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United States Department of Agriculture

Agricultural Research Service

Research Project: USING FUNCTIONAL AND APPLIED GENOMICS TO IMPROVE STRESS AND DISEASE RESISTANCE IN FRUIT TREES

Location: Appalachian Fruit Research Laboratory: Innovative Fruit Production, Improvement and Protection

Title: Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Authors
item Gasic, Ksenija - UNIVERSITY OF ILLINOIS
item Yuepeng, Han - UNIVERSITY OF ILLINOIS
item Kertbundit, Sunee - UNIVERSITY OF ILLINOIS
item Shulaev, Vladimir - VIRGINIA TECH
item Lezzoni, Amy - MICHIGAN STATE UNIVERSITY
item Stover, Ed
item Bell, Richard
item Wisniewski, Michael
item Korban, Schuyler - UNIVERSITY OF ILLINOIS

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 19, 2008
Publication Date: December 11, 2008
Citation: Gasic, K., Yuepeng, H., Kertbundit, S., Shulaev, V., Lezzoni, A., Stover, E.W., Bell, R.L., Wisniewski, M.E., Korban, S. 2009. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Molecular Breeding. 23:397-411.

Interpretive Summary: Breeding new varieties of fruit trees with specific traits is a long and costly endeavor. Once a cross is made, it can take 4 – 5 years before the offspring will bear fruit for evaluating or before it can be used for further crosses. It is not unreasonable for it to take up to 25 years or more to develop a new fruit variety. During that entire time, the various breeding lines need to be maintained in the field which is very costly and labor intensive. A typical tree fruit breeding program may have thousands of trees to maintain as crosses are made, selections are evaluated, elite parents defined, and further crosses are made and evaluated. Any technology that could either reduce the time to evaluation or lower the number of offspring that need to be maintained would greatly increase efficiency, lower costs, and result in the production of new varieties in a timely manner. The use of genetic markers in a breeding program can be used as a selection tool to identify specific traits in individuals, an approach referred to as marker-assisted-selection (MAS). This approach allows a breeder to screen germplasm while plants are still in a seedling stage, with many hundreds of trees occupying a small amount of bench space. Instead of planting all the offspring in the field for evaluation, MAS allows one to plant only 'elite' selections that are known to carry the genetic markers for the traits of interest. In order to use MAS, good genetic maps of tree fruit cultivars are needed. Microsatellites, also known as simple sequence repeats (SSRs) are short, repetitive sequences of DNA that are the tool of choice for making the genetic maps necessary to define molecular markers for specific traits. Tree fruits (apple, pear, cherry, peach, plums, etc.) and strawberries and roses belong in the taxonomic family, Rosaceae. Within the family, more SSRs have been defined for apple than for any other species. The purpose of the present study was to determine if the primers used to amplify SSRs in apple could also be used to identify similar SSRs in other tree fruit species. A total of 68 apple SSRs were used on 50 individual members of the Rosaceae representing 3 different genera and 14 species. Transferability of apple SSRs to other tree fruit species ranged from 20 percent in sweet cherry to 62 percent in pear. Rose and peach exhibited 40 and 44 percent transferability, respectively, while the strawberry genus exhibited 53 percent. Overall these finding suggest that many apple SSRs can be used on other members of the rose family to generate genetic maps. These SSRs can also be used in the future for comparative mapping and determining levels of genetic similarity within the members of the rose family.

Technical Abstract: Genic microsatellites or simple sequence repeats derived from expressed sequence tags (ESTs), referred to as EST–SSRs, are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus x domestica) EST database (over 300,000) provides a valuable resource for developing well-characterized DNA molecular markers. In this study, we have investigated the level of transferability of 68 apple EST-SSRs in 50 individual members of the Rosaceae family, representing three genera and fourteen species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the amplification product matched the in silico predicted size. When tested across the Rosaceae family, only 76 percent of these primer pairs produced amplification products. Transferability of apple EST-SSRs across the Rosaceae family ranged from 20 percent in sweet cherry to 62 percent in the closely related pear. Besides pear, the highest transferability of these apple EST-SSRs, at the genus level, was observed for rose and peach, 40 and 44 percent, respectively. Interestingly, the observed transferability across the genera Prunus and Fragaria was rather similar, 51 percent and 53 percent, respectively. Overall, these findings suggest that transferability of apple EST-SSRs across the Rosaceae family was good, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies.

Last Modified: 4/23/2014
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