Next-Generation Sequencing Technologies: Approaches and Applications for Crop Improvement

The persistent efforts toward attaining food security and balanced nutrition are challenged by the deteriorating natural resources, aberrant climate changes, and increase in population, hence calling for the utilization of innovative technologies to overcome the constraints of crop production. Crop improvement through multifaceted approaches that combine conventional and genomic technologies is necessary for developing biotic and abiotic stress-tolerant varieties with high yield and desirable nutritional quality. A detailed understanding of complex plant genome and genetic diversity is necessary to meet these challenges. Before 2004, genome sequencing was mostly dependent on Sanger sequencing technology, which though accurate was not high-throughput. The successful sequencing of Arabidopsis and rice genomes encouraged the sequencing of many other crop and model plants. Since then, sequencing technologies, accompanied by application of high-power computer technology have evolved at an astounding pace and developed into more advanced, innovative, and competitive next-generation sequencing (NGS) and Next-NGS technologies. The NGS technologies are low cost, rapid, and high-throughput. The advancement of NGS and Next-NGS technologies combined with automated phenotyping techniques have accelerated the crop improvement process. NGS technology enables the generation of reference genomes and re-sequencing of related species to understand the genetic diversity, transcriptome sequencing that provides insight into complex gene networks, metagenomics, as well as high-throughput genotyping methods like genotyping by sequencing (GBS) and QTL mapping which have been successfully used in crop improvement programs. In the present chapter, we briefly describe different generations of sequencing technologies, the current status of advanced NGS technologies, and their application in crop improvement including de novo nuclear/organellar genome assembly, re-sequencing, functional genomics, epigenetics, and marker development for introgression of important agronomic traits, population genetics, evolutionary biology, and pan-genomics.