Enhancing Efficiency in Tree-Fruit Breeding by Developing Trait-Predictive DNA Tests

Paul James Sandefur

Since 2009, consumption of fresh fruit in the U.S. has grown by 4% and is expected to increase 9% over the next five years. Simultaneously, the difficulties of fruit production have increased, with elevated input costs and continual threats from new pests and diseases. Successful development of new fruit cultivars is a sustained solution to production challenges. However, evaluation of genetic potential for many traits and subsequent selection of superior germplasm within fruit breeding programs is costly due to long juvenility periods, large plant size, and the requirement for several years of evaluation. The use of DNA-based information could improve breeding efficiency by enabling greater selection accuracy at reduced costs, but trait-predictive DNA tests are required. The objective of this work was to demonstrate an efficient approach in Rosaceae fruit crops for developing DNA tests to predict fruit quality trait levels. Demonstration trait targets were peach fruit acidity and blush coverage, sweet cherry fruit color and harvest time, and apple fructose content. For each trait locus, haplotypes based on single nucleotide polymorphism (SNP) markers and associated with breeding-relevant trait level differences were established. The SNP haplotypes were converted to simple sequence repeat assays to enable routine screening using various genotyping platforms. Each test’s trait-predictive potential was determined across RosBREED germplasm sets representative of breeding material with multiple years of phenotypic data. For peach, the fruit acidity test, Ppe-Acid, identified individuals with a maximum difference of 0.4% titratable acidity and the blush coverage test, Ppe-Rf-SSR, differentiated individuals with a maximum difference of 25% blush. For sweet cherry, the fruit color test, Pav-Rf-SSR, distinguished mahogany-type from blush-type individuals and the harvest time test, Pav-Fht-SSR, identified individuals varying in harvest date by up to two weeks. The apple fructose test, Md-Fructose, differentiated individuals varying in fructose content by up to 36 mg/ml. The approach established for the development of DNA tests is a simple, efficient process that utilized published research findings, freely available software, and straightforward protocols. Therefore, this approach can be used across traits and crops to enhance selection efficiency by facilitating development of trait-predictive DNA tests for routine use in breeding.

Enhancing Efficiency in Tree-Fruit Breeding by Developing Trait-Predictive DNA Tests

Files and links (1)

Abstract

Metrics

Details