Peanut being an important food, oilseed and fodder crop worldwide, its genetic improvement currently relies on genomics-assisted breeding (GAB). Since the level of marker polymorphism is limited in peanut, availability of a large number of DNA markers is the prerequisite for GAB. Therefore, we detected 4,309,724 single nucleotide polymorphisms (SNPs) from the whole genome re-sequencing (WGRS) data of 178 peanut accessions of Arachis along with the reference genome sequence of Tifrunner. SNPs were analyzed for the structural and functional features in order to conclude on their utility and employability in genetic and genomic studies. ISATGR278-18, a synthetic amphidiploid, showed the highest number of SNPs (2,505,266), while PI_628538 recorded the lowest number (19,058) of SNPs. A03 showed the highest number of SNPs, while the B08 recorded the lowest number of SNPs. The number of accessions required to record 50% of the total SNPs varied from 11 to 13 across the chromosomes. The rate of transitions was more than that of transversions. Among the various chromosomal contexts, intergenic and intronic regions carried more SNPs than the exonic regions. SNP impact analysis indicated 2,488 SNPs with high impact due to gain of stop codons, variations in splice acceptors and splice donors, and loss of start codons. Of the 4,309,723 SNPs, as high as 46,087 had the highest polymorphic information content (PIC) of 0.375. As an illustration of application, a drought and disease resistant accessions were compared with susceptible accessions to identify the SNPs with high impact substitutions. SNPs were also identified between the two sub-genomes (A and B). This SNP resource is being used for haplotype selection and allele mining for various genes and gene families. Overall, these structural and functional landscapes of the SNPs will be of immense importance for their utility in genetic and genomic studies including reverse genetics in peanut.

Current agricultural practices need to be modernized and strengthened to meet the food needs of the growing world population. Hence, new and advanced approaches keep on developing for the crop-improvement. Nano-enabled agriculture is a new such area. Genome editing using nanotechnology is used in agricultural research to improve stress tolerance, targeting, controlled release of pesticides, and improve photosynthetic efficiency. Genome editing is more accurate, faster, and cheaper than other transgenic approaches. Clustered regularly interspaced short palindromic repeats (CRISPRs) using nucleases are a customizable and successful method for genome editing. However, there are some limitations such as time-consuming and complex protocols, inevitable DNA integration into the host genome, potential tissue damage, and low transformation efficiency. To overcome these problems, nanoparticle-mediated gene delivery has emerged as an innovative technology. Combining current technologies such as speed breeding and CRISPR/Cas with nanotechnology can advance crop improvement programs. Recent advances in the development of genome editing tools have revolutionized the ability of researchers to genetically investigate and modify biological systems. However, genetic engineering of mature plants and their plastids remains a challenge due to the various physical barriers. Nanomaterials develop a nanoscale understanding of the mechanisms that can be used to achieve nanoparticle transport across plant cells and chloroplast membranes and identify highly efficient nanoparticle complexes for plant cell internalization. Researchers are creating a nanoparticle platform that enables electrostatic-grafting of genomic biomolecules used to genetically transform mature plants. In addition to the use of magnetic nanoparticles, carbon nanotubes are also an increasingly popular nano-tool for plant transfection. Carbon nanotubes merged with gene fragments have been shown to effectively transport transient and expression genes to the leaves of various plant species, including wheat, cotton, and arugula. Nanotechnology-based genomics is still in its infancy, but it has a promising future for crop improvement and modern agricultural research.

The molecular mechanisms behind the seed priming are still a mystery. However, advanced molecular tools such as genomics, transcriptomics, and proteomics have added significant information. Seed priming is a seed pre-soaking technique that is used to initiate pre-germination processes inside by activating the expression of certain genes. This study was designed to reveal important molecular mechanisms behind cotton seed priming. Seed priming completes into three phases: I. Imbibition phase, II. Lag phase, and III. Radicle emergence phase. Proteomic analysis revealed that GhAKT1 (K⁺ channel gene) was activated and expressed during phase I of primed seeds and facilitated the transport of K⁺ and elongation of embryonic cells in primed seeds. The repair and synthesis of new mitochondria were also observed in primed seeds by the resumption of respiratory activities. However, expression of ACT7 (Actin-gene) was also observed in primed seeds. In Phase II, more RNA transcripts were found than unprimed seeds. Several events were revealed, including the mitochondrial repair, synthesis of new mitochondria, and proteins. The embryonic expansion also began due to the expression of the GhAKT1 gene. The proteomic analysis also revealed the synthesis of α-amylase, β-amylase, protease, and isocitrate lyase in primed seeds which are required for degradation and translocation of reserve food. The end of Phase II and the start of Phase III marked by radicle protrusion through the testa/seed coat. During the third phase, there was a significant increase of actin proteins found in primed seeds which characterized cell division. Radicle cells elongation was also noted by following the activity of ACT7, and GhAKT1 genes.

The genes encoding α- and β-type subunits of 20S proteasome core protease are integral components of 26S proteasome complex in the ubiquitin-proteasome system (UPS). The 20S proteasome represents a catalytic particle that cleaves cytotoxic, denatured, damaged and unwanted proteins in an ATP/ubiquitin-dependent non-lysosomal pathway and is known to impart thermotolerance in model plants. In the present study, we identified a family of 67 genes (including 34 TaPA and 33 TaPB genes) encoding α- and β-subunits of 20S proteasome in bread wheat (Triticum aestivum L.). These genes were distributed on all the 21 wheat chromosomes, majority of them being in triplicate homoeologues. These wheat genes were orthologous to corresponding rice and Arabidopsis genes. The proteins encoded by each of the TaPA and TaPB genes contained 20 different motifs. These 20 motifs were present in corresponding proteins of Arabidopsis and rice. Phylogenetic analysis placed these genes in seven clusters, each with one of the seven α (α1-7) and one of the seven β (β1-7) subunits. Expression analysis suggested that 10 of the 67 genes were involved in heat stress response, whereas four genes were involved in drought tolerance at the seedling stage. Nine (9) genes were expressed under both heat and drought suggesting their involvement in response to multiple abiotic stresses. Future research on TaPA/TaPB genes will help in the development of climate-resilient wheat cultivars.

FIG. Schematic representation of the steps and programs used to identify 20S proteasome family genes in bread wheat.