Next Generation Sequencing Technologies: Applications in Crop Improvement

Whole genome sequencing of plants with large genome sizes was considered to be a major challenge about a decade ago. Thanks to the rapid developments in sequencing technologies, genome sequencing of any crop plant has now become faster, cheaper and technically less demanding. These sequencing technologies are undergoing never ending revolution with commercialization of next-next-generation technologies capable of sequencing thousands of millions of nucleotide bases in each run. Using these sequencing technologies it is possible to sequence or resequence entire plant genomes or sample entire transcriptomes in greater depth than ever before. Rather than sequencing individual genomes, now scientists envision the sequencing of hundreds of related genomes to sample genetic diversity within and between germplasm pools. The increasing availability of DNA sequence information in large number of crop plants enable the discovery of genes and molecular markers associated with diverse agronomic traits creating new opportunities for crop improvement. Such huge and accurate DNA sequence information impacts many of the current uses of molecular tools in plant evolution, phylogenetics, fingerprinting, linkage mapping and marker assisted selection and breeding. This review provides an overview of various NGS technologies that are currently available and near future arrivals along with their applications in de nova sequencing and resequencing, marker development, population genetics and evolutionary biology, organelle sequencing and translational biology of crop plants.