**2. Next-generation sequencing technologies**

Knowing the genome sequence of a species has an advantage in crop breeding. This became possible with the revolution of DNA sequencing technologies. The Sanger method [3] was the first-generation sequencing method based on DNA chain termination method of the singlepass sequencing of one clone at a time. With the advent of NGS technologies, the sequencing

of complete genome or transcriptome of a species/genotype has become possible within a few hours. Utilizing various NGS platforms that are based on diverse chemistry and detection methods, several crop genomes, including major Solanaceae crops have been sequenced [4– 7]. Among the various NGS technologies, three widely utilized platforms are Roche/454, Illumina Genome Analyzer (GA), and ABI SOLiD. The Roche/454 GSFLX chemistry is based on pyrosequencing and can produce up to 1 million reads of 600 bp to 1 kb [8]. The ABI SOLiD chemistry is based on emulsion polymerase chain reaction and sequencing by ligation technology, which can sequence up to 100 million reads of 50 bp in size [9]. The Illumina/Solexa GA based on sequencing by synthesis method produces 320 to 640 million reads of 100–150 bp [10].

plant-breeding practices have been carried out for producing new varieties that can withstand with such changing climatic conditions besides increasing the productivity. These timeconsuming practices could make considerable progress in crop improvement using selective germplasm, however, resulted in loss of biodiversity in the process. The recent advances in crop genomics, particularly the use of high throughput next-generation sequencing (NGS) technologies, look promising to identify causal genetic factors at genome by sequencing the whole genome and transcriptome of a species. As a result, the complete gene catalogue of a crop species and functional genes in different tissues could be identified besides allowing studying the genetic pathways involved in growth and development and biochemical pathways that eventually could be correlated with the crop phenotypes [1, 2]. Furthermore, the sequence data generated in vast amount provide a basis of genetic variation such as singlenucleotide polymorphisms (SNPs), which ultimately provide a relationship between genotype

The Solanaceae family comprises approximately 2500 flowering plant species under 102 genera. The family represents the third most economically important family after grasses and legumes. Among the most important plants of this family are the potato (*Solanum tuberosum*), eggplant (*Solanum melongena*), tomato (*Solanum lycopersicun*), and capsicum or pepper (*Capsicum annuum*). They serve as important food crops and consumed worldwide due to their high nutritional components. Solanaceae crops have high nutritional value due to the presence of quality proteins, mineral salts, starch, vitamins, and antioxidants. Tomato majorly contrib‐ utes to dietary nutrition globally with beneficial effects to human health mainly attributed to antioxidant compounds in the fruit such as lycopene and several other compounds such as carotenoids, zeaxanthin, and vitamin C. Capsicum fruits are rich source of metabolites that are beneficial for human health, such as carotenoids (provitamin A), vitamin C, vitamin A (which destroy free radicals), vitamin E, flavonoids, and capsaicinoids (anticancer agent). Although these compounds function as antioxidants and nutrients, they are used in traditional medicine also due to their enormous medicinal properties. Eggplant serves as an excellent source of antioxidants such as anthocyanins and several phenolics. Apart from this, it has a significant effect in reducing blood and liver cholesterol rates in humans. Worldwide, potato tubers are

the principal source of starch along with proteins, vitamins, and antioxidants.

toward translational research has been discussed.

**2. Next-generation sequencing technologies**

Here in this chapter, an attempt has been made to compile current research progress made based on NGS technology in four most important Solanaceae crop plants: tomato, potato, eggplant, and pepper. Furthermore, the application of NGS technology on those four crops

Knowing the genome sequence of a species has an advantage in crop breeding. This became possible with the revolution of DNA sequencing technologies. The Sanger method [3] was the first-generation sequencing method based on DNA chain termination method of the singlepass sequencing of one clone at a time. With the advent of NGS technologies, the sequencing

and phenotype in different species.

248 Next Generation Sequencing - Advances, Applications and Challenges

The third- and the fourth-generation sequencing technologies are being developed, the majority of which allow the detection of single molecules with real-time sequencing. The popular third-generation sequencing platforms are Ion Torrents/Life Technologies, Heli‐ Scope™/Helicos Biosciences, and PacBio RS/Pacific Biosciences. The fourth generation is nanopore sequencing technology (Roche/IBM and Oxford). Ion Torrent company introduced a very different approach in 2010 as "Personal Genomic Machine," which was later commer‐ cialized by Life Technology. The chemistry is based on the real-time detection of the pH change (release of hydrogen ions), with the incorporation of a nucleotide into a growing DNA strand by a silicon detector [11]. The technology provides an average read length of ∼ 200 bp. The HeliScope introduced by Helicos BioSciences was the first commercially available singlemolecule sequencing (SMS) platform [12]. The technology is based on highly sensitive fluorescence detection system with the incorporation of each nucleotide carrying fluorescent dye in the growing strand. The read length obtained ranges from 30 to 35 bp. PacBio RS, a single-molecule real-time (SMRT) sequencing technology, is based on the DNA sequencing by synthesis method and contains the provision of the real-time imaging of fluorescently tagged nucleotides for studying the sequence and structure of nucleic acid [13]. This technology not only can produce a comparatively longer DNA sequence (average read lengths of 5500−8500 bp) but also has wider application in epigenetics research as the technology is able to detect DNA methylation such as 4-methylctosine (mC), 5-mC, and 6-methyladenine (mA) [14].

The development of nanopore sequencing technology [15] begins an era of fourth-generation sequencing technology and has promised a cheap and fast method of sequencing. The principle involves threading a single-stranded DNA/RNA molecule electrophoretically through a nanopore that causes altering the pore's electrical properties and thereby modulating the ionic current through the nanopore. Braha et al. [16] designed a biosensor using "α-hemolysin," a toxin isolated from *Staphylococcus aureus.* The first commercial sequencing device was an‐ nounced by Oxford Nanopore Technologies in 2012. Later, the technology was adapted and commercialized by other companies like Roche with IBM, Electronic BioSciences, and NABsys [17, 18]. This technology has advantage as sample preparation is not needed and the trans‐ duction and recognition occur in real time, on a molecule-by-molecule basis. The technology produces very long reads (up to 10 kb), which could be are capable of inexpensive *de novo* sequencing.
