**7.3. Pungency**

**6. Genome-Wide Association Study (GWAS)**

270 Next Generation Sequencing - Advances, Applications and Challenges

association mapping in tomato [175].

ovary and normal fleshy fruit development.

**7.2. Tuber**

The advent of NGS technologies provides a large number of sequence variants (mainly SNPs) within a shorter period. These sequence variants can be utilized for QTL mapping, GWAS, and germplasm characterization. The establishment of an association between genotype and phenotype is a very challenging task. For crop improvement, it is necessary to determine the genetic basis of the agronomic trait. GWAS is a powerful technique for detecting natural variation and fine mapping of QTL underlying complex traits [174]. It requires a collection of individuals or a population of diverse genotypes and highly polymorphic markers that showed genome-wide distribution. This is a very robust method, in comparison to biparental cross-mapping, to map multiple traits simultaneously. In tomato, Shirasawa et al. [77] reported the whole genome resequencing of six tomato cultivars and detected 1.5 million SNPs by mapping the reads onto the reference genome (SL2.40). They utilized Illumina GoldenGate assay for genotyping of 1536 SNPs in 663 tomato accessions. There was no population structure observed when analyzing the genetic relationship using the STRUCTURE software. Further, they identified a total of nine SNP loci that were found to be associated with eight morpho‐ logical traits. To overcome the low polymorphism in cultivated tomato (*S. lycopersicum*), they used genome admixture of the cultivated and its wild ancestor (*S. pimpinellifolium)* for

**7. Next-generation sequencing toward translational research**

These TFs are consistently found to be involved in plant embryo development.

The transcriptome studies in Solanaceae crops such as potato revealed the identification of transcription factors associated with fruit development. A total of 632 lineage-specific genes were identified, of which 289 genes were asterid specific and 343 were potato specific [23]. They identified 290 genes, including *pectin esterase*, *lipoxygenase*, and *malate synthase*. *Leafy Cotyledon 1* (*LEC 1*) and transcriptional factor *B3* were found to be co-expressed in fruit tissues.

In tomato, using NGS technologies, several SNPs successfully differentiating between cherry type and round/beef type tomatoes were identified [80]. The SNP data revealed that cherry tomatoes share more SNPs with *S. pimpinellifolium*, a wild relative of the tomato. This revealed a close phylogenetic relationship of cherry tomato with the wild type. Several SNPs belonged to the chromosomal region that harbors genes/QTLs related to fruit weight, size, shape, and color, indicating that the SNPs may be used to explore the other fruit traits. In a miRNA study, it was observed that the transgenic tomato plants harboring AtMIR156b precursor resulted in abnormal flower and fruit morphology [130], indicating that mir156b plays crucial role in

The transcriptome of tuber tissue showed the presence of several transcripts that are specific for tuber. Around 90 genes were co-expressed in tuber, including the genes involved in starch

**7.1. Fruit traits (size, shape, ripening, and development)**

Pungency is a special and economically important quality trait only found in pepper fruits, and it has been studied extensively [7, 43]. NGS technology has a wide scope to explore this trait and provides insights into the capsaicinoid pathway revealing the genes/loci associated with pungency. The transcriptome profiling of *C. frutescens* revealed the identification of three structural genes, namely, dihydroxyacid dehydratase (DHAD), Thr deaminase (TD), and prephenate aminotransferase (PAT) involved in the capsaicinoid biosynthesis pathway [43]. They claimed the identification of several new candidate genes involved in the capsaicinoid pathway. The comparative transcriptomic study of pepper with potato and tomato showed that the different capsaicinoid pathway genes were expressed during placenta development at 16 DPA, 25DPA, and mature green stages of pepper fruits, but their orthologous genes hardly showed any expression in tomato and potato fruit [7]. The study confirmed the specificity of capsaicinoid pathway in the development of pungency in pepper fruit.
