Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 2, 2013
Publication Date: May 20, 2013
Citation: Riday, H., Johnson, D.W., Heyduk, K., Raasch, J.A., Darling, M.M., Sandman, J.E. 2013. Paternity testing in an autotetraploid alfalfa breeding polycross. Euphytica. DOI:10.1007/s10681-013-0938-7. Interpretive Summary: Paternity of plants produced in alfalfa breeding programs is often unknown. This missing information can make alfalfa breeding less efficient. In this study, an inexpensive DNA test is presented along with software that enables alfalfa breeders to determine unknown parentage in their alfalfa breeding programs. The DNA test and software are demonstrated on offspring of a 16-parent commercial alfalfa breeding polycross. Using the test, paternal assignment success rate was over 90%. Unexpectedly, 45% of progeny were the result of self-fertilization. Furthermore, a parent’s seed yield was positively associated with self-fertilization rates. These correlations suggest that selecting for increased seed yield may result in indirect selection for increased self-fertilization rates. Such a high level of self-fertilization has negative inbreeding implications with accompanying expected loss of plant vigor. Although the study was based on one polycross, the study cautions alfalfa breeders that heretofore unconsidered sources of inbreeding could be present in some breeding materials. Based on the test provided in this paper, alfalfa breeders have a tool for detecting, managing, and/or selecting against self-fertilization, if desired.
Technical Abstract: Determining unknown parentage in autotetraploid alfalfa (Medicago sativa L.) (2n = 4x = 32) can improve breeding gains. Exclusion analysis based paternity testing SAS code is presented, amenable to genotyping errors, for autotetraploid species utilizing co-dominant molecular markers with ambiguous dosage. Nineteen SSR loci were used to analyze more than 1100 progeny from a commercial, isolated, clonally replicated, 16-parent alfalfa breeding polycross which were pollinated by leafcutter bees (Megachile rotundata F.). Paternal assignment success rate was over 90%. Among typed progeny, 45% were the result of self-fertilization. Significant differences between the 15 parents that produced seed and were detected as fathers for total fertilizing pollen contribution (% deviation from expectation), self-fertilization rates (%), and outcrossing pollen contribution (% deviation from expectation) were detected. Physical within-cage distance between parental plants was correlated with outcrossing fertilizing pollen frequency (exponential decay function). Parental seed yield was positively correlated with total fertilizing pollen contribution, particularly with self-fertilization rates (41% self-fertilization and 15% outcrossing). These correlations suggest that selecting for increased seed yield may result in indirect selection for increased self-fertilization rates. Parental total fertilizing pollen contribution was 66% determined by outcrossing and 34% by self-fertilization. This study cautions alfalfa breeders that heretofore unconsidered sources of inbreeding could be present in some breeding materials. This study provides cost effective and easy to use molecular genetic tools for detecting, managing, and/or selecting against (through breeding) these sources of inbreeding.