Sequencing crop genomes: approaches and applications

Abstract

SummaryMany challenges face plant scientists, in particular those working on crop production, such as a projected increase in population, decrease in water and arable land, changes in weather patterns and predictability. Advances in genome sequencing and resequencing can and should play a role in our response to meeting these challenges. However, several barriers prevent rapid and effective deployment of these tools to a wide variety of crops. Because of the complexity of crop genomes, de novo sequencing with next-generation sequencing technologies is a process fraught with difficulties that then create roadblocks to the utilization of these genome sequences for crop improvement. Collecting rapid and accurate phenotypes in crop plants is a hindrance to integrating genomics with crop improvement, and advances in informatics are needed to put these tools in the hands of the scientists on the ground.

Nanodiagnostic Tools in Plant Breeding

“…This is due to the fact that it enables nanoparticles, nanofibers, and nanocapsules to carry foreign DNA and chemicals that change genes [2]. However, many plant genomes are complex, de novo sequencing with next-generation sequencing technologies is a process fraught with difficulties that then create roadblocks to the employment of these genome sequences for crop enhancement [3]. Nanotechnology can specifically target specific plant pathology problems in agriculture such as in plant-pathogen interactions and provide new techniques for crop disease management [4].…”

Sequencing Technologies and Their Use in Plant Biotechnology and Breeding

“…This information improves our understanding of the role of genes in development and evolution, and facilitates the discovery of related genes and functions across species (Messing & Llaca, 1998;Feuillet et al, 2011). Reference genomes are also important tools in the identification, analysis and exploitation of genetic diversity of an organism in plant population genetics and breeding (Varshney et al, 2009;Edwards & Batley, 2010;Jackson et al, 2011). The sequencing of the human genome and other vertebrates in the 90's provided the technological pathway for the initial sequencing of genomes in plants (International Human Genome Sequencing Consortium, 2001, Venter et al, 2001).…”

Dwarfing of Breadfruit (Artocarpus altilis) Trees: Opportunities and Challenges

“…The wealth of genetic diversity among breadfruit cultivars provides an important reservoir of genetic variation for developing dwarfing rootstocks. Phenotypic studies facilitated by Next Generation Sequencing (NGS) are generating a large volume of genomic and transcriptomic information for use as functional markers or breeding targets in many species with limited genome resources [142]. Morphological diversity in tree height and canopy shape exists in breadfruit cultivars throughout Oceania, but quantitative analysis is required with a focus on the tree architecture, yield and the resistance to wind damage.…”