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

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.5.722 ◽

2005 ◽

Vol 130 (5) ◽

pp. 722-728 ◽

Cited By ~ 26

Author(s):

Eric T. Stafne ◽

John R. Clark ◽

Courtney A. Weber ◽

Julie Graham ◽

Kim S. Lewers

Keyword(s):

Molecular Markers ◽

Genetic Mapping ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Maps ◽

Black Raspberry ◽

Sequence Repeat ◽

Red Raspberry ◽

Simple Sequence ◽

Mapping Populations

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 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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Classification of Kentucky Bluegrass (Poa pratensis L.) Cultivars and Accessions Based on Microsatellite (Simple Sequence Repeat) Markers

HortScience ◽

10.21273/hortsci.47.9.1356 ◽

2012 ◽

Vol 47 (9) ◽

pp. 1356-1366 ◽

Cited By ~ 14

Author(s):

Josh A. Honig ◽

Vincenzo Averello ◽

Stacy A. Bonos ◽

William A. Meyer

Keyword(s):

Ssr Markers ◽

Classification System ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Poa Pratensis ◽

Morphological Characteristics ◽

Kentucky Bluegrass ◽

Sequence Repeat ◽

Wide Range ◽

Simple Sequence

Kentucky bluegrass (Poa pratensis L.) is an important facultative apomictic temperate perennial grass species used for both forage and cultivated turf. Through apomixis, this species is able to propagate diverse and odd ploidy levels, resulting in many genetically distinct phenotypes. A wide range of diverse cultivars and accessions of kentucky bluegrass have been previously characterized based on pedigree, common turf performance, and morphological characteristics to create a kentucky bluegrass cultivar classification system. The objectives of the current study were to assess the amount of genetic divergence among kentucky bluegrass cultivars, experimental selections, and plant collections and revise/update the original pedigree, turf performance, and morphological characteristics kentucky bluegrass classification system using recently described kentucky bluegrass microsatellite [simple sequence repeat (SSR)] markers. In this study, 247 kentucky bluegrass cultivars, experimental selections, and collections were genotyped using 25 SSR markers. SSR markers showed a strong correlation between genetic relatedness as assessed by molecular markers and the original kentucky bluegrass classification system and also provided justification for a revision/update of the classification system. Traditional classification types that were supported by the current SSR analysis include BVMG, Compact, Compact-America, Julia, Mid-Atlantic, Midnight, and Shamrock types. Newly proposed classification types included Cynthia, Jefferson/Washington, Limousine, P-105, Sydsport, and three Eurasian types. The majority of cultivars, experimental selections, and collections were uniquely identified with the current set of SSR markers. Genetic relationships of individuals as assessed by SSR markers closely matched known pedigrees. The current set of SSR markers can be used to rapidly genotype and assign new cultivars/accessions to kentucky bluegrass classification types and assess genetic relatedness among individuals and should be considered for use in a kentucky bluegrass plant variety protection program.

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Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation

Plant Genetic Resources ◽

10.1079/pgr200461 ◽

2005 ◽

Vol 3 (1) ◽

pp. 45-57 ◽

Cited By ~ 52

Author(s):

M.L. Wang ◽

N.A. Barkley ◽

J.-K. Yu ◽

R.E. Dean ◽

M.L. Newman ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Transfer Rate ◽

Genetic Relatedness ◽

Expressed Sequence Tag ◽

Cynodon Dactylon ◽

Grass Species ◽

Cereal Crops ◽

Sequence Repeat ◽

Simple Sequence

A major challenge for the molecular characterization and evaluation of minor grass species germplasm is the lack of sufficient DNA markers. A set of 210 simple sequence repeat (SSR) markers developed from major cereal crops (self-pollinated wheat and rice, mainly self-pollinated sorghum and out-crossing maize) were evaluated for their transferability to minor grass species (finger millet, Eleusine coracana; seashore paspalum, Paspalum vaginatum; and bermudagrass, Cynodon dactylon). In total, 412 cross-species polymorphic amplicons were identified. Over half of the primers generated reproducible cross-species or cross-genus amplicons. The transfer rate of SSR markers was correlated with the phylogenetic relationship (or genetic relatedness) of these species. The average transfer rate of genomic SSR markers was different from the average transfer rate of expressed sequence tag (EST)-SSR markers. The level of polymorphism was significantly higher among species (67%) than within species (34%), and was related to the degree of out-crossing for each species. The level of polymorphism detected within species was 57% from self-incompatible species, 39% from out-crossing species and 20% from self-pollinated species. Genomic SSRs detected a higher level of polymorphism than EST-SSRs. The use of transferred polymorphic SSR markers for the characterization and evaluation of germplasm is discussed.

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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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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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