Revealing gene regulation and associations through biological networks

Traditionally, over the last 10,000 years, agriculture has relied on natural biological evolution and careful selection of plant varieties by farmers that was used as the founder material by plant breeders in the last 150 years for further genetic improvement. Plant breeders played an important role mainly by introgression of a trait of interest, through the transfer of genetic loci, into an elite crop line that exhibits high-yield performance across a wide range of conditions. Modern agriculture has relied on the use of biotechnologies and molecular biology to improve marker development and aid in the discovery of candidate loci or genes associated with desirable traits, thereby reducing the time required for selective breeding.In this review, we briefly describe the evolution of the methods used to identify candidate leads (gene, loci or regulatory regions) for crop improvement, starting by quantitative genetic methods. The development of co-expression and molecular networks will be described. It will be shown how network analysis can reinforced the discovery of candidate genes/loci more rapidly and with higher confidence. These improvements will serve to accelerate genetic engineering and molecular breeding as modern agriculture confronts the challenging times ahead, with the increase of abiotic stresses for crops as drought, heat, soil high salinity or waterlogging.Without taking in account possible losses due these growing stresses, the increase in crop yields needs to be significantly accelerated to feed the growing world population, following the FAO previsions.