Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily

Abstract

Cultivated strawberry (Fragaria 9 ananassa) together with other economically important genera such as Rosa (roses) and Rubus (raspberry and blackberry) belongs to the subfamily Rosoideae. There is increasing interest in the development of transferable markers to allow genome comparisons within the Rosaceae family. In this report, 122 new genic microsatellite (SSR) markers have been developed from cultivated strawberry and its diploid ancestor Fragaria vesca. More than 77% of the sequences from which the markers were developed show significant homology to known or predicted proteins and more than 92% were polymorphic among strawberry cultivars, representing valuable markers in transcribed regions of the genome. Sixtythree SSRs were polymorphic in the diploid Fragaria reference population and were bin-mapped together with another five previously reported but unmapped markers. In total, 72 loci were distributed across the seven linkage groups. In addition, the transferability of 174 Fragaria SSRs to the related Rosa and Rubus genera was investigated, ranging from 28.7% for genic-SSRs in rose to 16.1% for genomic-SSRs in raspberry. Among these markers, 33 and 16 were both localized in the diploid Fragaria reference map and cross-amplified in rose and raspberry, respectively. These results indicate that transferability of SSRs across the Rosoideae subfamily is limited. However, we have identified a set of Fragaria markers, polymorphic in the diploid reference population, which cross-amplified in both Rosa and Rubus, which represents a valuable tool for comparative mapping and genetic diversity analyses within the Rosoideae subfamily.Keywords Comparative mapping Á Synteny Á Strawberry Á Rose Á Raspberry Á Rosoideae Electronic supplementary material The online version of this article

Development of novel microsatellite markers for effective applications in Anthurium cultivar identification

“…SSR markers have been widely applied to construct linkage maps of the rice (McCouch et al 2002) and tomato (Frary et al 2005) genomes. Such markers can also be used to assist in selection in breeding and backcrossing for a specific trait or quantitative traits, in genotyping species (He et al 2003;Gong and Geng 2010;Zorrilla-Fontanesi et al 2011), and in cultivars identification (Tantasawat et al 2010;Zhang et al 2010) and serve as effective tools in plant germplasm diversity analysis (Guilford et al 1997;Gomez et al 2008;Mujaju et al 2010).…”

The History Of Genome Mapping In Fragaria Spp.

“…In genetic mapping of diploid Fragaria plants, F2 population obtained from self-pollination or intercross of F1 has been used most frequently (Williamson et al 1995;Davis & Yu 1997;Deng & Davis 2001;Sargent et al 2004Sargent et al , 2006Sargent et al , 2007Sargent et al , 2008Sargent et al , 2011Ruiz-Rojas et al 2010;Illa et al 2011;Zorrilla-Fontanesi et al 2011b;Koskela et al 2012). However, some outline maps of F. vesca and F. viridis were elaborated on the basis of backcross population (BC), generated by crossing F1 individual(s) with inbred parent used in the initial cross (Nier et al 2006;Cekic et al 2001;Albani et al 2004).…”

“…To overcome this obstacle, EST-SSR (Expressed Sequence Tag-SSR) primers were designed for coding regions of genes, resulting in development of polymorphic functional markers, informative not only within species, but also among genera. In total, 6125 EST-SSR markers were developed for Fragaria species and used for providing a linkage framework (Folta et Sargent et al 2006Sargent et al , 2007Sargent et al , 2008Spigler et al 2008;Vilanova et al 2008;Zorrilla-Fontanesi et al 2011b;Isobe et al 2012). Lately, SNP-based markers (Single Nucleotide Polymorphism), although diallelic and thus less polymorphic than SSRs, were recognised as providing valuable genetic information due to their abundance and ubiquity along the genome (Mammadov et al 2012).…”

“…americana 'WC6' population (Davis & Yu 1997 LGs with a total genetic distance of 448 cM. Subsequently, this reference map has been improved Illa et al 2011;Zorrilla-Fontanesi et al 2011b) and it latest version contains a total of 700 sequence tag sites derived from SSRs, genespecific markers, RFLPs, SNPs and ESTs, spanning along all seven linkage groups and covering a genetic distance of 442.8 cM .…”

The genetic diversity among strawberry breeding resources based on SSRs

“…SSR markers for strawberry were first developed using primer pairs that amplified characterized regions such as expressed sequence tags (ESTs) or genomic libraries, in contrast to other primer pairs that amplified anonymous DNA fragments (Ashley et al, 2003;Bassil et al, 2006;Gil-Ariza et al, 2006;James et al, 2003;Lewers et al, 2005;Monfort et al, 2006;Sargent et al, 2003). The completion of the genome sequence of diploid F. vesca allowed robust SSRs to be developed and mapped on the Fragaria reference map (Rousseau-Gueutin et al, 2011;Sargent et al, 2011;Zorrilla-Fontanesi et al, 2011). In this study, we assessed the genetic diversity of 160 strawberry accessions used for breeding in Korea, including 34 newly collected accessions.…”