a probable mediator of RNA polymerase transcription II protein, has potential interacting partners in Arabidopsis and signified the marked impact of this on the PI-471938 cultivar. Elevated activities in antioxidant enzymes indicate that the PI-471938 cultivar can restore the oxidation levels and sustain the plant during the stress. The discovery of this plant’s development of cross-stress tolerance could be used as a guide to foster ongoing genetic modifications in stress tolerance.

Water stress (WS) and heat stress (HS) have a negative effect on soybean plant growth and crop productivity. During WS, soybean plants opt for survival through ion homeostasis and the conformations of proteins are disconcerted as plant cells lose water while HS leads to difficulties in flowering and fruiting. Some of these changes include oxidative stress leading to the destruction of photosynthetic apparatus, macromolecules within cells and the onset of complex signaling cascades. Changes in the physiological characteristics, proteome, and certain metabolites investigated on molecular and cellular functions were studied in two soybean cultivars exposed to different heat and water stress conditions independently and in combination. Leaf protein composition was studied using 2-DE and complemented with MALDI TOF mass spectrometry. While two cultivars displayed genetic variation in response to water and heat stress, thirty-nine proteins were significantly altered in their relative abundance in response to WS, HS and combined WS+HS in both cultivars; a majority of them involved in metabolism, response to heat and photosynthesis showing significant cross-tolerance mechanisms. Functional analysis revealing a majority of heat responsive-proteins were more abundant during HS and combined stress (WS+HS) whereas these proteins were low to WS in cultivar PI 471938 and heat shock proteins were in low abundance to water, heat and combined stresses in cultivar R95-1705. Most protein abundances were not correlated with their expression at mRNA levels in PI cultivar, however, in cultivar R 95, the expression levels of transcript follow their relative abundance in proteins. Our systems bioinformatics analyses revealed that MED37C, a probable mediator of RNA polymerase transcription II protein showed potential interacting partners in Arabidopsis and our studies signifies the marked impact of this protein in PI cultivar. Elevated activities in antioxidant enzymes indicate that the PI-371938 cultivar has the ability to restore the oxidation levels and sustain the plant during the stress. Our study hypothesizes the plant’s development of cross-stress tolerance which will help foster the ongoing ventures in genetic modifications in stress tolerance.

Soybean exhibits markedly reduced growth and yields under flooding stress. To determine the functional roles of four soybean proteins in post-flooding recovery, the organ/stress specificity and time-dependency of their enzymatic activities were analyzed. Peroxidase activity decreased in root and hypocotyl exposed to flooding and cold stresses, but increased during the post-stress recovery period. In contrast, its activity increased in both root and hypocotyl under drought stress. Acid phosphatase activity was suppressed in root treated with flooding and cold stresses, and slightly increased during the recovery period; however, the opposite profile was observed in hypocotyl. In response to drought stress, it did not change in root, but was decreased in hypocotyl. Beta-ketoacyl reductase activity did not change in root under flooding conditions, but was decreased in hypocotyl, although the activity increased slightly during the recovery period. In addition, it was decreased in both organs under drought and cold stresses, but again increased during the recovery period. Nucleotidylyl transferase activity was increased in root under flooding and drought stresses, but was decreased in hypocotyl. It was decreased in response to cold stress, but exhibited a slight increase during the recovery period. Furthermore, the treatment with jasmonate and salicylate suppressed the activities of peroxidase and acid phosphatase in root and hypocotyl under flooding stress; however, the activity of acid phosphatase increased during the recovery period. Nucleotidylyl transferase activity in root was also elevated by treatment with jasmonate, but gradually decreased during the recovery period. These results suggest that jasmonate-induced changes in nucleotidylyl transferase activity may facilitate soybean root recovery after flooding stress.

Soybean is a nutritionally important crop that exhibits reductions in growth and yield under drought stress. To investigate soybean responses during post-drought recovery, a gel-free proteomic technique was used. Two-day-old soybeans were treated with drought stress for 4 days and recovered for 4 days. Root including hypocotyl was collected during the drought treatment and recovery stage. Seedling growth was suppressed by drought stress, but recovered following stress removal. The malondialdehyde content increased under drought stress, but decreased during the recovery stage. A total of 792 and 888 proteins were identified from the control and recovering seedlings, respectively. The identified proteins were related to functional categories of stress, hormone metabolism, cell wall, secondary metabolism, and fermentation. Cluster analysis indicated that abundances of peroxidase and aldehyde dehydrogenase were highly changed in the seedlings during the post-drought recovery. The activity of peroxidase decreased under drought conditions, but increased during recovery. In contrast, the activity of aldehyde dehydrogenase was increased in response to drought stress, but decreased during the recovery stage. These results suggest that peroxidase and aldehyde dehydrogenase play key roles in post-drought recovery in soybean by scavenging toxic reactive oxygen species and reducing the load of harmful aldehydes. Biological significance Post-drought recovery response mechanisms in soybean root including hypocotyl were analyzed using gel-free proteomic technique. A total of 643 common proteins between control and drought-stressed soybeans changed significantly in abundance over time. The proteins that changed during post-drought recovery were assigned to protein, stress, hormone metabolism, secondary metabolism, cell wall, redox, and glycolysis categories. The analysis revealed that peroxidase and aldehyde dehydrogenase were increased in protein abundance under drought stress. The enzyme activity of peroxidase decreased under drought but increased during recovery. The activity of aldehyde dehydrogenase was increased under drought stress but decreased during recovery stage. Peroxidase and aldehyde dehydrogenase reduce the toxic reactive oxygen species and aldehydes from the plant, respectively, and help to recover from drought stress. The study provides information about post-drought recovery mechanism in soybean.

Background Soybean is a nutritionally important source of proteins and oils. Organspecific analyses of the plants provided valuable information about physiological changes occurring in particular organ. However, studies on the vegetative stage soybean during the growth and development are lacking. Analyzing the growth stages of soybean at proteomic level is particularly important for understanding the growth dynamics. Objectives The main objective of this study was to investigate the organ-specific growth pattern of proteins during early growth stage. Methods Soybean (Glycine max L. cv Enrei) seeds were sown in each seedling case for 10 days and roots, hypocotyls, and leaves were collected. Proteins were extracted and analyzed by nano-liquid chromatography mass spectrometry. Mole percent abundance was calculated using emPAI values. To determine the functional role of the proteins identified in the MS analysis, functional categorization was performed using MapMan bin codes. Visualization of protein abundance ratio was performed using MapMan software. Enzyme activity and quantitative reverse transcription-polymerase chain reaction analyses were performed. Results A total of 357, 360, and 392 proteins were identified in root, hypocotyl, and leaf of vegetative stage soybean, respectively. Proteins related to stress, cell organization, transport, signaling, and mitochondrial electron transport chain decreased in root, hypocotyl, and leaf. Proteins related to protein metabolism, glycolysis, and cell wall were comparable in root and hypocotyl; however, in leaf, glycolysis and cell wall related proteins were decreased. Aldehyde dehydrogenase was decreased in abundance and activity in hypocotyl and leaf as compared to root. Major latex proteins 43 and 423 changed in abundance in an organ-specific manner. The mRNA expression level of major latex proteins exhibited a differential expression in the hypocotyl of soybean during flooding stress and recovery. Conclusion Our results suggest that aldehyde dehydrogenase and major latex proteins play key roles in growth of soybean in an organ-specific way.

The concentrations of trace metals were assessed using feathers of cattle egrets (Bubulcus ibis), collected within two industrial areas of Pakistan, Lahore and Sialkot. We found, in order of descending concentration: Zinc (Zn), Iron (Fe), Nickel (Ni), Copper (Cu), Cadmium (Cd), and Manganese (Mn), Chromium (Cr), Arsenic (As), and Lithium (Li), without any significant difference (except Fe, Zn, and Ni) between the two areas. The concentrations of trace metals, we recorded were among the highest ever reported in the feathers of avian species worldwide. The concentrations of Cr, Pb, Cd were above the threshold that affects bird reproductive success. The high contamination by heavy metals in the two areas is due to anthropogenic activities as well to natural ones (for As and Fe). The bioaccumulation ratios in eggs and feathers of the cattle egret, their prey, and the sediments from their foraging habitats, confirmed that avian feathers are a convenient and non-destructive sampling tool for the metal contamination. The results of this study will contribute to the environmental management of the Lahore and Sialkot industrial areas.

Climate change is a growing worldwide concern with respect to food security. Abiotic stresses are responsible for huge annual losses in agricultural productivity. In particular, flooding is a serious threat for many crops, including wheat and soybean, which exhibit dramatic reductions in growth and yield that result in the annual loss of billions of dollars. Flooding induces various adverse morphological and physiological effects, and forces plants to shift from aerobic to anaerobic metabolism through modifications at the molecular level. Proteomic analyses have greatly contributed to unraveling the flooding stress-response mechanisms that are adopted by different plant species, particularly soybean. The proteomic study of post-flooding recovery mechanisms has contributed to the search for flooding-responsive proteins and those that play essential roles in the transition from stress to post-stress conditions. This review summarizes the major findings from proteomic studies that have examined flooding stress-response mechanisms in important crop species. Furthermore, protein abundance changes and their significance during post-flooding recovery are discussed.

Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways. Biological significance This study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.

Soybean is an important legume crop that exhibits markedly reduced growth and yields under flooding conditions. To unravel the mechanisms involved in recovery after flooding in soybean root, gel-free proteomic analysis was performed. Morphological analysis revealed that growth suppression was more severe with increased flooding duration. Out of a total of 1645 and 1707 identified proteins, 73 and 21 proteins were changed significantly during the recovery stage following 2 and 4 days flooding, respectively. Based on the proteomic, clustering, and in silico protein-protein interaction analyses, six key enzymes were analyzed at the mRNA level. Lipoxygenase 1, which was increased at the protein level during the recovery period, was steadily down-regulated at the mRNA level. The peroxidase superfamily protein continuously increased in abundance during the course of recovery and was up-regulated at the mRNA level. HAD acid phosphatase was decreased at the protein level and down-regulated at the transcript level, while isoflavone reductase and an unknown protein were increased at both the protein and mRNA levels. Consistent with these findings, the enzymatic activity of peroxidase was decreased under flooding stress but increased significantly during the recovery sage. These results suggest that peroxidases might play key roles in post-flooding recovery in soybean roots through the scavenging of toxic radicals.

We investigated selected chlorinated pollutants (β-HCH, γ-HCH, DDDs, DDEs, o,p'-DDT, p,p'-DDT, heptachlor, aldrin, dieldrin, and endrin) in the Lahore and the Sialkot districts of Pakistan, using eggs of cattle egret (Bubulcus ibis) collected during May and June 2007. The pollutant with highest level and frequency was ΣDDT, followed by β-HCH, γ-HCH, heptachlor, aldrin, dieldrin, and endrin in descending order. The concentration(s) were significantly higher in Sialkot heronry for all the pollutants (except p,p'-DDT) than in Lahore. The values for DDTs, β-HCH, γ-HCH, and heptachlor were significantly higher (p0.05) in the egg(s) than in sediment(s) and in the chicks' diet, due to biomagnification. Among DDTs analogues, p,p'-DDD was the major contaminant with60 % of total DDT burden, reflecting the widespread aged as well as recent use of DDT as well as anaerobic degradation (DDD/DDE1 in many cases) in the nearby paddy soils. In few samples, p,p'-DDT/(DDD + DDE)0.5 suggested the recent emission patterns from surrounding contaminated areas of demolished DDT units and obsolete pesticide stores. The higher levels of HCHs (i.e., β-HCH) in the samples collected from Sialkot indicate exposure from long-term agricultural use. Overall, concentrations of all studied POPs were less than the threshold levels known to affect reproduction. Nevertheless, total DDTs and/or HCHs burdens in some eggs contained concentrations of greater than what would educe adverse effects on birds. This is among few studies on OCPs exposure to avian species, which provide the evidence of Pakistan's contribution toward the Global POPs emission.