Exploring Tomato Genes with a Microarray

Tomato is a very important food crop with a global production of over 150 million tons in 2009 as the fruit is consumed all around the world. The Tomato Genome Consortium produced a draft of the genome in late 2009, with a more complete version, release SL2.40, finished in early 2011. The International Tomato Annotation Group (ITAG) annotated almost 35k gene models in their annotation release ITAG 2.3 on the latest genome assembly. We describe here a microarray design to survey the gene models in ITAG 2.3 as well as represent genes from some common pathogens associated with tomato. The inclusion of pathogens allows for the study of host-pathogen interactions in a single experiment. Fusarium oxysporum and Verticillium dahlia are common soil fungi that cause wilt in tomatoes. Also included are some tomato-associated viruses: Tomato mosaic virus, Tobacco mosaic virus (TMV), and Tomato yellow leaf curl virus (TYLCV).