A Platform for Trait Development in Crop Plants

The science of genomics and transgenic technologies has shaped crop development enabling the introduction of new traits, particularly in grain and oilseed crops. In contrast, horticultural crops such as vegetables, fruits and ornamental species have been largely unmodified by genetic engineering presumably due to a lack of consumer acceptance in fresh products. Therefore, many horticultural breeding companies have turned to using mutagenesis as an approach to modify genes and develop new traits. Our research team has developed a collection of biological, genotyping and computational tools called “Deep Variant Scanning” (DVS) used to deliver induced variation from mutagenized plant populations. More specifically we have developed two EMS populations including TOMATO – 4,600 M2 lines @ 1SNP/50 bp and PEPPER – 3,400 M2 lines @ 1 SNP / 70 bp. The identification of desired mutants in candidate genes uses a proprietary technique that includes Illumina sequencing and high throughput genotyping that requires just 3 weeks to identify seed packages with the desired mutations. We have examined 46 genes covering >200 kbp and have identified multiple stop codons and highly deleterious mutations in virtually all genes we have examined. The DVS platform has value across crop species and is amenable to a wide range of diploid, polyploid, and obligate out-crossing plants. We are also adapting DVS to overcome chimerism in M1 plants and thus examine transient populations, where only the desired M1 plants containing the mutations are retained for selfing and allele fixation.