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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #291545

Title: Routine DNA testing

Author
item Peace, Cameron - Washington State University
item Bassil, Nahla

Submitted to: RosBREED Newsletter
Publication Type: Popular Publication
Publication Acceptance Date: 11/16/2012
Publication Date: N/A
Citation: N/A

Interpretive Summary: Routine DNA testing is done once you’ve identified useful DNA regions that can predict a trait of importance like large fruit size, for example, in your breeding program under your growing conditions. By then you are ready to screen the parents you are interested in using in your crosses or the progeny from the crosses that you have made. But how are DNA tests run routinely? Mostly when we refer to DNA tests we’re talking about location-specific DNA regions that are predictive for particular traits. For example, in the Washington State University apple and sweet cherry breeding programs, thousands of seedlings each year (and dozens of parents) are routinely screened with DNA tests that can predict superior fruit texture, storability, fruit size, and other traits. For selecting progeny that possesses traits of interest, the most economical way to conduct these tests is to run the most stringent DNA test on the family, eliminate the progeny at the young seedling stage if predicted to be inferior, and then run the next test on the remaining progeny. But testing costs are dropping to the point where the screening for multiple traits at the same time is becoming attractive. We discuss the usefulness of the large and expensive genotyping chips (containing = 6000 DNA tests) developed for apple, peach and cherry. In the future, we expect that refined composition of these DNA tests and the practical DNA information they provide will make chip use on parents and advanced selections an extremely compelling routine operation for all breeders.

Technical Abstract: Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your parent pool and/or various seedling families to gain insights into genetic potential that help with your crossing and selection decisions. But how are DNA tests run routinely? Mostly when we refer to DNA tests we’re talking about locus-specific markers predictive for particular traits - that is, targeting one trait locus at a time. For example, in the Washington State University apple and sweet cherry breeding programs, thousands of seedlings each year (and dozens of parents) are routinely screened with locus-specific markers for superior texture, storability, fruit size, and other traits. For seedling selection, the most economical way to conduct these tests is to run the most stringent DNA test on a family, cull the seedlings predicted to be inferior, and then run the next test on the remaining seedlings. But genotyping costs are dropping to the point where the multi-locus approach of Single Nucleotide Polymorphism (SNP) mini-array genotyping is becoming attractive. We discuss the usefulness of the large and expensive Infinium arrays developed for apple, peach and cherry. In the future, we expect that refined composition of these thousands-of-SNP arrays and the practical DNA information they provide, with streamlined centralized sample and data processing, will make SNP array use on parents and advanced selections an extremely compelling routine operation for all Rosaceae breeders.