Abstract The availability of pangenome and resequencing of wheat collections have facilitated the discovery of gene-trait associations in wheat. Yellow stripe-like (YSL) proteins play a key role in the uptake and translocation of metals and yet have not been fully identified and analyzed at the genome-wide level in wheat. In this study, 26 TaYSL genes were identified and divided into four distinct clades, each clade sharing similar domains and motif compositions. Most genes were upregulated under iron deficiency, whereas homoeologs of TaYSL1 were downregulated. Both SNP-based and haplotype-based association studies were used to dissect the role of TaYSLs underpinning grain iron contents (GFeC) and zinc contents (GZnC) in wheat. TaYSL6-2B and TaYSL16-1A haplotypes showed strong association with GFeC, and TaYSL14-6A showed strong association with GZnC in multiple field trials. The distribution of favorable haplotypes in global wheat collection of ∼3000 accessions showed that majority of haplotypes were more prevalent in landraces and winter wheat compared to modern cultivars and spring types, indicating their potential for use in breeding. The combination of favorable haplotypes of three YSL genes associated with GFeC and GZnC were very rare, and most of the wheat accessions has single or double favorable haplotypes. These findings provide the first comprehensive characterization of the TaYSL gene family in wheat and identify significant SNPs and elite haplotypes that can be utilized for genetic improvement and biofortification.

A high grain zinc wheat cultivar, Zincol-2016, was released in Pakistan to mitigate mineral malnutrition. Here, we used RNAseq based approach to reveal transcriptional landscape of its developing grains, and to identify genetic variants in zinc (Zn) and iron (Fe) homeostasis genes. Differential gene expression analysis identified 8370 differentially expressed genes (DEGs) over the course of grain filling. The profiling of 265 Fe/Zn homeostasis genes revealed the homeologs of TaNAS9 , TaFER1, TaNAAT2 , TaDMAS, TaZIFL5-A , TaZIFL5-D , TaZIP14-B , TaNRAMP3 , TaVIT1, TaPRI2-D , TabZIPF1-7B , TabZIPF1-7D , TabZIPF2-5A , and TabZIPF2-5B had increased expression in Zincol-2016 relative to other cultivars from expVIP database. The variant calling identified 358 SNPs and 34 InDels in the Fe/Zn homeostasis genes. Two of those SNPs in TaZIP14-B ( TraesCS3B02G140400 ), and TaNAAT2-B ( TraesCS1B02G300600 ), were associated with grain zinc and iron concentrations (GZnC and GFeC) in a diverse panel of 145 wheat cultivars. The Zincol-type alleles of both genes significantly increased GZnC and GFeC by 7.3 -8.6% and 5.9 -6.3%, respectively. In addition, 8 SNPs causing missense mutation and 2 InDels causing frameshift mutation were found unique to Zincol. The present study forms a basis for understanding the genetic basis of high GZnC and GFeC in Zincol-2016 and can help efforts to biofortify other wheat varieties.

Drug delivery systems based on ring-like 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) are increasingly used in the treatment of cancer. The influence of these carrier over the anticacerous potential of drug molecules is underway to investigation. So the current study is comparative design to elucidate the effect of inclusion complexation of metal-hydroxy flavones with HP-β-CD. The three hydroxy flavones named as, 5-Hydroxyflavone (5HF), 2′,4′,3,5,7-Pentahydroxyflavone (2′-PHF) and 3′,4′,3,5,7-Pentahydroxyflavone dihydrate (3′-PHF) and their Cu(II) and Fe(III) complexes were subjected to inclusion complexation with 2-hydroxylpropyl beta cyclodextrin (HP-βCD) having stability constants values with order of 103M-1 leading to their aqueous solubility. 3′-PHF-HP-βCD, Cu-3′-PHF-HP-βCD, Fe-3′-PHF-HP-βCD, 2′-PHF-HP-βCD, Cu-2′-PHF-HP-βCD, Cu-5HF-HP-βCD and Fe-5HF-HP-βCD complexes bound with DNA through intercalation while 5HF-HP-βCD exhibited electrostatic interaction of with DNA. Comparison of their anti-cancerous potential of M-HFs-HP-βCD complexes with that of M-HFs against U-87 cancerous cell lines revealed that intercalating 3′-PHF-HP-βCD, Cu-3′-PHF-HP-βCD, Fe-3′-PHF-HP-βCD, Cu-5HF-HP-βCD and Fe-5HF-HP-βCD led to less cancer cell viablity than their M-HFs counter parts. In antimicrobial assay, Cu-3′-PHF-HP-βCD, Cu-2′-PHF-HP-βCD exhibited excellent response against bacterial strains i.e.; Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. On other side, Fe-3′-PHF-HP-βCD, Cu-5HF-HP-βCD and Fe-2′-PHF-HP-βCD exhibited reasonable antimicrobial activities when compared with standard drug ampicillin. Thus, HP-βCD inclusion of M-HFs resulted in enhancement of their anti-cancerous and anti-microbial potentials.

Brinjal or eggplant ( Solanum melongena L.) of family Solanaceae is grown widely as cultivated crop worldwide due to their great economic importance. It plays a significant role in human diet and health and have both phenotypic and genotypic diversity as well. The estimation of genetic diversity in eggplant is important for selecting the best genotypes for making improvement in crop as well as to broaden the genetic variations in breeding programs. The present study is aimed at evaluating the evolutionary divergence pattern and genetic relationship among 33 genotypes of eggplant selected from different ecogeographical regions of the world based on a chloroplast gene. To achieve the main objective, rps 11 gene from eggplant genotypes was amplified, sequenced and analyzed by using bioinformatics tools. The constructed phylogram by MEGA X grouped the 33 genotypes into two main clusters (cluster 1 and cluster 2) irrespective of geographic divergence with a narrow genetic diversity of 0.01% revealing the monophyletic origin in these brinjal accessions. This may be due to their limited sequence variability in rps 11 sequences. Divergence ranged from 0.01 to 0.12 with an average of 0.04 on the basis of pair wise distance calculation. In phylogenetic tree, BARI-1, Grif-13962, 036693, 033836, 033839, Kemar and Viserba were the most similar genotypes with overall bootstrap value of 99%, while Badanjan and MK-95 genotypes showed distant relationship. The presented results of low genetic variation and close phylogenetic relatedness strongly suggest that rps 11 gene is a potential source for assessing the phylogeny and diversity analysis among brinjal germplasm. This study also concluded that genetic diversity does not depend upon the geographical origin of eggplant. Additionally, it is hoped that this information will help to guide future germplasm collecting and genetic relationship of eggplant.

Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson’s correlation coefficients between root phenotypes and expression of root-specific genes varied from −0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.

Medicinal plants in most of societies have been a source of quality health care. The indigenous populations are getting many ethnomedicinal products form local biodiversity. The current study aimed to investigate anti-diabetic plants in 8 villages (Patriata, Surasi, Charhan, Lower toppa, Ghikagali, Kashmir point, Pindi point and Shawala) of rural Murree. The methodology included preparation of questionnaire, identification of plants and phytochemical analysis. The informants were asked about vernacular name, part used and folk recipe. The quantitative study included fidelity level, use value and relative frequency of citation of plant species. Data indicated that 30% of patients use local herbs to treat diabetes. The most significant plant species were Berberis lycium with use value of 0.50 followed by Melia azedarach with use value of 0.43 and Himalaiella heteromalla with use value of 0.33. Himalaiella heteromalla was selected for phytochemical analysis. Total flavonoid content was 7.25±0.08mg (ethanol extract) and 6.03±0.13mg (chloroform extract) quercetin equivalent/gm of extract; total phenolic content was 53.92±0.47mg (ethanol extract) and 72.75±0.48mg (chloroform extract) quercetin equivalent/gm of extract; total β-Carotene content was 29.7μg/g in ethanol extract, and 27.26μg/g in chloroform extract while total lycopene content was 46.33μg/g (ethanol extract) and 41.54μg/g (chloroform extract) in H. heteromalla. The results suggest that medicinal plants of Murree region may be potential natural resources for antidiabetic compounds.

Background. Solanum melongena is a medicinally important vegetable crop that belongs to the family Solanaceae, which is cultivated worldwide. Methodology. In the present study, 22 eggplant varieties from the different ecogeographical regions were evaluated for nine quantitative and twenty-two qualitative morphological characters. A significant divergence was observed in all characters and wide regional variations for plant characteristics, flower, and fruit characteristics. Principle component analysis (PCA) was performed using PAST3 software to determine the relationship among eggplant accessions. Results. The principal component analysis showed that the first two principal component axes explained 97.17% of the total multivariate variation. Cluster analysis using the Unweighted Pair Group Method of Arithmetic Means (UPGMA) grouped the 22 eggplant accessions into two main clusters based on similarities in morphological characteristics. The study showed that the Solanum melongena accessions belonging to Pakistan and other geographical regions of the world possess marked variation in fruit weight, fruit shape, fruit color, leaf spine, number of locules in fruit, plant height, and flower color. Conclusion. Based on morphological diversity, the best cultivars of eggplant that show better yield can be selected for farmers.

Wheat (Triticum aestivum L.), being a staple food crop, is an important nutritional source providing protein and minerals. It is important to fortify staple cereals such as wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy-dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r = 0.90), compared to GFe (r = 0.68). Modern cultivars such as Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70, released before 1970, also exhibited higher values of GFe and GZn; however, their agronomic performance was poor. Multivariate analysis using eleven micronutrients (Fe, Zn, Al, Ca, Cu, K, Mg, Mn, Na, Se and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification and wider genetic diversity. Genetic gain analysis identified a significant increase in grain yield (0.4% year−1), while there was negative gain for GFe (−0.11% year−1) and GZn (−0.15% year−1) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had a strong association with plant height and grain yield (GY), while semi-dwarfing alleles had a negative effect on GFe and GZn contents. This study provided a valuable insight into the biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification.

Wheat (Triticum aestivum L.) being a staple food crop is an important nutritional source providing protein and minerals. It is important to fortify staple cereals like wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r=0.90), compared to GFe (r=0.68). Modern cultivars like Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70 released before 1970 also exhibited higher value of GFe and GZn, however their agronomic performance was poor. Multivariate analysis using ten micronutrients (Al, Ca, Cu, K, Mg, Mn, Na and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification trait and wider genetic diversity. Genetic gain analysis identified significant increase in grain yield (0.4% year-1), while there was negative gain for GFe (-0.11% year-1) and GZn (-0.15% year-1) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had strong association with plant height, and grain yield (GY), while semi-dwarfing alleles had negative effect on GFe and GZn contents. This study provided a valuable insight into biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification.

The plant microbiome influence plant health, yield and vigor and has attained a considerable attention in the present era. In the current study, native bacterial community composition and diversity colonizing Triticum aestivum L. rhizosphere at two distant geographical locations including Mirpur Azad Kashmir and Islamabad was elucidated. Based on IonS5™XL platform sequencing of respective samples targeting 16S rRNA gene that harbor V3-V4 conserved region revealed 1364 and 1254 microbial operational taxonomic units (OTUs) at ≥97% similarity and were classified into 23, 20 phyla; 70, 65 classes; 101, 87 orders; 189,180 families; 275, 271 genera and 94, 95 species. Respective predominant phyla accounting for 97.90% and 98.60% of bacterial community were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Gemmatimonadetes. Diversity indices revealed variations in relative abundance of bacterial taxa owing to distant geographical locations however predominant bacterial taxa at both locations were similar. These findings paved a way to dissect consequence of associated microbiota on future wheat production system.

Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all the available proteomic data we prioritized the novel proteins ideal for vaccine development using bioinformatics tools and techniques. Among the huge data, eight proteins passed all the barriers and were considered ideal candidates for vaccine development. These include: copper silver efflux system outer membrane protein (CusC), outer membrane porin protein (OmpN), Fe++ enterobactin transporter substrate binding protein (fepB), zinc transporter substrate binding protein (ZnuA), ribonuclease HI, tellurite resistant methyltransferase (the B), and two uncharacterized hypothetical proteins (WP_002918223 and WP_002892366). These proteins were also subjected to epitope analysis and were found best for developing subunit vaccine against K. pneumoniae. The study shows that the potential vaccine targets are sufficiently efficient being virulent, of outer membranous origin and can be proposed for the DNA third-generation vaccines development that would help to cope up infections caused by multidrug-resistant K. pneumoniae.

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

The present study was designed to analyze genetically somaclonal variants using biochemical and molecular markers. Efficient tissue culture protocol for Solanum melongena L. cv. Nirrala was developed. Maximum callus induction (100%) was observed for Murashige and Skoog (MS) media supplemented with 2.0 mg L−1 naphthalene acetic acid +0.5 mg L−1 6-benzylaminopurine; and nodal explants gave best callusing response (88.8%) as compared to internodes (88.3%) and leaves (87.7%). The best shooting was induced on nodal and internodal callus in the presence of 2.0 mg L−1 6-benzylaminopurine. Total soluble protein content of callus and regenerated variant plants was estimated for biochemical analysis, and largest amount of soluble protein was found in callus (6.54 mg g−1 fresh tissue) followed by variant plant grown on 2.0 mg L−1 6-benzylaminopurine (5.96 mg g−1 fresh tissue). Random amplification of polymorphic DNA technique was done with five decamer primers (OPC1-OPC5) and maximum polymorphism was detected by OPC 2 (26.99%) among all samples, whereas nodal callus on media containing 1.0 mg L−1 naphthalene acetic acid +1.0 mg L−1 6-benzylaminopurine showed highest polymorphism producing 22 bands, out of which 8 bands were polymorphic. The study shows that this marker system can provide better evaluation of genetic variation induced by tissue culture.

Tissue culture and genetic analysis of somaclonal variations of Solanum melongena L. cv. Nirrala Abbreviations BAP – 6-Benzylaminopurine; CTAB – Cetyltrimethylammonium bromide; 2,4-D – 2,4-dichlorophenoxyacetic acid; KN – kinetin; MS –Murashige and Skoog; NAA –Naphthalene acetic acid; TAE – tris acetate EDTA.