ARS | Publication request: Microsatellite (simple sequence repeat) marker-based paternity analysis of a seven-parent sugarcane polycross

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 2, 2010
Publication Date: June 7, 2010
Citation: Tew, T.L., Pan, Y.-B. 2010. Microsatellite (simple sequence repeat) marker-based paternity analysis of a seven-parent sugarcane polycross. Crop Science. 50:1401-1408.

Interpretive Summary: Sugarcane breeders prefer to make crosses with two known parents; however, they often encounter situations where the availability of desirable parents is limited. To maximize the number of high-value crosses with a limited parental source, sugarcane breeders must adopt the alternative crossing method called polycross, through which several parents are intercrossed by putting their flowers all together. One drawback of the polycross method is the loss of paternity information. This study was conducted on a seven-parent polycross to test if the paternity of their offspring could be determined using seven simple sequence repeat (SSR) markers. For each parent, 87 offspring were randomly taken and their DNA samples were extracted and subjected to a DNA fingerprinting process. As a control, DNA samples from all seven parents were also fingerprinted with the same set of SSR markers. DNA fingerprinting software was employed to view and score the fingerprints. A total of 51 DNA fingerprints was detected, 48 of which were not uniformly present among the parents as well as their offspring. Fifteen of these 51 fingerprints were present in only one parent and were highly useful in determining paternity. Overall, the paternity of 79 to 99% of the offspring was determined, depending upon the maternal parent. The fingerprinting data also indicated that self pollination had occurred, ranging from 0 to 45% across the seven parents, while the pollen contribution to polycross offspring from each parent ranged from 4 to 27%. This study has demonstrated that, by using this fingerprinting technology, sugarcane breeders now have the ability to increase the number of desirable crosses with minimal loss of pedigree information.

Technical Abstract: It is not feasible to make all possible cross combinations among elite parents used in sugarcane (Saccharum spp.) breeding programs, particularly within a single year. Hence, the polycross approach has been used to maximize the number of cross combinations that can be represented among progeny. The primary objection to using the polycross approach is the rapid loss of paternity information. Simple sequence repeat (SSR) marker-based paternity analysis is proposed as an effective molecular tool for identifying paternity of progeny from a seven-parent polycross. Using seven highly polymorphic SSR markers, 87 progeny from each elite parent were genotyped along with the parents, producing a total of 51 polymorphic SSR alleles, 15 of which were parent-specific. These alleles enabled the positive identification of the paternity for 79 to 99% of the progeny from the polycross, depending upon the maternal parent. Based on our analysis, the extent to which each parent contributed pollen, and thus was represented as a paternal parent, ranged from 4 to 27%. This molecular breeding approach to identify paternity among polycross progeny can be used in sugarcane breeding to maximize the number of desirable crosses with minimal loss of pedigree information.