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, 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.

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Simple Sequence Repeat (SSR) Markers for Raspberry and Blackberry

HortScience ◽

10.21273/hortsci.39.4.785d ◽

2004 ◽

Vol 39 (4) ◽

pp. 785D-785 ◽

Cited By ~ 1

Author(s):

Kim S. Lewers* ◽

Eric T. Stafne ◽

John R. Clark ◽

Courtney A. Weber ◽

Julie Graham

Keyword(s):

Molecular Markers ◽

Simple Sequence Repeat ◽

Mapping Population ◽

Black Raspberry ◽

Sequence Repeat ◽

Red Raspberry ◽

Simple Sequence Repeat Markers ◽

Cultivar Development ◽

Pcr Product ◽

Simple Sequence

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.

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Application of SSR markers in the construction of Australian barley genetic maps

Australian Journal of Agricultural Research ◽

10.1071/ar02222 ◽

2003 ◽

Vol 54 (12) ◽

pp. 1187 ◽

Cited By ~ 7

Author(s):

G. A. Ablett ◽

A. Karakousis ◽

L. Banbury ◽

M. Cakir ◽

T. A. Holton ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Maps ◽

Sequence Repeat ◽

Consensus Map ◽

Allele Size ◽

Marker System ◽

Different Sources ◽

Simple Sequence ◽

Mapping Populations

Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers.

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Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.2.0204 ◽

2004 ◽

Vol 129 (2) ◽

pp. 204-210 ◽

Cited By ~ 37

Author(s):

Riaz Ahmad ◽

Dan Potter ◽

Stephen M. Southwick

Keyword(s):

Molecular Markers ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sweet Cherry ◽

Prunus Persica ◽

Sequence Repeat ◽

Srap Markers ◽

Upgma Cluster Analysis ◽

Commercially Important ◽

Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

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Simple sequence repeat DNA markers in alfalfa and perennial and annual Medicago species

Genome ◽

10.1139/g97-115 ◽

1997 ◽

Vol 40 (6) ◽

pp. 887-895 ◽

Cited By ~ 52

Author(s):

Noa Diwan ◽

Arvind A. Bhagwat ◽

Gary B. Bauchan ◽

Perry B. Cregan

Keyword(s):

Ssr Markers ◽

Dna Markers ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Mammalian Species ◽

Genetic Maps ◽

Sequence Repeat ◽

Annual Medicago ◽

Medicago Species ◽

Simple Sequence

Simple sequence repeat (SSR) or microsatellite DNA markers have been shown to function well in plant and mammalian species for genetic map construction and genotype identification. The objectives of the work reported here were to search GenBank for the presence of SSR-containing sequences from the genus Medicago, to assess the presence and frequency of SSR DNA in the alfalfa (Medicago sativa (L.) L. &L.) genome, and to examine the function of selected markers in a spectrum of perennial and annual Medicago species. The screening of an alfalfa genomic DNA library and sequencing of clones putatively containing SSRs indicated approximately 19 000 (AT)n + (CT)n + (CA)n + (ATT)n SSRs in the tetraploid genome. Inheritance was consistent with Mendelian expectations at four selected SSR loci with different core motifs. Additionally, genotypes of a range of Medicago species, including 10 perennial subspecies of the M. sativa complex and other perennial and annual Medicago species, were analyzed at each of the loci to ascertain the presence, number, and size of SSR alleles at each locus in each genotype. These studies indicate that SSR markers can function in alfalfa for the construction of genetic maps and will also be useful in a range of Medicago species for purposes of assessing genetic relatedness and taxonomic relationships, and for genotype identification.Key words: microsatellites, SSR markers, simple sequence repeats, alfalfa, annual medics.

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Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars

Australian Journal of Agricultural Research ◽

10.1071/ar04190 ◽

2005 ◽

Vol 56 (3) ◽

pp. 301 ◽

Cited By ~ 47

Author(s):

D. Rungis ◽

D. Llewellyn ◽

E. S. Dennis ◽

B. R. Lyon

Keyword(s):

Gossypium Hirsutum ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Maps ◽

Sequence Repeat ◽

Gossypium Hirsutum L ◽

Breeding Populations ◽

Length Polymorphisms ◽

Low Levels ◽

Simple Sequence

Since their discovery in the 1980s microsatellite or simple sequence repeat (SSR) markers have been widely used in many species to generate relatively dense genetic maps or framework maps on which to anchor more abundant, but anonymous, markers such as amplified fragment length polymorphisms (AFLPs). They are typically highly polymorphic, robust, and often portable, particularly among different mapping populations or crosses and often to related species. They have been useful in species where low levels of genetic diversity limit the use of other markers. Cultivated cotton (Gossypium hirsutum L.) has a history of genetic bottlenecks that have considerably reduced its diversity, with the consequence that most molecular marker genetic linkage studies are done with inter-specific crosses. In this study we evaluated the potential for SSR markers to be used in marker-assisted selection (MAS) breeding in cotton by quantifying the level of polymorphism detected with a set of commercially available SSR markers between and within a collection of cotton cultivars being used in our breeding programs. Although the majority of these markers are polymorphic between the 2 tetraploid species of cotton, G. barbadense and G. hirsutum, they are not highly polymorphic (~5%) either among or within G. hirsutum cultivars. However, 6 of the 8 cultivars studied were found to be segregating for alleles of these SSR markers. This suggests that where polymorphisms exist, heterozygosity within cultivars is maintained by the breeding strategies adopted by many modern cotton breeders. Although SSRs clearly have utility in genetic studies using inter-specific crosses or in the introgression of wild germplasm, they will be more difficult to use for standard cotton breeding until greater numbers are available. The utility of some markers may be reduced in some breeding populations where heterozygosity remains in the parental material.

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Strawberry GenBank-derived and Genomic Simple Sequence Repeat (SSR) Markers and Their Utility with Strawberry, Blackberry, and Red and Black Raspberry

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.1.102 ◽

2005 ◽

Vol 130 (1) ◽

pp. 102-115 ◽

Cited By ~ 68

Author(s):

K.S. Lewers ◽

S.M.N. Styan ◽

S.C. Hokanson ◽

N.V. Bassil

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Gene Sequence ◽

Genomic Library ◽

Black Raspberry ◽

Sequence Repeat ◽

Coding Regions ◽

Polymorphism Detection ◽

Mining Methods ◽

Simple Sequence

Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. ×ananassa Duschene ex Rozier `Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5′UTR (80% polymorphic) or 3′UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.

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Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽

10.3390/plants8110471 ◽

2019 ◽

Vol 8 (11) ◽

pp. 471

Author(s):

Jae-Ryoung Park ◽

Won-Tae Yang ◽

Yong-Sham Kwon ◽

Hyeon-Nam Kim ◽

Kyung-Min Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Group Method ◽

Sequence Repeat ◽

Rice Varieties ◽

Red Pericarp ◽

Simple Sequence ◽

Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database

BMC Research Notes ◽

10.1186/1756-0500-5-362 ◽

2012 ◽

Vol 5 (1) ◽

pp. 362 ◽

Cited By ~ 27

Author(s):

Yongli Zhao ◽

Channapatna S Prakash ◽

Guohao He

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Public Database ◽

Simple Sequence

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Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

Phytopathology ◽

10.1094/phyto-07-15-0155-r ◽

2016 ◽

Vol 106 (4) ◽

pp. 362-371 ◽

Cited By ~ 20

Author(s):

P. Cheng ◽

X. M. Chen ◽

D. R. See

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Simple Sequence Repeat ◽

Puccinia Striiformis ◽

The United States ◽

Grass Species ◽

Cereal Crops ◽

Sequence Repeat ◽

Grass Hosts ◽

Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

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