Development of novel chloroplast microsatellite markers for Cucumis from sequence database

Abstract

The development of chloroplast microsatellite (cpSSR) markers in Cucumis species and analysis of their polymorphism and transferability were reported. Fifteen microsatellite markers, represented by mononucleotide repeats, were developed from the complete sequence of Cucumis sativus chloroplast genome. Intraspecific variation was successfully detected in C. sativus and C. melo and revealed mean 1.6 and 1.9 alleles per cpSSR locus, respectively. With the exception of two exon region-located cpSSR markers being monomorphic, each of the others amplified polymorphic fragments in C. sativus or C. melo. A total of 34 polymorphic loci were detected with these cpSSR markers in the two species. Transferability of the newly developed cpSSR markers was checked on an additional set of 41 Cucurbitaceae accessions (belonging to 12 different species), and except for two markers with no amplification in Cucurbita maxima, the others could be transferable to all the accessions tested. Of the 15 cpSSR markers, 14 markers generated fragments with expected band sizes and 13 markers detected interspecific polymorphism among the accessions. Intraspecific polymorphism was also observed within four Cucurbitaceae species excluding C. sativus and C. melo.

Characterization and development of chloroplast microsatellite markers for Gossypium hirsutum, and cross-species amplification in other Gossypium species

“…We identified cpSSRs throughout the whole chloroplast genome, but they were not evenly distributed, appearing to be concentrated in several areas. This result was consistent with those found in other plants (Wang et al, 2006;Pian et al, 2008;Hu et al, 2009;Pan et al, 2014). In addition, there were clear differences in the cpSSR number in different plants.…”

Development and evaluation of expressed sequence tag-derived microsatellite markers for hop genotyping

“…Theoretically, our results proved that bioinformatic tools and sequence databases are an effective way to find valid molecular markers for another species (e.g. Hu et al 2009). Generally, the new developed EST-SSR markers can be used as an effective tool for cultivar's identification, verification and purity declaration of hop (Humulus lupulus L.).…”

“…Restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), sequencetagged sites (STS), simple sequence repeat (SSR), intersimple sequence repeat (ISSR) and amplified fragment length polymorphism AFLP) were successfully used for DNA fingerprinting of hop genotypes (reviewed by Patzak 2001). The SSR method has been the most reliable for molecular genetic analysis of variability and evaluation of biodiversity in different plant species (Akkak et al 2009, Akritidis et al 2009, Hu et al 2009, Ma et al 2010. Therefore, microsatellite SSR markers have also been the most used for studies of molecular variability of hops (Jakše et al 2001, Čerenak et al 2004, Murakami et al 2006, Bassil et al 2008, Štajner et al 2008.…”

“…A new trend in molecular methods is to develop molecular markers in specific sequences, near or within structural genes. The use of ESTs is a new trend for SSR markers in all main crops (Feingold et al 2005, Hu et al 2009). The possibility to use polymorphism in structural genes was reported by Patzak et al (2007), Bassil et al (2008) and Castro et al (2008).…”

Utilization of a set of high-polymorphism DAMD markers for genetic analysis of a cucumber germplasm collection

“…This fact makes it emergent to develop new methods for germplasm study and to offer new genetic information for cucumber cross-breeding. Although several kinds of marker systems have been used to study the cucumber diversity to date (Kennard et al 1994;Fazio et al 2002;Wang et al 2007;Hu et al 2009a), new high-polymorphism molecular markers are demanded yet.…”