Rice (Oryza sativa, Indica) is an important staple food crop and a major route for heavy metals (HMs) such as Cadmium (Cd) and Arsenic (As). These HMs disturb plant-nutrient uptake and stunt the growth and final crop yield. Being emerging regulators, the role of lncRNAs in metal toxicity remains largely unknown. The present study identified HM-responsive lncRNA in hydroponically grown Huanghuazhan (HHZ) rice. The transcriptomic analysis revealed 3,303 lncRNAs in HHZ rice treated with Cd and As. We found that 288 lncRNA transcripts were upregulated and 253 were downregulated in CK vs Cd. Contrastingly, CK vs As showed 278 up- and 314 down-regulated lncRNAs, while Cd vs As showed 285 and 251 were up- and down-regulated lncRNAs. In addition, WGCNA analysis showed four enriched modules correlating the protein-coding (PCs) genes with lncRNAs transcriptionally. Subsequently, the expression of selected lncRNAs-PCs targets like MSTRG.24054.4 negatively correlated with LOC_Os08g15204.1 under Cd and As stress in the root. These results suggest that lncRNAs may regulate the expression of PCs in response to excessive Cd and As contamination. Similarly, the cis-regulatory network analysis indicated the involvement of a few lncRNAs that control the expression of As and Cd stress-related genes. Furthermore, GO and KEGG pathway analyses specified 951 GO terms in 21 pathways, respectively. Our findings pinpointed the role of lncRNAs in Cd and As tolerance, which might used as a reference for future functional-based research to mitigate Cd and/or As contamination from the environment.

Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members of the oxidoreductase enzyme family, play a critical role in protecting plants against abiotic stresses. This study demonstrated a comprehensive investigation of the POD gene family in B. napus. As a result, a total of 109 POD genes were identified across the 19 chromosomes and classified into five distinct subgroups. Further, 44 duplicate events were identified; of these, two gene pairs were tandem and 42 were segmental. Synteny analysis revealed that segmental duplication was more prominent than tandem duplication among POD genes. Expression pattern analysis based on the RNA-seq data of B. napus indicated that BnPOD genes were expressed differently in various tissues; most of them were expressed in roots rather than in other tissues. To validate these findings, we performed RT-qPCR analysis on ten genes; these genes showed various expression levels under abiotic stresses. Our findings not only furnish valuable insights into the evolutionary dynamics of the BnPOD gene family but also serve as a foundation for subsequent investigations into the functional roles of POD genes in B. napus.

Multiple abiotic stresses such as drought, salinity, heat, and cold stress prevailing in natural habitats affect plant growth and development. Different species modify their structural and functional traits to combat these abiotic stresses while growing in stressful environments. Cenchrus species, i.e., Cenchrus pennisetiformis, C. setiger, and C. prieurii are widely distributed grasses found growing all over the world. Samples from natural populations were collected from different ecological regions in the Punjab and Khyber Pakhtoonkhwa that were exposed to aridity, salinity, and cold, while one site was designated as normal control. In the present study, structural and functional modifications of three Cenchrus species under abiotic stresses were evaluated. It was expected that each Cenchrus species may evolve different strategies to cope with multiple abiotic stresses. All Cenchrus species responded differently whether growing in normal environment or stressful conditions. The most remarkable feature for survival in C. pennisetiformis under cold stress was increased inflorescence and increased stem and root lignification. C. prieurii showed better tolerance to saline and cold environments. C. setiger showed better development of leaf sheath anatomical traits. The structural and functional modifications in Cenchrus species such as development of mechanical tissues provided structural support, while dermal and parenchymatous tissues increased water storage capacity and minimized water loss. An increase in the concentration of organic osmolytes and ionic content aids turgor pressure maintenance and ionic content crucial for plant growth and development. It was concluded that structural and functional alterations in all Cenchrus species were very specific and critical for survival under different environmental stresses. The ecological fitness of these species relied on maintenance of growth and biomass production, and the development of mechanical, vascular, dermal and parenchyma tissues under stressful environmental conditions. Moreover, accumulation of beneficial ions (K+ and Ca2+) and organic osmolytes were critical in turgor maintenance, hence survival of Cenchrus spp.

Three Cenchrus species (C. biflorus, C. ciliaris, and C. orientalis) were collected from different ecological regions in the Punjab and Khyber Pakhtoonkhwa during July to September 2020 to evaluate tolerance to multiple abiotic stresses (aridity, salinity, and cold). Growth and biomass production was the maximum in C. biflorus, C. ciliaris, and C. orientalis under aridity stress. Aerenchyma formation and vascular tissue increased significantly in roots under aridity. In C. ciliaris, aerenchyma formation was recorded under cold stress. Root vascular tissue was higher under normal conditions (26.7%) and aridity (30.4%) stress in C. ciliaris. Stem parenchyma (29.1%) and vascular tissues (35.5%) showed an increase in C. biflorus under aridity, while mechanical tissue (33.6%) increased significantly under salinity stress. In C. biflorus and C. ciliaris, extensive sclerification was recorded in the stelar region under aridity stress. The stem radius of C. orientalis was greatest under salinity (27.0%) and cold (29.1%) stress, while parenchyma tissue was smaller (12.1%) under cold stress. Leaf thickness generally increased under abiotic stresses, and the maximum (43.0%) thickness was recorded in C. biflorus under aridity stress. Cenchrus biflorus, C. ciliaris, and C. orientalis showed strong association among morphological and leaf anatomical traits under aridity stress. Cenchrus orientalis showed high sclerification outside the vascular bundles of the leaf sheath. In saline conditions, vascular bundles were sclerified and enlarged. In and outside the vascular bundles of leaf blades, extensive sclerification was observed under cold stress conditions. Modifications in structural and functional traits were critical for the ecological success of Cenchrus species for survival in multiple environmental stresses.

Salt excretory halophytes are the major sources of phytoremediation of salt-affected soils. Cressa cretica is a widely distributed halophyte in hypersaline lands in the Cholistan Desert. Therefore, identification of key physio-anatomical traits related to phytoremediation in differently adapted C. cretica populations was focused on. Four naturally adapted ecotypes of non-succulent halophyte Cressa cretica L. form hyper-arid and saline desert Cholistan. The selected ecotypes were: Derawar Fort (DWF, ECe 20.8 dS m(-1)) from least saline site, Traway Wala Toba (TWT, ECe 33.2 dS m(-1)) and Bailah Wala Dahar (BWD, ECe 45.4 dS m(-1)) ecotypes were from moderately saline sites, and Pati Sir (PAS, ECe 52.4 dS m(-1)) was collected from the highly saline site. The natural population of this species was collected and carefully brought to the laboratory for different structural and functional traits. As a result of high salinity, Na+, Cl-, K+, and Ca2+ content significantly increased at root and shoot level. At root level, some distinctive modifications such as increased sclerification in vascular bundles, enlarged vascular bundles, metaxylem vessels, phloem region, and storage parenchyma (cortex) are pivotal for water storage under extreme arid and osmotic condition. At the stem level, enhanced sclerification in outer cortex and vascular bundles, stem cellular area, cortical proportion, metaxylem and phloem area, and at the leaf level, very prominent structural adaptations were thicker and smaller leaves with increased density of salt glands and trichomes at surface, few and large stomata, reduced cortical and mesophyll parenchyma, and narrow xylem vessels and phloem area represent their non-succulent nature. The ecotype collected from hypersaline environments was better adapted regarding growth traits, ion uptake and excretion, succulence, and phytoremediation traits. More importantly, structural and functional traits such as root length and biomass, accumulation of toxic ions along with K+ in root and shoot, accumulation of Ca2+ in shoot and Mg2+ in root, excretion of toxic ions were the highest in this ecotype. In conclusion, all these alterations strongly favor water conservation, which certainly contributes to ecotypes survival under salt-induced physiological drought.

Salinity stress is one of the major abiotic stresses that affect plant growth and development worldwide. This study aimed to investigate the anatomical attributes of widely distributed halophytic halophytes which are economically important due to their numerous bioactive compounds of high nutritive value. The members of the family Cyperaceae are of high importance among halophytes due to their ability to grow in a diverse range of environments. The study of anatomical attributes of C. exaltatus Retz. in varying salt-affected habitats is a novel approach and has not been reported earlier. For this purpose, different populations of C. exaltatus were collected from a diverse range of saline habitats and analyzed for variation in their morphoanatomical attributes in response to varying degree of salinity. The results showed that C. exaltatus can grow under higher salinity levels, but excessive salts of growth medium caused a reduction in overall plant growth. The anatomical modifications along salinity gradient observed in C. exaltatus included an increase in the size of vascular bundles, formation of lysigenous aerenchyma cavities, and high intensity of sclerification. These modifications enabled C. exaltatus to survive in a saline environment and provide a useful resource for the revegetation of coastal areas and hypersaline -degraded rangelands in Pakistan. Overall, this study provides insight into the anatomical attributes of C. exaltatus and its ability to survive in hypersaline environments. The findings of this study may have practical applications for the cultivation of halophytes in saline soils for the purpose of food and feed production, as well as for the restoration of degraded ecosystems.

The present research was carried out to determine the spatiotemporal variation in accumulation of different nutritional and medicinal components in Dicliptera bupleuroides from the Soone valley in the Salt Range of Punjab, Pakistan. Most of the biochemical attributes were higher in the spring season than those in the other seasons; this might have been due to high soil pH during spring. High amounts of minerals and high pH are necessary for the synthesis of alkaloids, phenols, flavonoids, and fibers. Proteins, N, dry matter, fats and nitrogen free extract (NFE) were higher in summer, which might have been due to considerable availability of macro-nutrients during this season due to high moisture content because of high rainfall during the season. Spatial variation showed that phenols and flavonoids were associated with the population from Khabeki site (despite enough minerals and moisture availability) which might have been due to physical injuries caused by grazing and cutting. Minerals, proteins and N were also associated with the Khabeki population probably due to large amounts of minerals and moisture retention in the soil of the site and prevalent optimum environmental conditions therein. Alkaloids, fats, moisture and some minerals were associated with Anga and Knotti Garden sites which might have been due to high pH and prolonged salt stressed conditions at both sites.

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Phosphoenolpyruvate carboxylase (PEPC) gene family is essential in regulating plant growth and abiotic stress response. Based on the sequenced Brassica napus genomes, a comprehensive analysis of PEPC homolog genes identified 15 in B. napus. These genes were categorized into four subgroups: PTBC-II, PTPC-III, PTPC-IV, and PTPC-V; genes in each subgroup displayed conserved gene structures and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Cis-elements and expression analyses revealed that BnaPEPC homologs might respond to abiotic stresses. The expression of a few BnaPEPC genes (BnaPEPC2, BnaPEPC4, BnaPEPC6, BnaPEPC9) was induced in response to IAA, ABA, JA, and GA in leaf while in root BnaPEPC6 and BnaPEPC9 was significantly responsive to all applied hormone stresses. BnaPEPC2, BnaPEPC4, BnaPEPC6, BnaPEPC9, and BnaPEPC10 showed significant responses to cold, heat, drought, and salinity in leaf tissues, while BnaPEPC1, BnaPEPC2, BnaPEPC6, and BnaPEPC9 exhibited highest expression levels in root tissues under cold, heat, drought, and salt stress. The present study provides new information to decipher the evolution and function of PEPC genes in B. napus.

Brassica napus is an important oil crop and cold stress severely limits its productivity. To date, several studies have reported the regulatory genes and pathways involved in cold-stress responses in B. napus. However, transcriptome-scale identification of the regulatory genes is still lacking. In this study, we performed comparative transcriptome analysis of cold-tolerant C18 (CT - C18) and cold-sensitive C6 (CS - C6) Brassica napus genotypes under cold stress for 7 days, with the primary purpose of identifying cold-responsive transcription in B. napus. A total of 6061 TFs belonging to 58 families were annotated in the B. napus genome, of which 3870 were expressed under cold stress in both genotypes. Among these, 451 TFs were differentially expressed (DE), with 21 TF genes expressed in both genotypes. Most TF members of the MYB (26), bHLH (23), and NAC (17) families were significantly expressed in the CT - C18 genotype compared with the CS - C6 B. napus genotype. GO classification showed a significant role in transcription regulation, DNA-binding transcription factor activity, response to chitin, and the ethylene-activated signaling pathway. KEGG pathway annotation revealed these TFs are involved in regulating more pathways, resulting in more tolerance. In conclusion, the results provide insights into the molecular regulation mechanisms of B. napus in response to freezing treatment, expanding our understanding of the complex molecular mechanisms in plants' response to freezing stress.

Sugarcane (Saccharum spp. hybrids) is a worldwide acclaimed important agricultural crop used primarily for sugar production and biofuel. Sugarcane’s genetic complexity, aneuploidy, and extreme heterozygosity make it a challenging crop in developing improved varieties. The molecular breeding programs promise to develop nutritionally improved varieties for both direct consumption and commercial application. Therefore, to address these challenges, the development of simple sequence repeats (SSRs) has been proven to be a powerful molecular tool in sugarcane. This study involved the collection of 285216 expressed sequence tags (ESTs) from sugarcane, resulting in 23666 unigenes, including 4547 contigs. Our analysis identified 4120 unigenes containing a total of 4960 SSRs, with the most abundant repeat types being monomeric (44.33%), dimeric (13.10%), and trimeric (39.68%). We further chose 173 primers to analyze the banding pattern in 10 sugarcane accessions by PAGE analysis. Additionally, functional annotation analysis showed that 71.07%, 53.6%, and 10.3% unigenes were annotated by Uniport, GO, and KEGG, respectively. GO annotations and KEGG pathways were distributed across three functional categories: molecular (46.46%), cellular (33.94%), and biological pathways (19.6%). The cluster analysis indicated the formation of four distinct clusters among selected sugarcane accessions, with maximum genetic distance observed among the varieties. We believe that these EST-SSR markers will serve as valuable references for future genetic characterization, species identification, and breeding efforts in sugarcane.

Plant performance is mainly estimated based on plant architecture, leaf features and internal microstructural changes. Olive (Olea europaea L.) is a drought tolerant, oil yielding, and medium sized woody tree that shows specific structural and functional modifications under changing environment. This study was aimed to know the microstructural alteration involving in growth and yield responses of different Olive cultivars. Eleven cultivars were collected all over the world and were planted at Olive germplasm unit, Barani Agricultural Research Institute, Chakwal (Punjab) Pakistan, during September to November 2017. Plant material was collected to correlate morpho-anatomical traits with yield contributing characteristics. Overall, the studied morphological characters, yield and yield parameters, and root, stem and leaf anatomical features varied highly significantly in all olive cultivars. The most promising cultivar regarding yield was Erlik, in which plant height seed weight and root anatomical characteristics, i.e., epidermal thickness and phloem thickness, stem features like collenchymatous thickness, phloem thickness and metaxylem vessel diameter, and leaf traits like midrib thickness, palisade cell thickness a phloem thickness were the maximum. The second best Hamdi showed the maximum plant height, fruit length, weight and diameter and seed length and weight. It also showed maximum stem phloem thickness, midrib and lamina thicknesses, palisade cell thickness. Fruit yield in the studied olive cultivars can be more closely linked to high proportion of storage parenchyma, broader xylem vessels and phloem proportion, dermal tissue, and high proportion of collenchyma.

Context Allelopathy is recognised as a potential technology to control weeds, and could also be a suitable approach for enhancement of crop yield. Aims The study was conducted to investigate the allelopathic role of Averrhoa carambola leaf extract on growth, anatomical and physiological features of three wheat lines, namely 3094, 7076 and A2011. Methods Three dilutions i.e. 0% (control), 15% and 30% of the leaf aqueous extract were applied at 15 day intervals (total five applications) on wheat lines until maturity. Key results All wheat lines showed differential behaviour to allelochemicals of A. carambola leaf extract. Increased root area was accompanied by a high proportion of storage parenchyma tissues and enlarged vascular bundles in line 3094. Disintegration of root cortical parenchyma and complete transformation of chlorenchyma into sclerenchyma in stem was recorded in all wheat lines, particularly at the highest concentration of leaf extract. Line 7076 showed very different behaviour, as it possessed a proportionally enlarged root cortex, enlarged stem vascular bundles and increased leaf thickness, primarily at the highest concentration of leaf extract. Line A2011 was relatively more sensitive, indicating a significant reduction (P < 0.05) in root and stem area and deformed leaves. Conclusions A low concentration (15%) of leaf extract promoted growth and development, whereas a higher concentration caused significant reduction in growth and anatomical attributes. Implications A lower dose of Averrhoa leaf extract promoted growth and development in all wheat lines, and hence can be used as a growth promoter. A higher concentration is important for eradicating unwanted plants.

Chrysopogon serrulatus (false beard-grass) is a dominant component of vegetation in the foothills of the Himalayas. To study whole plant morphology, individuals of C. serrulatus were collected from three plots at each of six locations spanning from 400 to 1,400 m. The population colonizing the highest elevation showed noticeable morphological modifications in different plant organs. Roots showed increased xeromorphy, specifically increased metaxylem number and area. In the stem, especially outside of the vascular tissue, there was intensive sclerification indicative of increased xeromorphy as a survival strategy. At the highest elevation, leaves were wider; aerenchyma formation and increased sclerification were noted in the leaf sheath; and a greater proportion of storage parenchyma was observed in the leaf blade, all indicators of succulence. In contrast, leaves at lower elevations had xeric morphological features such as increased epidermal thickness, sclerification and more developed metaxylem area. In conclusion, shifting of morphological features in below- and above-ground plant parts of C. serrulatus were linked to shifts in environmental factors along this elevation gradient, thus enabling the successful distribution of this species along this elevation gradient.

Salinity, drought, and temperature stresses are major environmental threats that change the plants' distributional pattern in natural ecosystems. Cenchrus prieurii (Kunth) Maire is a typical desert grass species that can colonize different habitats i.e., cool mountains, arid and semiarid regions. It was hypothesized that wide adaptability potential in Cenchrus prieurii may be linked to plasticity in morpho-anatomical features. Cenchrus prieurii populations were collected from different habitats of the Punjab, Khyber Pakhtoonkhwa and Azad Jammu and Kashmir, which were exposed to multiple environmental stresses, i.e., aridity, salinity, waterlogging and cool temperature and were evaluated for foliar structural modifications. All populations showed morpho-anatomical modifications that were related to water conservation. The Thal Desert populations such as collected from inter-dune flats (DID), marginal area (DMA) and loamy sand (DLS) were superior in midrib, lamina, epidermal and mesophyll thicknesses, and phloem area. The populations facing cold stress like foothill region (CFH) showed thicker lamina, epidermal, thickness, and larger vascular bundles and metaxylem vessels. The population from highest elevation (CHE) collected from the coolest habitats showed the largest parenchymatous cells. The sand dune population (DSD) was collected from the driest area had the thinnest leaves (midrib and lamina), epidermis layer and mesophyll, the smallest parenchymatous cells, bulliform cells, metaxylem vessels and vascular bundles. Another specific feature of SDS population was the formation of large aerenchymatous cavities and numerous microhairs in leaf sheath. Plasticity in anatomical traits was significantly high in all populations, and this might be a strong reason for successful colonization and adaptability of this species to a variety of habitat types, hence contributing significantly to its wide distributional range.

Using halophytes for phytoremediation is an environmentally friendly technique, now gaining importance all over the world. Fagonia indica Burm. f. (Indian Fagonia) is primarily distributed in salt-affected lands of the Cholistan Desert and surrounding habitats. Four populations with three replications from salt-affected habitats were collected from natural habitats to evaluate structural and functional adaptation for salinity tolerance and phytoremediation of hypersaline habitats. The populations collected from the highest saline sites Pati Sir (PS) and Ladam Sir (LS) had restricted growth habit, increased accumulation of K+ and Ca2+ along Na+ and Cl−, more excretion of Na+ and Cl−, increased cross-sectional area of root and stem, larger exodermal and endodermal cells in roots, and broad metaxylem area. Sclerification in stem was high in population. Specific modifications in leaves were reduced stomatal area and increased adaxial epidermal cell area. Important traits associated with phytoremediation potential of F. indica populations (Pati Sir and Ladam Sir) were deeper roots and taller plants, increased density of salt glands on leaf surface, and high excretion of Na+. Additionally, higher bio-concentration factor, translocation factor, and dilution factor for Na and Cl− in same Ladam Sir and Pati Sir population were identified as key phytoremediation attributes. The plants of F. indica colonizing high salinities (Pati Sir and Ladam Sir) were, therefore, more efficient in phytoremediation of saline soils as these populations accumulated and/or excrete toxic salts. Density of salt glands remarkably increased in the Pati Sir population collected from the highest salinity. This population accumulated and excreted the highest amount of Na+ and Cl−. The dilution factor of Na+ and Cl− ions was also the highest in this population. Anatomical modifications such as root and stem cross-sectional areas, proportion of storage parenchyma, and broad metaxylem vessels were the maximum in Pati Sir population. These modifications indicate not only better salt tolerance of the Pati Sir population but also better in accumulation and excretion of toxic salts. This population can potentially rehabilitate hypersaline uncultivated lands through green reclamation.

Herbicides are widely used to kill weeds and increase crop production all over the world. Nevertheless, some weeds show certain structural modifications in response to herbicide application that impart mostly partial or sometimes complete tolerance to these noxious plants. The present study was focused on morpho-anatomical modifications in the root, stem, and leaves of Dactyloctenium aegyptium (L.) Willd. treated with different herbicides and to examine whether it possesses tolerance against herbicides. Two pre- and four post-emergence herbicides were applied to D. aegyptium at the recommended dose in a randomized complete block design (RCBD). Pre-emergence herbicide Bromoxynil enhanced root growth (30%), leaves per plant (3%), and leaf fresh weight (17.2%). Increased stem epidermal thickness (100%) was the most notable feature among anatomical attributes. Post-emergence herbicides generally increased stem epidermal thickness 33–56%), leaf sheath thickness (5%), and root area in roots. Other modifications included increased sclerenchymatous thickness in the stem (133–255%), and epidermal thickness (100–200%) in the leaf blade. These characters assisted D. aegyptium to cope with herbicide toxicity. Collectively, pre-emergence herbicides more effectively controlled D. aegyptium compared with post-emergence herbicides.

Man is using plants for curing different diseases for several hundred years. In Pakistan, rangelands and forests are the major sources of medicinal plants, and the residents of different areas including those of the Vanhar Valley depend upon local plants for the medication of several diseases. However, this study was planned to enlist the indigenous medicinally important flora, which will help in conservation of the vanishing knowledge about the indigenous plants of the area by proper documentation. In order to document the uses of indigenous plants, some surveys were conducted for the collection of all available species. For the documentation of uses of these indigenous plant species, 55 experts were interviewed and their knowledge was documented. A total of 41 species belonging to 25 families were recorded from the Vanhar Valley. High numbers of species of families Fabaceae, Amaranthaceae and Asteraceae were used for the cure of several diseases like sexual disorders, piles, asthma, sputum, stomach disorders, diabetes, etc. It was evident that the older people had most of the knowledge about the indigenous plants of the Valley, while the young lacked such knowledge due to the death of older people without documenting or transferring the knowledge to them. With conservation of the knowledge, these plants can be used as a low-cost and effective treatment of many common diseases.