Meta QTL analysis for dissecting abiotic stress tolerance in chickpea

BACKGROUND

Chickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea.

RESULTS

A meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc. CONCLUSION: The results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.

Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)

The grain-filling stage in Triticum aestivum (wheat) is highly vulnerable to increasing temperature as terminal heat stress diminishes grain quality and yield. To examine the mechanism of terminal heat tolerance, we performed the biochemical and gene expression analyses using two heat-tolerant (WH730 and WH1218) and two heat-sensitive (WH711 and WH157) wheat genotypes. We observed a significant increase in total soluble sugar (25%-47%), proline (7%-15%), and glycine betaine (GB) (22%-34%) contents in flag leaf, whereas a decrease in grain-filling duration, 1000-kernel weight (8%-25%), and grain yield per plant (11%-23%) was observed under the late-sown compared to the timely sown. The maximum content of osmolytes, including total soluble sugar, proline, and GB, was observed in heat-tolerant genotypes compared to heat-sensitive genotypes. The expression of 10 heat-responsive genes associated with heat shock proteins (sHsp-1, Hsp17, and HsfA4), flavonoid biosynthesis (F3'-1 and PAL), β-glucan synthesis (CslF6 and CslH), and xyloglucan metabolism (XTH1, XTH2, and XTH5) was studied in flag leaf exposed to different heat treatments (34, 36, 38, and 40°C) at 15 days after anthesis by quantitative real-time polymerase chain reaction. A significant increase in the relative fold expression of these genes with increasing temperature indicated their involvement in providing heat-stress tolerance. The high differential expression of most of the genes in heat-tolerant genotype "WH730" followed by "WH1218" indicates the high adaptability of these genotypes to heat stress compared to heat-sensitive wheat genotypes. Based on the previous results, "WH730" performed better in terms of maximum osmolyte accumulation, grain yield, and gene expression under heat stress.

Strategies for economic utilization of rice straw residues into value-added by-products and prevention of environmental pollution

Rice straw management, along with the prevalent practice of residue burning, poses multifaceted challenges with substantial environmental and human health implications. After harvest, a considerable amount of straw is left behind, often disposed of through burning, releasing several pollutants into the environment. Carbon dioxide (CO2) dominates at 70%, accompanied by methane (CH4) at 0.66%, carbon monoxide (CO) at 7%, and nitrous oxide (N2O) at 2.09%. This process further compounds issues by depleting soil nutrients like nitrogen and organic matter. This review focuses on strategies for residue management and using straw as value-added by-products. We address research gaps and offer potential recommendations for rice straw management using economically feasible and practical routes. We elaborate that to improve rice straw digestibility, utilization in mushroom cultivation, and other value-added products, low silica (Si) rice varieties must be developed using modern technologies including marker-assisted selection breeding or genome editing. Developing low Si rice could also reduce arsenic uptake by rice, as rice plants use the same transporters for the uptake of both elements. Conversely, silica is also indispensable for quality rice production; hence, optimizing silicon content in rice is worth investigating. More research is required to understand the extent of silicon's effect on the utilization of straw for various purposes. This review also discusses the importance of educating farmers about the straw burning issue and its environmental consequences. We highlight the significance of tailoring rice straw management methods to local suitability, moving away from a universal approach. More extension work is needed to encourage farmers to opt for environmentally and economically sound options for rice straw management. Policy intervention to incentivize farmers and develop technologies for the widespread use of rice straw for various industries and product development could help in the management of rice straw and will also create a circular economy.

Nanoparticles as novel elicitors in plant tissue culture applications: Current status and future outlook

Plant tissue culture is the primary, fundamental, and applied aspect of plant biology. It is an indispensable and valuable technique for investigating morphogenesis, embryogenesis, clonal propagation, crop improvements, generation of pathogen-free plants, gene transfer and expression, and the production of secondary metabolites. The extensive use of various nanoparticles (NPs) in fields such as cosmetics, energy, medicine, pharmaceuticals, electronics, agriculture, and biotechnology have demonstrated positive impacts in microbial decontamination, callus differentiation, organogenesis, somatic variations, biotransformation, cryopreservation, and enhanced synthesis of bioactive compounds. This review summarizes the current state of knowledge with regard to the use of nanoparticles in plant tissue culture, with a particular focus on the beneficial outcomes. The positive (beneficial) and negative (toxic) effects of engineered NPs in tissue culture medium, delivery of transgenes, NPs toxicity concerns, safety issues, and potential hazards arising from utilization of nanomaterials in agriculture through plant tissue culture are discussed in detail, along with the future prospects for these applications. In addition, the potential use of novel nanomaterials such as graphene, graphite, dendrimers, quantum dots, and carbon nanotubes as well as unique metal or metalloid NPs are proposed. Further, the potential mechanisms underlying NPs elicitation of tissue culture response in different applications are critically evaluated. The potential of these approaches in plant nanobiotechnology is only now becoming understood and it is clear that the role of these strategies in sustainably increasing crop production to combat global food security and safety in a changing climate will be significant.

Physiological traits and expression profile of genes associated with nitrogen and phosphorous use efficiency in wheat

BACKGROUND

Nitrogen (N) and phosphorous (P) play a very important role in the growth and development of wheat as well as major constituents of biological membranes. To meet the plant's nutritional demand these nutrients are applied in the form of fertilizers. But the plant can utilize only half of the applied fertilizer whereas the rest is lost through surface runoff, leaching and volatilization. Thus, to overcome the N/P loss we need to elucidate the molecular mechanism behind the N/P uptake.

METHODS

In our study, we used DBW16 (low NUE), and WH147 (high NUE) wheat genotypes under different doses of N, whereas HD2967 (low PUE) and WH1100 (high PUE) genotypes were studied under different doses of P. To check the effect of different doses of N/P, the physiological parameters like total chlorophyll content, net photosynthetic rate, N/P content, and N/PUE of these genotypes were calculated. In addition, gene expression of various genes involved in N uptake, utilization, and acquisition such as Nitrite reductase (NiR), Nitrate transporter 1/Peptide transporter family (NPF2.4/2.5), Nitrate transporter (NRT1) and NIN Like Protein (NLP) and induced phosphate starvation (IPS), Phosphate Transporter (PHT1.7) and Phosphate 2 (PHO2) acquisition was studied by quantitative real-time PCR.

RESULTS

Statistical analysis revealed a lower percent reduction in TCC, NPR, and N/P content in N/P efficient wheat genotypes (WH147 & WH1100). A significant increase in relative fold expression of genes under low N/P concentration was observed in N/P efficient genotypes as compared to N/P deficient genotypes.

CONCLUSION

Significant differences in physiological data and gene expression among N/ P efficient and deficient wheat genotypes could be useful for future improvement of N/P use efficiency.

Effect of stem structural characteristics and cell wall components related to stem lodging resistance in a newly identified mutant of hexaploid wheat (Triticum aestivum L.)

In wheat, lodging is affected by anatomical and chemical characteristics of the stem cell wall. Plant characteristics determining the stem strength were measured in lodging tolerant mutant (PMW-2016-1) developed through mutation breeding utilizing hexaploid wheat cultivar, DPW-621-50. Various anatomical features, chemical composition, and mechanical strength of the culms of newly developed lodging-tolerant mutant (PMW-2016-1) and parent (DPW-621-50), were examined by light microscopy, the Klason method, prostate tester coupled with a Universal Tensile Machine, and Fourier Transform Infrared Spectroscopy. Significant changes in the anatomical features, including the outer radius of the stem, stem wall thickness, and the proportions of various tissues, and vascular bundles were noticed. Chemical analysis revealed that the lignin level in the PMW-2016-1 mutant was higher and exhibited superiority in stem strength compared to the DPW-621-50 parent line. The force (N) required to break the internodes of mutant PMW-2016-1 was higher than that of DPW-621-50. The results suggested that the outer stem radius, stem wall thickness, the proportion of sclerenchyma tissues, the number of large vascular bundles, and lignin content are important factors that affect the mechanical strength of wheat stems, which can be the key parameters for the selection of varieties having higher lodging tolerance. Preliminary studies on the newly identified mutant PMW-2016-1 suggested that this mutant may possess higher lodging tolerance because it has a higher stem strength than DPW-621-50 and can be used as a donor parent for the development of lodging-tolerant wheat varieties.

Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.)

The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding α- and β-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for α- (PA) and β-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (α1-7) and BnPB (β1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus, and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.

Development and characterization of nitrogen and phosphorus use efficiency responsive genic and miRNA derived SSR markers in wheat

Among all the nutrients, nitrogen (N) and phosphorous (P) are the most limiting factors reducing wheat production and productivity world-wide. These macronutrients are directly applied to soil in the form of fertilizers. However, only 30-40% of these applied fertilizers are utilized by crop plants, while the rest is lost through volatilization, leaching, and surface run off. Therefore, to overcome the deficiency of N and P, it becomes necessary to improve their use efficiency. Marker-assisted selection (MAS) combined with traditional plant breeding approaches is considered best to improve the N and P use efficiency (N/PUE) of wheat varieties. In this study, we developed and evaluated a total of 98 simple sequence repeat (SSR) markers including 66 microRNAs and 32 gene-specific SSRs on a panel of 10 (N and P efficient/deficient) wheat genotypes. Out of these, 35 SSRs were found polymorphic and have been used for the study of genetic diversity and population differentiation. A set of two SSRs, namely miR171a and miR167a were found candidate markers able to discriminate contrasting genotypes for N/PUE, respectively. Therefore, these two markers could be used as functional markers for characterization of wheat germplasm for N and P use efficiency. Target genes of these miRNAs were found to be highly associated with biological processes (24 GO terms) as compared to molecular function and cellular component and shows differential expression under various P starving conditions and abiotic stresses.

Nanotechnology-enabled biofortification strategies for micronutrients enrichment of food crops: Current understanding and future scope

Nutrient deficiency in food crops severely compromises human health, particularly in under privileged communities. Globally, billions of people, particularly in developing nations, have limited access to nutritional supplements and fortified foods, subsequently suffering from micronutrient deficiency leading to a range of health issues. The green revolution enhanced crop production and provided food to billions of people but often falls short with respect to the nutritional quality of that food. Plants may assimilate nutrients from synthetic chemical fertilizers, but this approach generally has low nutrient delivery and use efficiency. Further, the overexposure of chemical fertilizers may increase the risk of neoplastic diseases, render food crops unfit for consumption and cause environmental degradation. Therefore, to address these challenges, more research is needed for sustainable crop yield and quality enhancement with minimum use of chemical fertilizers. Complex nutritional disorders and 'hidden hunger' can be addressed through biofortification of food crops. Nanotechnology may help to improve food quality via biofortification as plants may readily acquire nanoparticle-based nutrients. Nanofertilizers are target specific, possess controlled release, and can be retained for relatively long time periods, thus prevent leaching or run-off from soil. This review evaluates the recent literature on the development and use of nanofertilizers, their effects on the environment, and benefits to food quality. Further, the review highlights the potential of nanomaterials on plant genetics in biofortification, as well as issues of affordability, sustainability, and toxicity.

Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum L.)

Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.

Physical localization of 45S rDNA in Cymbopogon and the analysis of differential distribution of rDNA in homologous chromosomes of Cymbopogon winterianus

Cymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of C. winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosomes 1. The development of C. winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of C. winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of C. winterianus.

Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR markers (miRNA-SSRs) in wheat, which were found as key players in various abiotic stresses. In the present study, we identified 104 heat-stress-responsive miRNAs reported in various crops. Out of these, 70 miRNA-SSR markers have been validated on a set of 20 terminal heat-tolerant and heat-susceptible wheat genotypes. Among these, only 19 miRNA-SSR markers were found to be polymorphic, which were further used to study the genetic diversity and population structure. The polymorphic miRNA-SSRs amplified 61 SSR loci with an average of 2.9 alleles per locus. The polymorphic information content (PIC) value of polymorphic miRNA-SSRs ranged from 0.10 to 0.87 with a mean value of 0.48. The dendrogram constructed using unweighted neighbor-joining method and population structure analysis clustered these 20 wheat genotypes into 3 clusters. The target genes of these miRNAs are involved either directly or indirectly in providing tolerance to heat stress. Furthermore, two polymorphic markers miR159c and miR165b were declared as very promising diagnostic markers, since these markers showed specific alleles and discriminated terminal heat-tolerant genotypes from the susceptible genotypes. Thus, these identified miRNA-SSR markers will prove useful in the characterization of wheat germplasm through the study of genetic diversity and population structural analysis and in wheat molecular breeding programs aimed at terminal heat tolerance of wheat varieties.