Plant Bioinformatics: Next Generation Sequencing Approaches

Abstract

The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. Bioinformatic resources and web databases are essential for the most effective use of genetic, proteomic, metabolomic and phenome information important in increasing agricultural crop productivity. During this decade, remarkable advances in DNA and RNA sequencing technologies have emerged with the advent of next-generation sequencing (NGS). NGS technologies now allow virtually millions of bases to be sequenced in one sample, at very low costs relative to traditional Sanger sequencing. As costs and capabilities of these methods continue to be reduced, we are only beginning to see the possibilities of NGS, which are developing in parallel with online and computer availability of a wide range of biological datasets, and allowing us to address a variety of questions not possible before. As techniques and data continue to improve and grow, we are rapidly moving to the point where every plant, not just select ‘model plants’, is open to the power of NGS applications. Re-sequencing allows the identification of an unlimited number of markers and analysis of germplasm allelic diversity based on allele mining. The availability of NGS information is enabling genome editing (i.e. site-specific mutations) to obtain gene sequences desired by plant breeders. This chapter presents a brief synopsis of NGS technologies and the development of typical applications of such methods in the fields of molecular marker development, hybridisation and introgression, biodiversity, phylogenetic, evolutionary and ecological studies, polyploid genetics, proteomics and applications for large genebank collections. The information is set out under the molecular biology divisions of DNA-based resources and sequencing, RNA and variation analysis, proteomics, structural proteins, post-translation modifications, and plant bioactive peptides. This chapter illustrates how next-generation sequencing-derived information can be used to tailor genomic tools for different needs and application to crop improvement, and how such developments should assist in better crop and food security. Finally, a list of present and future perspectives and research are detailed, which in time should enable the full potential of bioinformatics to be achieved, and utilised in crop improvement programmes.