Journal articles: 'Simple Sequence Repeat (SSR)'

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SINGH, ALOK KUMAR, N. K. SINGH, V. K. SINGH, D. P. SINGH, and N. P. SINGH. "Tools for simple sequence repeat (SSR) markers." AGRICULTURE UPDATE 11, no. 2 (May 15, 2016): 163–72. http://dx.doi.org/10.15740/has/au/11.2/163-172.

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Krenz, J. D., R. D. Semlitsch, H. C. Gerhardt, and P. A. Mahoney. "Isolation and characterization of simple sequence repeat loci in the gray tree frog, Hyla chrysoscelis." Genome 42, no. 4 (August 1, 1999): 676–80. http://dx.doi.org/10.1139/g98-166.

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A gray tree frog (Hyla chrysoscelis) genomic library was constructed and characterized with regard to the incidence and complexity of simple sequence repeat (SSR) loci. The partial genomic library, containing approximately 10 000 clones with an average-sized insert of 350 bp, was screened with six SSR repeat oligonucleotides (AC, AG, ACG, AGC, AAC, and AAG). Screening identified 31 unique positive clones containing 41 SSR loci. Sequences of tandemly arrayed dinucleotide repeats were more common (36 of 41) than trinucleotide repeats. Twenty-six loci were identified using the AC dinucleotide probe, while 7 loci were identified using the AG dinucleotide probe. An additional 3 AT dinucleotide loci were serendipitously identified. The AT repeats generally comprised the longest dinucleotide repeat loci. The SSR repeat loci reported here should provide potent markers for identity, parentage, and short-lineage determinations in large-scale experiments using gray tree frogs.Key words: Hyla chrysoscelis, simple sequence repeat, SSR, gray tree frog, microsatellite.

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Kwon, Yong-Sham, Eun-Kyung Park, Kyung-Mi Bae, Seung-In Yi, Soon-Gi Park, and Il-Ho Cho. "Use of Simple Sequence Repeat (SSR) Markers for Variety Identification of Tomato (Lycopersicon esculentum)." Journal of Plant Biotechnology 33, no. 4 (December 30, 2006): 289–95. http://dx.doi.org/10.5010/jpb.2006.33.4.289.

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SAPTADI, DARMAWAN, R. R. SRI HARTATI, ASEP SETIAWAN, BAMBANG HELIYANTO, and SUDARSONO SUDARSONO. "PENGEMBANGAN MARKA SIMPLE SEQUENCE REPEAT UNTUK Jatropha spp." Jurnal Penelitian Tanaman Industri 17, no. 4 (June 19, 2020): 140. http://dx.doi.org/10.21082/jlittri.v17n4.2011.140-149.

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ABSTRAKPemuliaan tanaman jarak pagar (Jatropha curcas L.) untukmenghasilkan varietas berdaya hasil dan berkadar minyak tinggi perludilakukan. Penggunaan marka molekuler dapat membantu mempercepattercapainya tujuan pemuliaan tanaman jarak pagar. Marka simple sequencerepeat (SSR) merupakan marka ko-dominan yang efektif untuk mendu-kung program pemuliaan tanaman, tetapi penerapannya pada jarak pagarmasih terbatas. Penelitian yang dilakukan bertujuan untuk : (i) merancangprimer spesifik SSR menggunakan aksesi DNA jarak pagar yang tersediadi GenBank DNA database dan (ii) mengevaluasi efektivitas pasanganprimer yang dirancang untuk menghasilkan marka SSR yang polimorfikuntuk jarak pagar dan J. multifida. Dua puluh delapan pasang primerspesifik SSR telah berhasil dirancang menggunakan aksesi DNA asal jarakpagar yang ada di GenBank DNA database. DNA genomik jarak pagar danJ. multifida yang diisolasi dapat digunakan sebagai templat untukamplifikasi PCR. Dari 28 pasang primer yang dikembangkan, semuanyamampu menghasilkan marka SSR dari genom jarak pagar dan hanya 19pasang primer yang menghasilkan marka SSR dari genom J. multifida.Dari 19 pasangan primer spesifik SSR yang dievaluasi mampu dihasilkan44 alel dengan ukuran produk amplifikasi berkisar antara 100-360 bp.Sebanyak 35 alel (79,5%) yang diamati merupakan alel yang polimorfik.Marka SSR yang didapatkan tidak polimorfik intra-aksesi jarak pagar atauintra-aksesi J. multifida tetapi polimorfik untuk inter-aksesi kedua spesies.Karena marka SSR yang dihasilkan bersifat polimorfik untuk aksesi jarakpagar dengan aksesi J. multifida maka dapat digunakan sebagai markauntuk mendeteksi hasil persilangan F 1 inter-spesies J. curcas x J. multifida.Kata kunci : Jatropha curcas L., jarak pagar, J. multifida, DNA berulang,rancangan primerABSTRACTDevelopment of Simple Sequence Repeat Markers forJatropha spp.Breeding of physic nut (Jatropha curcas L.) to obtain new varietiesthat are high in yield and oil content needs to be conducted. Molecularmarker could be used to assist breeding of physic nut (J. curcas). Simplesequence repeat (SSR) marker is a co-dominant marker and theoretically itcould be used to support physic nut breeding program. However, onlylimited information has been available regarding molecular analysis ofphysic nut. The objectives of this research were: (i) to design SSR specificprimer based on DNA sequences available in the GenBank DNA databaseand (ii) to evaluate effectiveness of the primer pairs to produce polymor-phic SSR markers for J. curcas and J. multifida. Twenty eight primer pairswere designed and developed using physic nut DNA available in theGenBank DNA database. Total genomic DNA isolated from J. curcas andJ. multifida could be used as DNA templates for PCR amplification. Of the28 primer pairs developed in this research yielded SSR marker using J.curcas genomic DNA, while only 19 out of 28 pairs yielded SSR markersusing J. multifida genomic DNA. As many as 44 alleles with the size ofamplified products ranged from 100-360 bp were identified. Thirty fivealleles (79.5%) out of 44 identified ones were polymorphic. Results ofanalysis indicated that identified SSR markers generated using thedesigned primers were not polymorphic intra accession of J. curcas norintra-accession of J. multifida either. However, the generated SSR markerswere polymorphic for inter-accession of the two Jatropha species. Sincethe generated markers were only polymorphic for J. curcas and J.multifida, they could be used as markers for identifying interspecific F 1hybrids derived from crossing between J. curcas and J. multifida.Key words: Jatropha curcas L., physic nut, J. multifida, DNA repeatsequence, primer design

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van der Nest, M. A., E. T. Steenkamp, B. D. Wingfield, and M. J. Wingfield. "Development of simple sequence repeat (SSR) markers in Eucalyptus from amplified inter-simple sequence repeats (ISSR)." Plant Breeding 119, no. 5 (October 2000): 433–36. http://dx.doi.org/10.1046/j.1439-0523.2000.00515.x.

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Sipahi, Hülya, Ayşen Yumurtaci, and Zafer Mert. "Development of novel markers, using computationally extracted classi type EST-SSRs, in wheat leaf rust fungus Puccinia triticina." Genetika 47, no. 3 (2015): 917–26. http://dx.doi.org/10.2298/gensr1503917s.

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This study focused on the development of EST-simple sequence repeats markers and the detection of their transferability and their utility for evaluating wheat leaf rust pathogen diversity. A total of 44,407 publicly available EST sequences derived from Puccinia triticina were computationally mined. Di-nucleotide repeat density covered the vast majority of assembled ESTs (45%). The tri-repeat motif (TCT) and penta-repeat motif (TTCTT) were the most repeated motif. A set of 103 Class I type sequences containing simple sequence repeats were further analyzed by BLASTX similarity. Nineteen primer pairs flanking regions of EST-SSRs were designed. Of the 19 primer pairs tested, 10 successfully amplified fragments. Their polymorphism was evaluated with 8 Puccinia triticina (Pt) single-uredinal isolates collected from the different regions of Turkey. These newly developed EST-SSR primer pairs can be implicated as stable markers for pathogen diversity analysis. It was also shown that some leaf rust EST-SSR markers were capable of cross-amplification in P. graminis f. sp. tritici.

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Lewers*, Kim S., Eric T. Stafne, John R. Clark, Courtney A. Weber, and Julie Graham. "Simple Sequence Repeat (SSR) Markers for Raspberry and Blackberry." HortScience 39, no. 4 (July 2004): 785D—785. http://dx.doi.org/10.21273/hortsci.39.4.785d.

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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.

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Melis, Roberta, Paige Bradley, Tami Elsner, Margaret Robertson, Elisabeth Lawrence, Steve Gerken, Hans Albertsen, and Ray White. "Polymorphic SSR (Simple-Sequence-Repeat) Markers for Chromosome 20." Genomics 16, no. 1 (April 1993): 56–62. http://dx.doi.org/10.1006/geno.1993.1140.

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Robinson, A. J., C. G. Love, J. Batley, G. Barker, and D. Edwards. "Simple sequence repeat marker loci discovery using SSR primer." Bioinformatics 20, no. 9 (February 12, 2004): 1475–76. http://dx.doi.org/10.1093/bioinformatics/bth104.

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Bornet, B., C. Muller, F. Paulus, and M. Branchard. "Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L.)." Genome 45, no. 5 (October 1, 2002): 890–96. http://dx.doi.org/10.1139/g02-061.

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Inter simple sequence repeat (ISSR) sequences as molecular markers can lead to the detection of polymorphism and also be a new approach to the study of SSR distribution and frequency. In this study, ISSR amplification with nonanchored primer was performed in closely related cauliflower lines. Fourty-four different amplified fragments were sequenced. Sequences of PCR products are delimited by the expected motifs and number of repeats, which validates the ISSR nonanchored primer amplification technique. DNA and amino acids homology search between internal sequences and databases (i) show that the majority of the internal regions of ISSR had homologies with known sequences, mainly with genes coding for proteins implicated in DNA interaction or gene expression, which reflected the significance of amplified ISSR sequences and (ii) display long and numerous homologies with the Arabidopsis thaliana genome. ISSR amplifications revealed a high conservation of these sequences between Arabidopsis thaliana and Brassica oleracea var. botrytis. Thirty-four of the 44 ISSRs had one or several perfect or imperfect internal microsatellites. Such distribution indicates the presence in genomes of highly concentrated regions of SSR, or "SSR hot spots." Among the four nonanchored primers used in this study, trinucleotide repeats, and especially (CAA)5, were the most powerful primers for ISSR amplifications regarding the number of amplified bands, level of polymorphism, and their nature. Key words: inter simple sequence repeat (ISSR), nonanchored primer, DNA marker sequence, SSR, cluster of SSRs.

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Hou, Benjun, Suping Feng, and Yaoting Wu. "Systemic Identification ofHevea brasiliensisEST-SSR Markers and Primer Screening." Journal of Nucleic Acids 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/6590902.

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This research aimed to systematically identify and preliminarily validate theHevea brasiliensisexpressed sequence tag (EST) information using Simple Sequence Repeat (SSR) and provide evidence for further development of SSR molecular marker. The definition of general SSR features ofHeveaEST splicing sequences and development of SSR primers founded the basis of diversity analysis and variety identification forHeveatree resource. 1134 SSR loci were identified in the EST splicing sequence and distributed in 840 Unigene. The occurrence rate of SSR loci was 23.9%, and the average distribution distance of EST-SSR was 2.59 kb. The major repeat type was mononucleotide repeat motif, which accounted for 38.89%, while the corresponding value was 36.95% for dinucleotide repeat motif and 18.17% for trinucleotide repeat motif; the proportion of other motifs was only 5.99%. The superior repeat motifs for mononucleotide, dinucleotide, and trinucleotide were A/T, AG/CT, and AAG/CTT, respectively. 739 pair of primers were designed for 1134 SSR loci. PCR amplification was performed onHeveaReyan5-11, Reyan87-6-47, and PR107, and 180 pairs of primers were selected which were able to amplify polymorphism bands.

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van Zijll de Jong, Eline, Kathryn M. Guthridge, German C. Spangenberg, and John W. Forster. "Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes." Genome 46, no. 2 (April 1, 2003): 277–90. http://dx.doi.org/10.1139/g03-001.

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Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

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Gürcan, K., S. A. Mehlenbacher, and N. V. Bassil. "HIGHLY INFORMATIVE SIMPLE SEQUENCE REPEAT (SSR) MARKERS FOR FINGERPRINTING HAZELNUT." Acta Horticulturae, no. 845 (October 2009): 103–8. http://dx.doi.org/10.17660/actahortic.2009.845.10.

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Im, Chak Han, Kyung-Hee Kim, Hee Jeong Je, Asjad Ali, Min-Keun Kim, Wan-Kyu Joung, Sang Dae Lee, HyunYeol Shin, and Jae-San Ryu. "Multiplex Simple Sequence Repeat (SSR) Markers Discriminating Pleurotus eryngii Cultivar." Korean Journal of Mycology 42, no. 2 (June 30, 2014): 159–64. http://dx.doi.org/10.4489/kjm.2014.42.2.159.

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Dracatos, Peter M., Jeremy L. Dumsday, Rhiannon S. Olle, Noel O. I. Cogan, Mark P. Dobrowolski, Masahiro Fujimori, Hywel Roderick, Alan V. Stewart, Kevin F. Smith, and John W. Forster. "Development and characterization of EST-SSR markers for the crown rust pathogen of ryegrass (Puccinia coronata f.sp. lolii)." Genome 49, no. 6 (June 1, 2006): 572–83. http://dx.doi.org/10.1139/g06-006.

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The causative organism of crown rust in ryegrasses (Puccinia coronata f.sp. lolii) is an obligate biotroph that causes significant economic losses within the temperate grazing industries of dairy, meat, and wool production. This study reports on the development, transferability, and utility of gene-associated simple sequence repeat (SSR) molecular markers for crown rust. Analysis of 1100 expressed sequence tag (EST) sequences from a urediniospore-derived cDNA library detected 55 SSR loci. The majority of EST-SSR arrays contained perfect trinucleotide repeats with consistently low repeat numbers, and the motifs (ACC)n and (CAT)n were most commonly represented. DNA extraction from single pustules, in conjunction with multiple displacement amplification, provided the basis for PCR-based screening to evaluate genetic marker performance. An example of the identification of intraspecific genetic diversity was obtained from the analysis of 16 P. coronata isolates originating from the United Kingdom, Australia, New Zealand, and Japan. A subset of 12 robust EST-SSR markers was informative for determination of pathogen diversity within and between these localities. It was also demonstrated that crown rust EST-SSR markers were capable of cross-amplification in closely related fungal taxa (Puccinia spp.) and filamentous fungi within the Ascomycota.Key words: Puccinia coronata, simple sequence repeat, expressed sequence tags, urediniospore, genetic diversity, pathogen.

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Akkaya, M. S., A. A. Bhagwat, and P. B. Cregan. "Length polymorphisms of simple sequence repeat DNA in soybean." Genetics 132, no. 4 (December 1, 1992): 1131–39. http://dx.doi.org/10.1093/genetics/132.4.1131.

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Abstract The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.

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Taramino, Graziana, and Scott Tingey. "Simple sequence repeats for germplasm analysis and mapping in maize." Genome 39, no. 2 (April 1, 1996): 277–87. http://dx.doi.org/10.1139/g96-038.

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Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population. Key words : simple sequence repeats, microsatellites, maize, germplasm analysis, mapping.

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Kashia, Yechezkel, and David G. King. "Has Simple Sequence Repeat Mutability Been Selected to Facilitate Evolution?" Israel Journal of Ecology and Evolution 52, no. 3-4 (April 12, 2006): 331–42. http://dx.doi.org/10.1560/ijee_52_3-4_331.

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While adaptation and speciation begin with heritable variation, the underlying processes of mutation remain poorly understood. One particularly interesting source for prolific and adaptively meaningful variation is presented by the exceptionally high mutability of simple sequence repeats (SSRs: microsatellites and minisatellites). Frequent mutations at SSR sites alter the number of tandem repeats and create extensive polymorphism. Although most SSR variants are commonly presumed to be neutral, SSR variation has been shown to influence many biochemical, morphological, physiological, and behavioral characters, with at least a few examples offering evidence of response to selection. The type and degree of phenotypic variation depend upon each SSR's motif and on its location in exon, intron, or regulatory region, but the generation of abundant repeat-number variation is intrinsic to all of these repetitive sequences. Given the widespread distribution of SSRs within most genomes and their potential to modify almost any aspect of gene function, we believe that SSR mutability can facilitate evolutionary adaptation. Furthermore, we argue that the properties of SSRs allow natural selection to favor, indirectly, the mutability of these sites, in contrast to a conventional expectation that selection normally minimizes mutation rates by balancing the cost of deleterious mutations against the cost of replication fidelity. We believe that SSR mutability is not an "accident" of DNA replication, but has been adjusted and selected for this role. SSRs thus have a true biological function as general-purpose "tuning knobs" whereby mutations provide reversible adjustment for many quantitative and qualitative traits.

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Kumpatla, Siva P., and Snehasis Mukhopadhyay. "Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species." Genome 48, no. 6 (December 1, 2005): 985–98. http://dx.doi.org/10.1139/g05-060.

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Simple sequence repeat (SSR) markers are widely used in many plant and animal genomes due to their abundance, hypervariability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) in public databases permits rapid and economical discovery of SSRs. Most of such efforts to date focused on mining SSRs from monocotyledonous ESTs. In this study, we have computationally mined and examined the abundance of SSRs in more than 1.54 million ESTs belonging to 55 dico tyledonous species. The frequency of ESTs containing SSRs among species ranged from 2.65% to 16.82%. Dinucleotide repeats were found to be the most abundant followed by tri- or mono-nucleotide repeats. The motifs A/T, AG/GA/CT/TC, and AAG/AGA/GAA/CTT/TTC/TCT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. Most of the mononucleotide SSRs contained 15–25 repeats, whereas the majority of the di- and tri-nucleotide SSRs contained 5–10 repeats. The comprehensive SSR survey data presented here demonstrates the potential of in silico mining of ESTs for rapid development of SSR markers for genetic analysis and applications in dicotyledonous crops.Key words: simple sequence repeats, expressed sequence tags, SSRs, ESTs, bioinformatics, mining, survey, dicotyledonous species, markers.

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Pinto, Fernanda de Oliveira, Mirian Perez Maluf, and Oliveiro Guerreiro-Filho. "Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance." Pesquisa Agropecuária Brasileira 42, no. 3 (March 2007): 377–84. http://dx.doi.org/10.1590/s0100-204x2007000300011.

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The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

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Liu, Jianfeng, Bowen Yang, Yuetong Ming, Yuchu Zhang, and Yunqing Cheng. "Identification of Expressed Sequence Tag-simple Sequence Repeat Markers from the De Novo Transcriptome Sequence of Red Raspberry (Rubus idaeus L.)." HortScience 52, no. 4 (April 2017): 554–59. http://dx.doi.org/10.21273/hortsci11680-16.

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Rubus idaeus has remarkable economic and cultural value. Developing efficient simple sequence repeat (SSR) markers is necessary for the molecular breeding of red raspberry. In this study, SSR mining was performed using the de novo transcriptome sequence of R. idaeus. In total, 14,210 SSR sequences were identified from 11,158 SSR-containing unigenes. In all the SSR sequences, mononucleotide, dinucleotide, and trinucleotide repeats were the most common, and their number and percentage were 1323 (9.31%), 6752 (47.52%), and 4897 (34.46%), respectively. Of the mononucleotide and dinucleotide repeats, A/T, AG/CT, AT/AT, and AC/GT were more abundant and accounted for 9.09%, 37.82%, 6.51%, and 3.14% of the total repeat number, respectively. In the trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats, the nucleotide (NT) patterns AAG/CTT, AAAG/CTTT, AAAAG/CTTTT, and AAGAGG/CCTCTT were the most frequent, and accounted for 14.11%, 0.38%, 0.57%, and 0.23% of the total SSRs, respectively. Of the 480 SSR-containing unigenes with gene ontology (GO) annotation, the classification results showed that they were mainly involved in binding, catalytic, and transporter molecular functions. Most of the 3441 SSR-containing unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were involved in the following top five pathways: metabolic, RNA transport, spliceosome, protein processing in the endoplasmic reticulum, and mRNA surveillance. Thirty pairs of primers derived from the red raspberry transcriptome were randomly selected to assess their polymorphism by using 15 red raspberry germplasms, in which the polymorphism information content (PIC) values ranged from 0.50 to 0.86, with a mean of 0.73, thereby indicating a high level of polymorphism. The unweighted pair group method with arithmetic mean clustering results indicated that the thirty pairs of primers could precisely distinguish the germplasms. This study reveals the SSR distribution characteristics of red raspberry and provides a scientific basis for further genetic diversity studies and genetic linkage map construction for this species.

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Burgess, Treena, Michael J. Wingfield, and Brenda W. Wingfield. "Simple Sequence Repeat Markers Distinguish among Morphotypes of Sphaeropsis sapinea." Applied and Environmental Microbiology 67, no. 1 (January 1, 2001): 354–62. http://dx.doi.org/10.1128/aem.67.1.354-362.2001.

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ABSTRACT Sphaeropsis sapinea is a fungal endophyte ofPinus spp. that can cause disease following predisposition of trees by biotic or abiotic stresses. Four morphotypes of S. sapinea have been described from within the natural range of the fungus, while only one morphotype has been identified on exotic pines in the Southern Hemisphere. The aim of this study was to develop robust polymorphic markers that could be used in both taxonomic and population studies. Inter-short-sequence-repeat primers containing microsatellite sequences and degenerate anchors at the 5′ end were used to target microsatellite-rich areas in an S. sapinea isolate. PCR amplification using an annealing temperature of 49°C resulted in profiles containing 5 to 10 bands. These bands were cloned and sequenced, and new short-sequence-repeat (SSR) primer pairs were designed that flanked microsatellite-rich regions. Eleven polymorphic SSR markers were tested on 40 isolates of S. sapinearepresenting different morphotypes as well as on 2 isolates of the closely related species Botryosphaeria obtusa. The putative I morphotype was found to be identical to B. obtusa. Otherwise, the markers clearly distinguished the remaining three morphotypes and, furthermore, showed that the C morphotype was more closely related to the A than the B morphotype. The B morphotype was the most genetically diverse, and the isolates could be further divided based on their geographic origins. Sequencing of different alleles from each locus showed that the most polymorphic markers had mutations within a microsatellite sequence.

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Ramsay, L., M. Macaulay, S. degli Ivanissevich, K. MacLean, L. Cardle, J. Fuller, K. J. Edwards, et al. "A Simple Sequence Repeat-Based Linkage Map of Barley." Genetics 156, no. 4 (December 1, 2000): 1997–2005. http://dx.doi.org/10.1093/genetics/156.4.1997.

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AbstractA total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F1 of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

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Nicot, N., V. Chiquet, B. Gandon, L. Amilhat, F. Legeai, P. Leroy, M. Bernard, and P. Sourdille. "Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)." Theoretical and Applied Genetics 109, no. 4 (May 14, 2004): 800–805. http://dx.doi.org/10.1007/s00122-004-1685-x.

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Subramanian, Subbaya, Vamsi M. Madgula, Ranjan George, Satish Kumar, Madhusudhan W. Pandit, and Lalji Singh. "SSRD: Simple Sequence Repeats Database of the Human Genome." Comparative and Functional Genomics 4, no. 3 (2003): 342–45. http://dx.doi.org/10.1002/cfg.289.

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Simple sequence repeats are predominantly found in most organisms. They play a major role in studies of genetic diversity, and are useful as diagnostic markers for many diseases. The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance. The data includes the abundance and distribution of SSRs in the coding and non-coding regions of the genome, as well as their association with the UTRs of genes. The exact locations of repeats with respect to genomic regions (such as UTRs, exons, introns or intergenic regions) and their association with STS markers are also highlighted. The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats. SSRD is available through two websites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr.

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Wadl, Phillip A., Xinwang Wang, John K. Moulton, Stan C. Hokanson, John A. Skinner, Timothy A. Rinehart, Sandra M. Reed, Vincent R. Pantalone, and Robert N. Trigiano. "Transfer of Cornus florida and C. kousa Simple Sequence Repeats to Selected Cornus (Cornaceae) Species." Journal of the American Society for Horticultural Science 135, no. 3 (May 2010): 279–88. http://dx.doi.org/10.21273/jashs.135.3.279.

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Cross-species transferability of simple sequence repeats (SSRs) is common and allows SSRs isolated from one species to be applied to closely related species, increasing the use of previously isolated SSRs. The genus Cornus consists of 58 species that are ecologically and economically important. SSRs have previously been isolated from C. florida and C. kousa. In this study, 36 SSRs were tested on taxa from 18 Cornus species and hybrids for cross-species transferability and genetic diversity was calculated for each locus using polymorphism information content (PIC). Cross-species transferability of SSR loci was higher in more closely related species and PIC values were high. Evidence was found for conserved primer sites as determined by the amplification of SSR loci in the taxa examined. Polymerase chain reaction products were cloned and sequenced for three SSR loci (CF48, CF59, and CF124) and all individuals sequenced contained the appropriate repeat. Phylogenetic relationships of 14 Cornus species were inferred using nucleotide sequences of SSR locus CF48. The most parsimonious tree resulting from this analysis was in concordance with phylogenies based on matK and internal transcribed spacer sequences. The SSR loci tested in this study will be useful in future breeding, population, and genetic studies within Cornus.

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Diwan, Noa, Arvind A. Bhagwat, Gary B. Bauchan, and Perry B. Cregan. "Simple sequence repeat DNA markers in alfalfa and perennial and annual Medicago species." Genome 40, no. 6 (December 1, 1997): 887–95. http://dx.doi.org/10.1139/g97-115.

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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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Ramzan, Musarrat, Sadia Sarwar, Naheed Kauser, Rabia Saba, Iqtidar Hussain, Anis Ali Shah, Muhammad Naveed Aslam, Jawaher Alkahtani, and Mona S. Alwahibi. "Assessment of Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers to reveal genetic diversity among Tamarix ecotypes." Journal of King Saud University - Science 32, no. 8 (December 2020): 3437–46. http://dx.doi.org/10.1016/j.jksus.2020.10.003.

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Dong, Li, Yuhan Sun, Keqi Zhao, Jing Zhang, Yuwei Zhang, Xiuyu Li, Shouhua Xun, Jiangtao Zhang, Shaoming Wang, and Yun Li. "Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China." Forests 10, no. 8 (July 30, 2019): 644. http://dx.doi.org/10.3390/f10080644.

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Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

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Saal, B., and Günter Wricke. "Development of simple sequence repeat markers in rye (Secale cereale L.)." Genome 42, no. 5 (October 1, 1999): 964–72. http://dx.doi.org/10.1139/g99-052.

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Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.

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Burgess, T. I., M. J. Wingfield, and B. D. Wingfield. "Global distribution ofDiplodia pineagenotypes revealed using simple sequence repeat (SSR) markers." Australasian Plant Pathology 33, no. 4 (2004): 513. http://dx.doi.org/10.1071/ap04067.

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Martínez-Gómez, P., R. Sánchez-Pérez, T. Paredes, and F. Dicenta. "VARIETAL TRACEABILITY IN ALMOND PRODUCTS BY SSR (SIMPLE SEQUENCE REPEAT) MARKERS." Acta Horticulturae, no. 1028 (March 2014): 255–58. http://dx.doi.org/10.17660/actahortic.2014.1028.41.

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El-Rawy, M., A. Taghian, H. El-Aref, B. Abd El-fatah, and S. El-Sanousy. "GENETIC DIVERSITY IN WHEAT GENOTYPES USING SIMPLE SEQUENCE REPEAT (SSR) MARKERS." Research Journal of Applied Biotechnology 2, no. 1 (June 1, 2016): 127–38. http://dx.doi.org/10.21608/rjab.2016.59913.

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Chen, Chunxian, Jude W. Grosser, Milica Ćalović, Patricia Serrano, Gemma Pasquali, Julie Gmitter, and Fred G. Gmitter. "Verification of Mandarin and Pummelo Somatic Hybrids by Expressed Sequence Tag–Simple Sequence Repeat Marker Analysis." Journal of the American Society for Horticultural Science 133, no. 6 (November 2008): 794–800. http://dx.doi.org/10.21273/jashs.133.6.794.

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Somatic hybridization is a powerful tool for the genetic improvement of citrus rootstocks, and it is part of an efficient in vitro-based breeding system described here. An essential component of the system is the requirement of confirming tetraploidy and the combination of the two donor genomes. Expressed sequence tag–simple sequence repeat (EST-SSR) markers provide a means to accomplish both of these objectives, and their application to a population of pummelo [Citrus grandis (L.) Osbeck] + mandarin (C. reticulata Blanco) somatic hybrids developed for the specific purpose of providing alternative rootstocks for sour orange (Citrus aurantium L.) is detailed. Nineteen new somatic hybrids were produced from various mandarin and pummelo parents, and their ploidy level and the complementation of their nuclear genomes were confirmed using four EST-SSR markers. These markers were selected from markers previously mapped in sweet orange [C. sinensis (L.) Osbeck] and trifoliate orange [Poncirus trifoliata (L.) Raf.] and prescreened for suitable allelic polymorphism within the mandarin and pummelo lines used. After polymerase chain reaction amplification of sequences from the parents and putative hybrids, the products were separated on a genetic sequencer and visualized electronically. Additionally, EST-SSR markers identified the unexpected zygotic origin of a presumed nucellar embryogenic callus line. Integration of EST-SSR techniques for high-throughput genotyping with previously developed approaches to somatic hybrid creation increases substantially the effectiveness and efficiency of this in vitro-based breeding system for citrus rootstock improvement.

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Sutoro, Sutoro, Puji Lestari, Andari Risliawati, Kristianto Nugroho, and R. Neni Iriany. "Evaluasi Keragaman Genetik Jagung Inbrida Berdasarkan Sepuluh Marka Simple Sequence Repeat." Jurnal AgroBiogen 13, no. 2 (March 7, 2018): 83. http://dx.doi.org/10.21082/jbio.v13n2.2017.p83-90.

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Keragaman genetik jagung inbrida diperlukan untuk mendapatkan jagung hibrida yang berpotensi hasil tinggi. Keragaman inbrida dapat dievaluasi melalui analisis molekuler dengan marka simple sequence repeat (SSR). Tujuan enelitian ini adalah mengevaluasi keragaman genetik jagung inbrida yang berlatar belakang genetik berbeda dengan marka SSR dan mengelompokkannya sebagai panduan untuk pembentukan jagung hibrida. Sebanyak sepuluh marka SSR digunakan untuk mengelompokkan 32 jagung inbrida yang memiliki latar belakang genetik yang berbeda. Analisis dilakukan di Laboratorium Biologi Molekuler, Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, pada bulan Maret 2017. Data polimorfisme SSR pada jagung inbrida dianalisis secara statistik dan filogeninya menggunakan perangkat lunak NTSYS. Hasil analisis keragaman genetik menunjukkan adanya perbedaan antarinbrida, termasuk inbrida yang dihasilkan dari satu populasi jagung bersari bebas. Total sepuluh marka SSR mampu membedakan alel homozigot dan heterozigot jagung inbrida. Dari hasil pengelompokan jagung inbrida pada tingkat kesamaan 68% diperoleh dua klaster. Klaster pertama terdiri atas 30 inbrida, sedangkan klaster kedua hanya terdiri atas inbrida Al-46 dan 22-9-5-4-17-5. Pasangan inbrida dengan jarak genetik terjauh adalah inbrida 22-9-5-4-17-5 dan 23-4-9-7-2-9, dan inbrida CML161/Nei 9008 dan 22-9-5-4-17-5. Inbrida tersebut potensial untuk dijadikan sebagai tetua dalam menghasilkan hibrida karena jarak genetiknya yang relatif jauh.

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da Maia, Luciano Carlos, Dario Abel Palmieri, Velci Queiroz de Souza, Mauricio Marini Kopp, Fernando Irajá Félix de Carvalho, and Antonio Costa de Oliveira. "SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation." International Journal of Plant Genomics 2008 (July 27, 2008): 1–9. http://dx.doi.org/10.1155/2008/412696.

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Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.

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Jarret, R. L., L. C. Merrick, T. Holms, J. Evans, and M. K. Aradhya. "Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai)." Genome 40, no. 4 (August 1, 1997): 433–41. http://dx.doi.org/10.1139/g97-058.

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Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.Key words: Citrullus, watermelon, simple sequence repeats, genetic diversity.

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Mott, I. W., S. R. Larson, and B. S. Bushman. "Simple sequence repeat (SSR) markers for Elymus, Pseudoroegneria and Pascopyrum species (Triticeae: Gramineae)." Plant Genetic Resources 9, no. 4 (May 17, 2011): 489–94. http://dx.doi.org/10.1017/s1479262111000694.

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The Triticeae tribe (Poaceae) includes several important cereal crops, cultivated forages, annual and perennial grass weeds and ecologically diverse native North American grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 polyploid perennial grass species occurring worldwide. The genomic constitutions of approximately 40% of the Elymus species are unknown. Molecular markers are needed to facilitate genetic analysis of diversity and functional traits in these species. We have developed simple sequence repeat (SSR) markers for use in Elymus based on Elymus expressed sequence tag sequences. To test the polymorphic content and transferability of these SSRs, 100 SSR primer pairs were tested on 84 plants representing seven North American Elymus, Pseudoroegneria and Pascopyrum species. The number of bands produced from each of the SSRs ranged from 1 to 11 with an average of 4.3 bands/SSR. A subset of the 23 most polymorphic SSRs produced 142 bands, an average of 6.2 bands/SSR. Binary data from the 100 SSRs successfully separated all individuals into their respective accessions in a neighbour-joining phylogram with a 100% confidence interval. Analysis of molecular variance showed that 29.9% of the total variation was within and 70.1% was among the accessions. These SSRs will be a useful tool for investigating genetic diversity, genome constitutions and molecular mapping in Elymus and other Triticeae grasses.

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Chen, Song Bo, Xin Lu Xie, Gong Li, and Hai Jin Liu. "Data Mining for Simple Sequence Repeats in Expressed Sequence Tags from Japanese Flounder (Paralichthys olivaceus)." Advanced Materials Research 765-767 (September 2013): 274–77. http://dx.doi.org/10.4028/www.scientific.net/amr.765-767.274.

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Based on ESTs of Japanese flounder (Paralichthys olivaceus) in the public database, EST-SSR makers were developed after mining and evaluating SSRs in them by bioinformatics methods. 5 927 non-redundant ESTs of Japanese flounder were screened and 390 SSRs were mined out. The frequency of these EST-SSRs was 7.95% and the average distance of distribution was 7.9 kb in non-redundant ESTs. The dinucleotide repest motif was dominant type (59.02%) with repeat motif AC being the most common (16.91%). The distribution of trinucleotide, tetranucleotide and hexanucleotide repeats were dispersive. 30 primer pairs for EST-SSRs were designed, 27 primer pairs showed the amplification, and 17 primer pairs showed polymorphisms, the rates of polymorphic EST-SSRs were 62.96% with the alleles per locus ranging from 2 to 6 (mean 3.5). The observed (HO) and expected (HE) heterozygosities of these EST-SSRs were 0.280.92 and 0.31550.8033, respectively. Two EST-SSR loci significantly deviated from the HardyWeinberg equilibrium (HWE) expectation, and theremaining 15 loci were in HWE. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of Japanese flounder.

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Khasa, P. D., C. H. Newton, M. H. Rahman, B. Jaquish, and B. P. Dancik. "Isolation, characterizaton, and inheritance of microsatellite loci in alpine larch and western larch." Genome 43, no. 3 (June 1, 2000): 439–48. http://dx.doi.org/10.1139/g99-131.

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Microsatellite loci or simple sequence repeat loci (SSRs) were isolated in alpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.). In total, 14 SSR loci were characterized; two [(TCT)4, A7] came from published Larix DNA sequence data, one (CA)17 was obtained from a partial non-enriched alpine larch total genomic DNA library, and the remaining 11 loci were obtained from larch genomic DNAs enriched for (CA)n repeats. The SSR regions in these clones could be divided into three categories: perfect repeat sequences without interruption, imperfect repeat sequences with interruption(s), and compound repeat sequences with adjacent tandem simple dinucleotides. Eight of the 14 loci analyzed were found to be polymorphic and useful markers after silver-staining polyacrylamide gel electrophoresis. In addition, several SSR primers developed for alpine larch were able to successfully amplify polymorphic loci in its related species, western larch, and among other closely related taxa within the Larix genus. The inheritance of microsatellite loci was verified by analysis of haploid megagametophyte and diploid embryo tissues of progeny obtained from controlled crosses between western larch and alpine larch. All microsatellite loci analyzed had alleles that segregated according to expected Mendelian frequencies. Two species-specific markers (UAKLly10a and UAKLla1) allow easy and rapid identification of specific genetic entry of alpine larch and western larch at any stage in the sporophyte phase of the life cycle. Therefore, these markers are efficient in identifying the parental species and to validate controlled crosses between these two closely related species. These results are important in tree improvement programs of alpine larch and western larch aimed at producing genetically improved hybrid stock for reforestation in Western Canada and U.S.A.Key words: database search, enriched library, inheritance, Larix, microsatellites, simple sequence repeats, PCR.

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Wang, Xiaoli, Zhiyong Wang, Li Liao, Xinyi Zhang, and Changjun Bai. "Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers." HortScience 50, no. 6 (June 2015): 797–800. http://dx.doi.org/10.21273/hortsci.50.6.797.

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Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

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Gil, Jinsu, Yurry Um, Jae Kyung Byun, Jong Wook Chung, Yi Lee, and Chan Moon Chung. "Genetic Diversity Analysis of Wood-cultivated Ginseng using Simple Sequence Repeat Markers." Korean Journal of Medicinal Crop Science 25, no. 6 (December 31, 2017): 389–96. http://dx.doi.org/10.7783/kjmcs.2017.25.6.389.

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Yu, Ju-Kyung, Trevor M. Dake, Sukhwinder Singh, David Benscher, Wanlong Li, Bikram Gill, and Mark E. Sorrells. "Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat." Genome 47, no. 5 (October 1, 2004): 805–18. http://dx.doi.org/10.1139/g04-057.

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Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260 000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.Key words: wheat, EST, SSR mapping.

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Fu, Yong-Bi, and Gregory W. Peterson. "Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species." Botany 88, no. 5 (May 2010): 537–43. http://dx.doi.org/10.1139/b10-019.

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One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

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Stafne, Eric T., John R. Clark, Courtney A. Weber, Julie Graham, and Kim S. Lewers. "Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry." Journal of the American Society for Horticultural Science 130, no. 5 (September 2005): 722–28. http://dx.doi.org/10.21273/jashs.130.5.722.

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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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Zhu, Lei, Huayu Zhu, Yanman Li, Yong Wang, Xiangbin Wu, Jintao Li, Zhenli Zhang, et al. "Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species." Horticulturae 7, no. 6 (June 8, 2021): 143. http://dx.doi.org/10.3390/horticulturae7060143.

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Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

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Feng, Suping, Helin Tong, You Chen, Jingyi Wang, Yeyuan Chen, Guangming Sun, Junhu He, and Yaoting Wu. "Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis." BioMed Research International 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/317912.

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Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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Lee, Eun-Jung, Gyoungju Nah, Min-Jung Yook, Soo-Hyun Lim, Tae-Sun Park, DoKyoung Lee, and Do-Soon Kim. "Phylogenetic Relationship ofEchinochloaSpecies Based on Simple Sequence Repeat and Phenotypic Marker Analyses." Weed Science 64, no. 3 (September 2016): 441–54. http://dx.doi.org/10.1614/ws-d-15-00187.1.

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Echinochloaspecies are among the most troublesome weeds in rice cultivation, and grow in a broad habitat range in Korea. Although various ecotypes ofEchinochloahave been collected as germplasm for future studies, it has been difficult to classify them due to their high level of morphological similarity. This study was thus conducted to develop and investigate the phylogenetic relationships between 77Echinochloaaccessions with the use of 23 simple sequence repeat (SSR) markers and 24 morphological traits. Of 77Echinochloaaccessions, including 57 accessions from Korea and 5 reference species, late watergrass was clearly clustered as a distinctive group from barnyardgrass and otherEchinochloaspecies. In this analysis, we also identified core genetic and morphological markers that can be used for the future identification and classification ofEchinochloaspecies. Five out of 23 SSR makers produced distinctive bands that discriminate late watergrass from barnyardgrass and otherEchinochloaspecies. Four morphological traits of the reproductive organs were the most influential contributors for classifyingEchinochloaspecies. Although there was no clear consensus generated in this study between SSR markers and morphological trait analyses, our results support the potential use of the selected SSR markers and morphological traits in future studies ofEchinochloa.

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Yu, Ju-Kyung, Jodie Mangor, Lucy Thompson, Keith J. Edwards, Mary B. Slabaugh, and Steven J. Knapp. "Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower." Genome 45, no. 4 (August 1, 2002): 652–60. http://dx.doi.org/10.1139/g02-025.

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Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.Key words: microsatellites, Helianthus, Compositae, DNA polymorphisms.

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Shen, Qing, Hua Bian, Hai-yan Wei, Li Liao, Zhi-yong Wang, Xiao-yan Luo, Xi-peng Ding, Zhenbang Chen, and Paul Raymer. "Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers." Journal of the American Society for Horticultural Science 145, no. 4 (July 2020): 228–35. http://dx.doi.org/10.21273/jashs04860-19.

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Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

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Journal articles on the topic 'Simple Sequence Repeat (SSR)'

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