Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer reviewed journal
Publication Acceptance Date: 2/25/2006
Publication Date: 5/1/2006
Citation: Hale, A.L., Farnham, M.W., Menz, M.A. 2006. Use of PCR-based markers for differentiating elite broccoli inbreds. Journal of the American Society for Horticultural Science. 131:418-423. Interpretive Summary: Many genetic markers derived from DNA fingerprints have been utilized by public and private plant breeders to increase the efficiency of selecting for desirable traits. In some crops, such as broccoli, recently developed marker systems have not been extensively tested and compared to older and more established methods to determine relative efficiency and cost-effectiveness. Previous studies tend to utilize a single type of marker to assist in selection. The aim of this study was to compare three different types of genetic markers to determine which marker or combination of marker types was the most effective in differentiating 24 elite broccoli varieties. The names of the three marker types compared are sequence related amplified polymorphisms, amplified fragment length polymorphisms, and simple sequence repeats. The first two marker types generated more markers than the third, thus they were the efficient types for differentiating varieties. However, it was determined that using a combination of all 3 marker types in combination provided the greatest power to differentiate among the varieties . While the results of this study with broccoli, show sequence related amplified polymorphisms are an equally effective marker system as the more widely accepted amplified fragment length polymorphism system, our results indicate a combination of systems is more effective, probably because the weakness of one system is complemented by the strengths of the other. In future studies, to obtain more accurate results, we would advise breeders to use more than one marker system.
Technical Abstract: Private and public vegetable breeders are interested in using current and emerging PCR-based marker systems in their respective improvement programs. However, before new systems are employed to replace existing ones, the new systems must prove to be efficient and cost-effective alternatives. Sequence related amplified polymorphisms (SRAPs), amplified fragment length polymorphisms (AFLPs), and simple sequence repeats (SSRs) were compared for their ability to differentiate individuals of a diverse group of 24 elite broccoli inbreds. Genomic DNA was assayed using 24 AFLP, 24 SRAP, and 44 SSR primer pairs. In this assessment, SSRs produced an average of only 2 bands per primer, with 25% of these bands being monomorphic, and the remaining bands detecting very few differences among the inbreds. Although the AFLP method resulted in a lower rate (63%) of polymorphism than the SSRs, it produced about 20 bands per primer. SRAPs produced an average of 14 bands per primer with 82% of these bands being polymorphic. Since AFLP and SRAP markers had a higher multiplex ratio and SSRs were frequently monomorphic, AFLP and SRAPs were more effective in differentiating the elite broccoli inbreds examined in this study. Similarity matrices were generated from the AFLP and SRAP data, and resulting dendographs were compared.