Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry

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 (Dirlewanger et al., 2002), 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. Blackberries reside in the subgenus Rubus (formerly Eubatus Focke). Modern eastern north american blackberry cultivars are comprised of many species, including R. allegheniensis Porter, R. argutus Link., R. cuneifolius Pursh., R. frondosus Bigel., R. rubrisetus Rydb. (=R. trivialis L.), and R. pergratus Blanch., as well as european blackberry species such as R. ulmifolius var. inermis Focke, R. thyrsiger Banning and Focke, and R. procerus P.J. Muell. Blackberry is a highly heterozygous plant and many current cultivars are tetraploid. Interest in development of molecular markers and maps has been limited, because of the Received for publication 30 Dec. 2004. Accepted for publication 1 Mar. 2005. The authors wish to thank Ms. Kate Rappaport for SSR testing reactions and Ms. Tina Sphon for reaction analyses. Thanks also to Dr. Tad Sonstagard for managing, and to the Beltsville Area Research Center for supporting the genotyping facility. Thanks also go to the North American Bramble Growers ̓Association for partial funding of this research. The authors also wish to thank Drs. Jim Ballington, Lisa J. Rowland, and Freddi Hammerschlag plus the anonymous reviewers for their helpful comments. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the Univ. of Arkansas, Cornell Univ., the Scottish Crops Research Inst., or the U.S. Dept. of Agriculture. 1To whom reprint requests should be addressed. E-mail: [email protected]. gov. varied reproductive strategies [sexual, facultatively apomictic, and obligately apomictic (Hall, 1990)], cytological conditions (autoand allo-polyploidy), and inheritance strategies (disomic and tetrasomic) (Lopez-Medina et al., 2000) of polyploid blackberries. Also, polyploid plants often display problems with reproducibility and amplification in polymerase chain reactions (PCR) (Buteler et al., 1999; Diwan et al., 1997; Röder et al., 1995). However, because eastern north american blackberries for the most part are not apomictic (Hall, 1990), sexual recombination can be assumed. Although alloploidy in Rubus is more common than autoploidy (Ourecky, 1975), various degrees of meiotic irregularity occur in north american species, and the high percentage of multivalents observed in tetraploid species suggests that both autoand allopolyploidy are involved (Einset, 1947). The desire to incorporate relatively new and exciting traits of commercial importance such as thornlessness and fruit production on first-year canes (primocane fruiting) has led to greater interest in molecular marker analysis in blackberries. Simple sequence repeat (SSR) markers are repeats of short nucleotide sequences, usually equal to or less than six bases in length, that vary in number (Rafalski et al., 1996). SSR markers have become quite useful in various aspects of molecular genetic studies in the past decade, including assessment of