Silicon (Si), the quasi-essential element occurs as the second most abundant element in the earth’s crust. Biological importance of Si in plant kingdom has become inevitable particularly under stressed environment. In general, plants are classified as high, medium, and low silicon accumulators based on the ability of roots to absorb Si. The uptake of Si directly influence the positive effects attributed to the plant but Si supplementation proves to mitigate stress and recover plant growth even in low accumulating plants like tomato. The application of Si in soil as well as soil-less cultivation systems have resulted in the enhancement of quantitative and qualitative traits of plants even under stressed environment. Silicon possesses several mechanisms to regulate the physiological, biochemical, and antioxidant metabolism in plants to combat abiotic and biotic stresses. Nevertheless, very few reports are available on the aspect of Si-mediated molecular regulation of genes with potential role in stress tolerance. The recent advancements in the era of genomics and transcriptomics have opened an avenue for the determination of molecular rationale associated with the Si amendment to the stress alleviation in plants. Therefore, the present endeavor has attempted to describe the recent discoveries related to the regulation of vital genes involved in photosynthesis, transcription regulation, defense, water transport, polyamine synthesis, and housekeeping genes during abiotic and biotic stress alleviation by Si. Furthermore, an overview of Si-mediated modulation of multiple genes involved in stress response pathways such as phenylpropanoid pathway, jasmonic acid pathway, ABA-dependent or independent regulatory pathway have been discussed in this review.

The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F₄ populations and correlated with the phenotypic disease index.

Bacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species. We resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes. From our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome.

Late blight (LB) is a devastating disease in tomato (Solanum lycopersicum), which is caused by the oomycete Phytophthora infestans (Mont.) de Bary. In this study, the LB-resistance gene Ph-3 was evaluated using a pathogenic isolate of P. infestans from Korea. Molecular mapping of the TG328 and TG591 regions, which are tightly linked to the Ph-3 locus, was performed using F₆ families derived by crossing the LB-resistant accession “L3708” (Solanum pimpinellifolium) with the LB-susceptible accession “AV107-4” (S. lycopersicum). The map indicated that the Ph-3 locus also conferred high resistance to the Korean isolate of P. infestans. To identify the putative Ph-3 gene, the ultracontig SL2.4ch09 of the S. pimpinellifolium draft-genome sequence, which contained the TG328 and TG591 clone sequences, was investigated. Four tandemly duplicated putative Ph-3 homologs (designated as Ph-3a, Ph-3b, Ph-3c, and Ph-3d in this study) belonging to the coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) class of pathogen resistance genes were identified in a flanking region of TG328 and TG591. TG591 sequences and partial sequences of Ph-3c and Ph-3d were tandemly repeated. Protein sequences of Ph-3 homologs showed high sequence homology with Rpi-vnt1.1 and Rpi-vnt1.3, the CC-NBS-LRR LB-resistance genes in potato. Ph-3c and Ph-3d showed the highest protein sequence homology (80%) to Rpi-vnt1.1 and Rpi-vnt1.3, whereas Ph-3a and Ph-3b showed 70% homology to these genes. A set of sequence characterized amplified region (SCAR) markers that could distinguish each copy of the Ph-3 gene homolog were developed, and allelic compositions of the Ph-3 locus were compared between “L3708” and a variety of LB-susceptible tomato accessions. These SCAR markers proved useful, not only for studying the organization of the Ph-3 homologs in an individual tomato plant, but also for selection of the LB-resistance allele.

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.