Functional Genomics For Crop Improvement

Abstract

Plant breeding has had a tremendous influence on crop improvement. However, due to dwindling germplasm resources, identification of variability for incorporation into new cultivars is becoming more difficult. Therefore, there has been recourse to alternative approaches including mutagenesis, tissue culture and genetic transformation to aid breeding programs. Furthermore, with the vast repertoire of genome-wide data from different expression profiling techniques such as microarrays, more subtle understanding of gene expression is being obtained and is further helping plant breeders to entertain a different selection approach based on expression quantitative traits to maximize combinations of genes capable of conferring high performance. In this chapter, we review some of the aspects of plant breeding and the influence functional genomics has on breeding programs. Some of the challenges to functional genomics and breeding come from establishment of high-throughput transformation systems to assess gene function, which is limiting functional characterization of numerous genes in their respective crops. Therefore, this chapter also focuses on the need to gain better understanding of the development of gene transfer systems for crop plants to make use of the array of available gene information data.

Reticulate Evolution in AA-Genome Wild Rice in Australia

“…Natural variations in genes for agronomically important traits are limited in cultivated rice germplasm. In-plant breeding, desirable germplasm is sourced from wild species, landraces, and distant relatives, or for new traits through induced mutation or genetic manipulation ( Ganeshan et al, 2010 ). The Australian wild rice populations include the earliest branching AA genome lineages and, therefore the most genetically and geographically distinct from the other AA genome wild relatives of cultivated rice.…”

Pulse Crops: Biotechnological Strategies to Enhance Abiotic Stress Tolerance

“…Even today, plant breeding is pivotal in the development of improved varieties. However, erosion of naturally occurring genetic variability has limited the development of newer cultivars with improved qualities by plant breeders [103]. The toolbox of plant breeders has therefore expanded with the use of novel germplasm resources, made available from both de novo as well as from induced sources.…”

“…Studies such as the cDNA-AFLP transcriptome analyses are valuable since they allow for gene discovery under abiotic stress challenges, as recently reported in wheat, wherein temporal and spatial specificity of induced transcripts under low temperature exposure occurred [127]. The cDNA-AFLP profiling is a low-cost alternative for gene discovery, especially in laboratories with limited resources [103] and will be valuable for pulse crop transcript profiling under abiotic stress challenges.…”

Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance

“…This implies that there are likely many more novel candidate genes involved in LT acclimation/tolerance, which have thus far not been identified or associated with LT exposure. Among the available gene expression profiling approaches (for review see Ganeshan et al 2009b), differential display PCR (DDRT-PCR) (Liang and Pardee 1992) and cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) (Bachem et al 1996) offer the unique possibility of identifying novel transcripts associated with LT exposure. Moreover, cDNA-AFLP is more stringent, reproducible and cost-effective than other methods since low-abundance transcripts can be detected and also allows the opportunity to distinguish among homologous genes (Reijans et al 2003;Vuylsteke et al 2007).…”