Implementation of simple sequence repeat markers to genotype Florida strawberry varieties

Abstract

Simple sequence repeats (SSRs or microsatellites) are frequently used as a robust, rapid, and relatively inexpensive means of genotyping. Recent reports in cultivated strawberry (Fragaria 9 ananassa) have identified a widely applicable set of SSRs that permits discrimination of closely-related genotypes. In the present study this same set of SSRs is analyzed in cultivars commonly grown in the state of Florida, as well as advanced breeding selections from the University of Florida program. Nine primer pairs have been used to produce discrete SSR patterns for all lines tested, including diagnostic sets that distinguish between closely-related cultivars and/or breeding selections. A comparison of markers to known pedigrees is presented, along with analysis of relative relatedness between lines studied. We also detail important technical considerations for transferability and limitations of these technologies between laboratories. The resulting genotype data for cultivars commonly used in Florida are accessible as supplemental data in graphic format and allow comparison with other cultivars. Users can thus select the most diagnostic SSRs to test the lines in question. These resources provide new tools for breeders and nurseries to authenticate genotypes, follow inheritance patterns and enforce patent protection. As important, this report underscores the strengths and weaknesses of applying the original methodologies to a different plant population in independent laboratories.

Characterization of strawberry (Fragaria × ananassa Duch.) cultivars and hybrid clones using SSR and AFLP markers

“…This primer pair was also the most informative by Honjo et al (2011). According to the number of alleles in this study, the primer pairs ARSFL-009 (20), ARFSL-010 (16) and ARFSL-011 (17) were highly informative also and the number of obtained alleles was higher as compared to the studies of Dangl et al (2007) and Brunings et al (2010), where 26 and 45 genotypes were investigated, …”

“…Dangl et al (2007) suggested using the primer ARSFL-009, followed by primers ARSFL-010 and ARSFL-011 for cultivar identification according to their highest number of alleles and unique peak profiles. The primer pair EMFv-104 distinguished 36 genotypes in this study and was most informative in the study of Brunings et al (2010) as well with the ability to distinguish 24 genotypes. The least informative primer pairs in this study were EMFax-381827 and EMFv-125 as both were able to distinguish only 12 genotypes.…”

“…Each of these systems has their own technical limitations. While microsatellites exhibit co-dominant inheritance, RAPD and AFLP markers are usually dominant (Brunings et al, 2010).…”

Studies Using DNA Markers in Fragaria × ananassa: Genetic Analysis, Genome Structure, and Cultivar Identification

“…In the cultivated strawberry, the SSR markers selected for genotyping by Govan et al (2008) were tested for their reproducibility in two other laboratories (Brunings et al, 2010). Although Govan et al (2008) had used multiplex PCR, Brunings et al (2010) examined the signals detected by each primer pair individually.…”

“…Although Govan et al (2008) had used multiplex PCR, Brunings et al (2010) examined the signals detected by each primer pair individually. The comparison of allele sizes of common cultivars detected in different laboratories revealed some discrepancies, including missing or additional signals, and 1-2 bp shifts, as shown in grapes.…”