Genotype-phenotype interactions play an important role in agronomy. However, these interactions are complex to identify because expressed at different molecular scales and are strongly influenced by environmental factors. Although high-throughput technologies generate more comprehensive insights, our knowledge remains fragmentary to elucidate the molecular mechanisms that govern the expression of complex traits. This objective can be achieved by integrating information from different levels into an integrative model in order to understand the functioning of the whole biological system. Today, the Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge. We have developed AgroLD (www.agrold.org) relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community. AgroLD is now an RDF (Resource Description Format) knowledge base of 130M triples created by annotating and integrating more than 55 datasets with 10 ontologies. AgroLD's objective is to offer a domain-specific knowledge platform to solve complex biological questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. Thus, the AgroLD platform provides several entry points, in order to allow a large number of users accessing it.