Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.)

Abstract

Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8 Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100 bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2 %) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7 % of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2 % of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species. Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.

Development of chloroplast‐specific microsatellite markers for molecular characterization of alloplasmic lines and phylogenetic analysis in wheat

“…() observed 51.9% in sorghum and Wang et al. () reported 34.38% in cabbage. Therefore, these results confirmed the universal application of cpSSR markers in wild relatives of wheat.…”

“…, Wang et al. ). In the present study, we have utilized the chloroplast‐specific cpSSR primers, which ensure PCR products amplified only from the chloroplast genome.…”

“…SSRs are mostly flanked with conserved nucleotide sequences, which allow designing primers for PCR amplification of highly variable SSR loci constitutively in different genotypes of a species or even in related species (Wang et al. ). However, SSR mining in organelle genome has not been well studied in plants even though chloroplast and mitochondria of several plants species have been sequenced (Sonah et al.…”

Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

“…It has been well recognized that some molecular markers (including microsatellite markers) can be transferable from different genotypes within or between species or even between genera (Wang et al, 2012). Such interspecific or intergeneric transferability for markers will provide some useful genetic information for poorly-studied related species, contributing to conservation, genetic assessment, and construction of linkage maps.…”

Development of 34 New Microsatellite Markers from Actinidia arguta: Intra- and Interspecies Genetic Analysis

“…The transferability of SSRs to other Actinida species showed average value of 77% ranged from 57% (A. macrosperma) to 90% (A. chinensis). A little higher transferability than other genus such as Prunus (mean=59%) and Allium (mean=59%) reveals that genetic distances are relatively low between tested Actinidia species (Lee et al 2011;Wang et al 2012).…”