When Mike and I started G2, one of the things on the "immediate" list was some sort of marker-assisted breeding project. The problem was that setting up a molecular marker lab is relatively expensive, and starting a breeding company was already going to take all of our energies. How could we possibly consider doing both? Well ...public domain PCR marker sequences exist for many loci coding for disease-resistance (DR) in tomatoes. All of the common DR loci are available --- VFNTA as well as the spotted wilt virus (Sw-5), a problem disease in the southeastern US. More, I did my MS in plant breeding with a tomato breeder at Purdue, the late Dr. Ed Tigchelaar.
One of our academic colleagues --- Dr. Rick Vierling (a soybean breeder at Purdue, and head of the genetics lab at the Indiana Crop Improvement Association) --- expressed an interest in working with us to convert those PCR markers to SNPs (single-nucleotide polymorphisms) and then screen for multiple DR loci in a multiplexed SNP-based microarray assay. For those of you out there who aren't molecular geneticists, what Vierling's team did was to combine 7 or 8 assays into a single assay. We could now quickly screen tomato seedlings for DR alleles, and thus only evaluate segregating populations in the field that we already knew were DR --- resistant to most of the common tomato diseases.
So, we started a tomato project to combine the best commercial and public domain sources of DR with the best commercially-adapted varieties having appropriate horticultural type --- including good flavor in most environments --- with the best-tasting heirloom tomatoes. If you grow heirloom tomatoes, you know that they are generally a challenge to produce because they lack disease-resistance. This may be acceptable to a backyard gardener, but severely limits the commercial production of heirlooms. Our goal was to produce DR F1 hybrid tomatoes which have an heirloom tomato flavor and texture.
How did we do? The assay development results can be viewed here: http://tgc.ifas.ufl.edu/2009/Shi%20SNP%20Multiplex.pdf This is a PDFed Powerpoint presentation by Dr. Ainong Shi, who was the lead scientist working in Vierling's lab at the time.
All of this occurred within 2 years of the project start. Two years after that, we are now beginning to make experimental hybrids between G2 inbreds. We have tomato inbreds in developement which look and taste like heirlooms, but which include multiple DRs --- V, F, N, T, A, Sw-5. Not all of our inbreds are resistant to every one of these diseases --- we didn't get that lucky on our first try! However, the ones which we will continue to develop contain at least 3 DR loci. We continuing to inbreed and refine, and to evaluate both F1s and inbreds for taste, quality, and commercial produce-ability. This summer will see the first of those hybrids in the field, but it is a late planting.
The real tests begin in the summer of 2011.