Reaping the Benefits of Next-generation Sequencing Technologies for Crop Improvement — Solanaceae

Abstract

Next-generation sequencing NGS technologies make possible the sequencing of the whole genome of a species decoding a complete gene catalogue and transcriptome to allow the study of expression pattern of entire genes. The huge data generated through whole genome and transcriptome sequencing not only provide a basis to study variation at gene sequence such as single-nucleotide polymorphism and InDels and expression level but also help to understand the evolutionary relationship between different crop species. Furthermore, NGS technologies have made possible the quick correlations of phenotypes with genotypes in different crop species, thereby increasing the precision of crop improvement. The Solanaceae family represents the third most economically important family after grasses and legumes due to high nutritional components. The current advances in NGS technology and their application in Solanaceae crops made several progresses in the identification of genes responsible for economically important traits, development of molecular markers, and understanding the genome organization and evolution in Solanaceae crops. The combination of high-throughput NGS technologies with conventional crop breeding has been shown to be promising in the Solanaceae translational genomics research. "s a result, NGS technologies has been seen to be adopted in a large scale to study the molecular basis of fruit and tuber development, disease resistance, and increasing quantity and quality of crop production.Keywords: Solanaceae, NGS, capsicum, eggplant, tomato, potato . IntroductionIn developing countries, population and food security are the two major issues. These problems get worse with the sudden climate changes that hamper production, yield, and quality of food crops. Therefore, to keep in mind the food security for billions of peoples, an initiative is required for improving the quality and yield of important crops. Several traditional 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. "s 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 [ , ]. 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 and phenotype in different species...

A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae

“…The Solanaceae include economically important crops such as tomato, potato, pepper and eggplant ( 3 , 4 ). Since the reference genomes of potato, tomato and pepper were released ( 5–7 ), many follow-up studies and large-scale resequencing projects of major breeding lines have been performed.…”