This Small Business Innovation Research Phase I project will test a low-cost approach to developing DNA-based diagnostic tests. Molecular diagnostics are now used in medicine to detect genetic disorders, cancers, and infectious diseases. However, high costs of development associated with expensive gene discovery and gene sequencing efforts preclude many lower-value applications. In particular, custom uses in agriculture, food processing, and environmental biology are economically unfeasible. The approach outlined here alleviates this problem. It circumvents the need for gene discovery and extensive DNA sequencing, and instead uses DNA marker technologies as a rapid and inexpensive means to find unique base pair sequences that are either linked to, or diagnostic for, a trait or genotype of interest. Polymorphic DNA fragments genetically linked to desirable genes are partially sequenced to identify underlying base pair variation. In turn, that variation is used to design a diagnostic test employing the Polymerase Chain Reaction (PCR) technique and sequence specific primers that will amplify the diagnostic DNA sequence if it is present in a test sample. The Phase I effort is designed to test the feasibility of the concept. It will do so by developing two such tests; one designed to measure the purity of hybrid seed, and a second designed to screen cattle for a trait affecting meat quality.If successful, the proposed research will broaden the use of DNA-based diagnostics in agriculture, food processing, environmental biology, and related fields. Specifically, these molecular tools hold promise for use in: (1) plant and animal breeding to improve the effectiveness with which desirable traits are combined and moved through breeding programs; (2) quality testing of agricultural and food products to ensure genetic identity and safety; and (3) biodiversity conservation to help protect and restore populations of threatened and endangered species.
