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Some raspberry and blackberry breeders are interested in using molecular markers to assist with selection. Simple Sequence Repeat markers (SSRs) have many advantages, and SSRs developed from one species can sometimes be used with related species. Six SSRs derived from the weed R. alceifolius, and 74 SSRs from R. idaeus red raspberry `Glen Moy' were tested on R. idaeus red raspberry selection NY322 from Cornell Univ., R. occidentalis `Jewel' black raspberry, Rubus spp. blackberry `Arapaho', and blackberry selection APF-12 from the Univ. of Arkansas. The two raspberry genotypes are parents of an interspecific mapping population segregating for primocane fruiting and other traits. The two blackberry genotypes are parents of a population segregating for primocane fruiting and thornlessness. Of the six R. alceifolius SSRs, two amplified a product from all genotypes. Of the 74 red raspberry SSRs, 56 (74%) amplified a product from NY322, 39 (53%) amplified a product from `Jewel', and 24 (32%) amplified a product from blackberry. Of the 56 SSRs that amplified a product from NY322, 17 failed to amplify a product from `Jewel' and, therefore, detected polymorphisms between the parents of this mapping population. Twice as many detected polymorphisms of this type between blackberry and red raspberry, since 33 SSRs amplified a product from NY322, but neither of the blackberry genotypes. Differences in PCR product sizes from these genotypes reveal additional polymorphisms. Rubus is among the most diverse genera in the plant kingdom, so it is not surprising that only 19 of the 74 raspberry-derived SSRs amplified a product from all four of the genotypes tested. These SSRs will be useful in interspecific mapping and cultivar development.

Primers to 43 genes, including those involved in the phenylpropanoid and volatile pathways, cell wall, ethylene and polyamine metabolism, and from Prunus linkage group (LG) 6 were tested in red raspberry (Rubus idaeus) cultivars Latham and Glen Moy, and 40 were polymorphic. Thirty-seven genes were subsequently mapped in the ‘Latham’ × ‘Glen Moy’ population and were placed across all seven Rubus LG. This brings to 97 the total number of genic markers mapped in this Rubus mapping population. Fifteen genes are associated with existing quantitative trait loci for ripening, cane diseases, including yellow rust (Phragmidium rubi-idaei), cane botrytis (Botrytis cinerea), spur blight (Didymella applanata), and cane spot (Elsinoe veneta) or fruit color in R. idaeus and can be used for identifying bacterial artificial chromosome clones for physical mapping studies. A cluster of four genes from Prunus LG6 mapped together to Rubus LG3, suggesting that there may be sufficient synteny between these Rosaceae over small genomic regions that can be exploited in future studies.

Twelve microsatellites were isolated from simple sequence repeat (SSR)-enriched genomic libraries of ‘Meeker’ red raspberry (Rubus idaeus) and ‘Marion’ blackberry (Rubus hybrid). These primer pairs plus one developed from a GenBank red raspberry sequence were evaluated in 48 raspberry and 48 blackberry genotypes. Only RhM031 did not generate a product in raspberry, whereas RiG001 failed to amplify in blackberry and hybrid accessions. The number of polymerase chain reaction products per primer pair in the 12 SSRs that successfully amplified was higher in blackberry genotypes and their hybrids than in raspberry, ranging from three to 29 in blackberry (average, 14.4) and from one to 15 in red raspberry (average, 7.5). Diversity estimates were determined for 10 of 12 SSRs that amplified up to two products in 44 red raspberry genotypes. The best SSR loci based on high observed and expected heterozygosities, high polymorphism information content, and low inbreeding coefficient were RiM019, RhM003, and RhM011. They mapped to three different linkage groups (5, 2, and 7, respectively) in red raspberry and differentiated the unique genotypes identified with the 12 SSRs in each crop type.

Scottish wild red raspberry (Rubus idaeus) plants at 12 sites were re-examined 10 years after initial studies had been carried out to examine the decline in population size and to address an earlier finding that demonstrated significant population differentiation over a small scale. Ten simple sequence repeat (SSR) loci were screened on the plants and a total of 80 alleles were detected, half of which were unique to a particular population, with all populations containing unique SSR alleles. Only 18 of the 80 alleles present in the wild were found in cultivated raspberries, highlighting the genetic diversity available for future breeding. This finding makes the decline in population number observed a concern, as this unique diversity is being eroded, primarily due to human impact. An additional 17 unique alleles were identified in the cultivars that were not present in the wild individuals studied. Gene flow into one lowland site was identified by the gain of one new allele into progeny at the site, but three alleles were also lost from parents to progeny. SSR markers were used to estimate the levels of outcrossing in wild red raspberry for the first time, and confirmed that the populations studied were outcrossing, intermating populations. The nonsignificant global F _IS value indicates that red raspberry is an outbreeder (global F _IS = −0.117), but significant population differentiation was observed [global F _ST = 0.348 (P < 0.001)]. Diversity in this crop's wild relative and the population differentiation observed may have use in the future for breeding aimed at addressing climate change scenarios, and consideration should be given to means of conserving the diversity revealed by these studies.

Interest in molecular markers and genetic maps is growing among researchers developing new cultivars of Rubus L. (raspberry and blackberry). Several traits of interest fail to express in seedlings or reliably in some environments and are candidates for marker-assisted selection. A growing number of simple sequence repeat (SSR) molecular markers derived from Rubus and Fragaria L. (strawberry) are available for use with Rubus mapping populations. The objectives of this study were to test 142 of these SSR markers to screen raspberry and blackberry parental genotypes for potential use in existing mapping populations that segregate for traits of interest, determine the extent of inter-species and inter-genera transferability with amplification, and determine the level of polymorphism among the parents. Up to 32 of the SSR primer pairs tested may be useful for genetic mapping in both the blackberry population and at least one of the raspberry populations. The maximum number of SSR primer pairs found useable for mapping was 60 for the raspberry population and 45 for the blackberry population. Acquisition of many more nucleotide sequences from red raspberry, black raspberry, and blackberry are required to develop useful molecular markers and genetic maps for these species. Rubus, family Rosaceae, is a highly diverse genus that contains hundreds of heterozygous species. The family is one of the most agronomically important plant families in temperate regions of the world, although they also occur in tropical and arctic regions as well. The most important commercial subgenus of Rubus is Idaeobatus Focke, the raspberries, which are primarily diploids. This subgenus contains the european red raspberry R. idaeus ssp. idaeus L., as well as the american black raspberry R. occidentalis L. and the american red raspberry R. idaeus ssp. strigosus Michx. Interspecific hybridization of these, and other raspberry species, has led to greater genetic diversity and allowed for the introgression of superior traits such as large fruit size, fruit firmness and quality, disease resistance, and winter hardiness.