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Perry B. Cregan - One of the best experts on this subject based on the ideXlab platform.
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automated sizing of fluorescent labeled Simple Sequence Repeat ssr markers to assay genetic variation in soybean
Theoretical and Applied Genetics, 1997Co-Authors: N Diwan, Perry B. CreganAbstract:Simple Sequence Repeat (SSR) allele sizing provides a useful tool for genotype identification, pedigree analysis, and for estimating genetic distance between organisms. Soybean [Glycine max (L.) Merr.] cultivars are identified for Plant Variety Protection (PVP) purposes by standard pigmentation and morphological traits. However, many commercial soybeans arise from a limited number of elite lines and are often indistinguishable based on these traits. A system based on SSR markers would provide unique DNA profiles of cultivars. Fluorescent labeling of alleles combined with automated sizing with internal size standards in each gel lane was used as an alternative to standard [32P] labeling to assess genetic variability in soybean. Allelic frequencies at 20 SSR loci were determined in 35 soybean genotypes that account for greater than 95% of the alleles in North American soybean cultivars based upon pedigree analysis. An average of 10.1 alleles per locus (range: 5–17), with a mean gene diversity of 0.80 (range: 0.50 to 0.87) were observed at the 20 SSR loci. The 20 loci successfully distinguished modern soybean cultivars that are identical for morphological and pigmentation traits, as well as 7 soybean genotypes reported to be indistinguishable using 17 RFLP probes. Pedigrees of 7 cultivars were studied to estimate stability of SSRs in soybean across generations. Of the 7 pedigrees 6 had one locus in the progeny with an allele(s) that was not present in either parent. These new alleles are most likely the result of mutation. The mutation rate of SSR alleles in soybean was similar to that reported in humans. To avoid difficulty associated with mutation, DNA fingerprint data should be determined from the bulk of 30-50 plants of a cultivar.
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integration of Simple Sequence Repeat dna markers into a soybean linkage map
Crop Science, 1995Co-Authors: Mahinur S. Akkaya, Arvind A. Bhagwat, Randy C Shoemaker, James E Specht, Perry B. CreganAbstract:A total of 40 Simple Sequence Repeat (SSR) or microsatellite DNA markers were mapped in a soybean [Glycine max (L.) Merrill] mapping population that consisted of 60 F 2 plants from a cross between near isogenic lines of the cultivars Clark and Harosoy. The first objective of study was to determine the map location of SSR loci in relation to 13 classical loci controlling pigmentation and morphological traits, seven isozyme loci, and a total of 118 RFLP and RAPD markers. The second objective was to determine if the microsatellite loci were randomly distributed in the soybean genome. Linkage analysis with MAPMAKER 3.0b yielded 29 linkage groups with a total map length of 1486 centimorgans (cM). This compares with a map length of 1056 cM if the SSR markers were removed from the data set. Thirty-four of the microsatellite loci were placed in linkage groups. SSR loci were linked to loci controlling nine of the 13 classical traits, and two of seven isozyme loci. Eighteen of the 29 linkage groups contained at least one SSR locus. While this result suggested that the microsatellite loci were randomly distributed throughout the soybean genome, two clusters of five and four SSR loci, spanning 23.4 and 33.6 cM, respectively, were detected. These results indicated a relatively limited amount of clustering of soybean SSR loci, and demonstrated that microsatellite genetic markers should provide an excellent complement to RFLP and RAPD markers for use in soybean molecular biology, genetics, and breeding research. Because SSR markers detect only single genetic loci and are highly polymorphic, they can be extremely informative in pedigree tracing studies, in the analysis of progeny from multiparent matings, in a wide range of mapping applications, and in genotype identification.
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Methodology of generation and characteristics of Simple Sequence Repeat DNA markers in avocado (Persea americana M.)
Euphytica, 1994Co-Authors: Uri Lavi, Mahinur S. Akkaya, Arvind A. Bhagwat, E. Lahav, Perry B. CreganAbstract:Generation of Simple Sequence Repeat (SSR) DNA markers was based on the construction of genomic DNA library of avocado (Persea americana M.). The library was screened with the four dinucleotide probes (AG), (AT), (GC) and (CA). Positive clones were Sequenced to validate the presence of Simple Sequence Repeats (SSR) and to generate polymerase chain reaction (PCR) primers based on the Sequences flanking the Simple Sequence Repeat. Twenty six different pairs of primers which yield a PCR product in the initial screening were synthesized. The SSR A1E11 was found to have eleven alleles while A3F8 has eight alleles. The SSRs in avocado were found to be inherited in a Mendelian fashion.
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length polymorphisms of Simple Sequence Repeat dna in soybean
Genetics, 1992Co-Authors: Mahinur S. Akkaya, Arvind A. Bhagwat, Perry B. CreganAbstract: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.
Prabhakar K. Ranjekar - One of the best experts on this subject based on the ideXlab platform.
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identification of inter Simple Sequence Repeat issr markers associated with seed size in wheat
Theoretical and Applied Genetics, 2001Co-Authors: Jetty S S Ammiraju, Vidya S. Gupta, Bhushan B Dholakia, Dipak K Santra, Harpreet Singh, M D Lagu, S A Tamhankar, H S Dhaliwal, V S Rao, Prabhakar K. RanjekarAbstract:The feasibility of identifying inter-Simple Sequence Repeat markers associated with seed weight in hexaploid wheat was tested using 113 recombinant inbred lines developed by the single-seed descent method, from a cross between Rye selection111, an Indian genetic stock obtained through the introgression of genes for bold seed size from rye, and Chinese Spring having small seed size. Three markers were associated with low seed size with gene effects of 14.8%, 9.5%, and 6%, while four markers with contributions of 8%, 4.66%, 2.92% and 2.61% were found to be linked to high seed size, together contributing 31% of the phenotypic variance in seed size. Nulli-tetrasomic and di-telosomic analysis revealed the presence of three low seed size QTL-associated markers on three chromosomes, 6BL, 2DL, and 1DS respectively. This study clearly demonstrates that ISSRs are highly useful for finding markers associated with major and minor genes controlling agronomically important traits in wheat.
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Genetic diversity and phylogenetic relationship as revealed by inter Simple Sequence Repeat (ISSR) polymorphism in the genus Oryza
Theoretical and Applied Genetics, 2000Co-Authors: S P Joshi, Ramesh K. Aggarwal, Prabhakar K. Ranjekar, Vidya S. Gupta, Darshan S. BrarAbstract:Inter Simple Sequence Repeat (ISSR) polymorphism was used to determine genetic diversity and phylogenetic relationships in Oryza. Forty two genotypes including 17 wild species, representing AA,BB,CC,EE,FF,GG,BBCC,CCDD, and HHJJgenomes, two cultivated species, Oryza sativa (AA) and Oryza glaberrima (AA), and three related genera, Porteresia coarctata, Leersia and Rhynchoryza subulata, were used in ISSR analysis. A total of 30 ISSR primers were screened representing di-, tri-, tetra- and penta-nucleotide Repeats, of which 11 polymorphic and informative patterns were selected to determine the genetic diversity. The consensus tree constructed using binary data from banding patterns generated by ISSR-PCR clustered 42 genotypes according to their respective genomes. ISSR analysis suggests that the genus Oryza may have evolved following a polyphyletic pathway; Oryza brachyantha (FF genome) is the most divergent species in Oryza and Oryza australiensis (EE genome) does not fall under the Officinalis complex. DNA profiles based on ISSR markers have revealed potential diagnostic fingerprints for various species and genomes, and also for individual accessions/cultivars. Additionally ISSR revealed 87 putative genome/species-specific molecular markers for eight of the nine genomes of Oryza. The ISSR markers are thus useful in the fingerprinting of cultivated and wild species germplasm, and in understanding the evolutionary relationships of Oryza.
Garth R Anderson - One of the best experts on this subject based on the ideXlab platform.
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Genomic instability of human aberrant crypt foci measured by inter-(Simple Sequence Repeat) PCR and array-CGH.
Mutation research, 2006Co-Authors: Sadir J Alrawi, Robert E Carroll, Hank C Hill, John F Gibbs, Dongfeng Tan, Bruce M Brenner, Norma J Nowak, Helen Swede, Daniel L Stoler, Garth R AndersonAbstract:Aberrant crypt foci (ACF) are the earliest identifiable neoplastic lesions in the colon. Thirty-two ACFs were examined for genomic instability in forms detectable either by inter-(Simple Sequence Repeat) PCR or by array comparative genomic hybridization [array-CGH]. One-fourth of ACFs revealed moderate instability by inter-(Simple Sequence Repeat) PCR; none showed amplifications or deletions on array-CGH. The absence of genomic events detectible by BAC array-CGH indicates early events in colorectal tumor progression are typically smaller than the approximate 150 kb size of a BAC clone insert.
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Analysis of inter-(Simple Sequence Repeat) PCR products from human colorectal cancers.
Oncology research, 2005Co-Authors: Neng Chen, Daniel L Stoler, Smitha S. Dutt, Gerald P. Jahreis, Miguel A. Rodriguez-bigas, Nicholas J. Petrelli, Garth R AndersonAbstract:Genomic instability is a fundamental characteristic of solid tumors, and understanding genomic instability should significantly clarify the process of tumorigenesis. We adapted the sampling technique of inter-(Simple Sequence Repeat) PCR [inter-(SSR) PCR] to measure genetic alterations between Simple Sequence Repeats in colorectal tumors. It becomes important to precisely define both normal and altered inter-(SSR) PCR products. BLAT searches of 131 cloned inter-(SSR) PCR Sequences reveal that inter-(SSR) PCR products are located on almost all the chromosomes except chromosome Y, indicating that inter-(SSR) PCR samples a representative diverse range of the genome. We confirm that a change in the pattern of the inter-(SSR) PCR products as seen on gel electrophoresis reflects a true alteration within the genome.
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Intrachromosomal genomic instability in human sporadic colorectal cancer measured by genome-wide allelotyping and inter-(Simple Sequence Repeat) PCR.
Cancer research, 2001Co-Authors: Garth R Anderson, Bruce M Brenner, Helen Swede, Neng Chen, W. Michael Henry, Jeffrey Conroy, Matthew J. Karpenko, Jean Pierre J. Issa, Jeremy D. Bartos, Joslyn K. BrunelleAbstract:We have used genome-wide allelotyping with 348 polymorphic autosomal markers spaced, on average, 10 cM apart to quantitate the extent of intrachromosomal instability in 59 human sporadic colorectal carcinomas. We have compared instability measured by this method with that measured by inter-(Simple Sequence Repeat) PCR and microsatellite instability assays. Instability quantitated by fractional allelic loss rates was found to be independent of that detected by microsatellite instability analyses but was weakly associated with that measured by inter-(Simple Sequence Repeat) PCR. A set of seven loci were identified that were most strongly associated with elevated rates of fractional allelic loss and/or inter-(Simple Sequence Repeat) PCR instability; these seven loci were on chromosomes 3, 8, 11, 13, 14, 18, and 20. A lesser association was seen with two loci flanking p53 on chromosome 17. Coordinate loss patterns for these loci suggest that at least two separate sets of cooperating loci exist for intrachromosomal genomic instability in human colorectal cancer.
Steven J. Knapp - One of the best experts on this subject based on the ideXlab platform.
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pcr multiplexes for a genome wide framework of Simple Sequence Repeat marker loci in cultivated sunflower
Theoretical and Applied Genetics, 2003Co-Authors: Shunxue Tang, Venkata K Kishore, Steven J. KnappAbstract:Simple Sequence Repeat (SSR) and other DNA Sequence-tagged site markers can be genotyped more rapidly and cost efficiently by simultaneously amplifying multiple loci (multiplex PCR). The development of PCR-multiplexes for a nearly genome-wide framework of 78 SSR marker loci in cultivated sunflower (Helianthus annuus L.) is described herein. The most outstanding single-locus SSR markers in the public collection (300 out of 1,089) were identified and screened for polymorphisms among 24 elite inbred lines, preparatory to selecting SSR markers for testing in multiplex PCRs. The selected SSR markers produced robust PCR products, amplified a single locus each, were polymorphic among elite inbred lines (minimum, mean and maximum heterozygosities were 0.08, 0.53 and 0.85, respectively), and supply a dense genome-wide framework of predominantly or completely codominant, single-locus DNA markers for molecular breeding and genomics research in sunflower. Thirteen six-locus multiplex PCRs were developed for 78 SSR marker loci strategically positioned throughout the sunflower genome (three to five per linkage group) by identifying compatible SSR primer combinations and optimizing multiplex PCR protocols. The multiplexed SSR markers, when coupled with 17 complementary SSR marker loci, create a 'standard genotyping' set ideal for first-pass scans of the genome, as are often needed when screening bulked-segregant DNA samples or mapping phenotypic trait loci. The minimum, mean and maximum heterozygosities of the multiplexed SSR markers were 0.38, 0.62 and 0.83, respectively. The PCR-multiplexes increase genotyping throughput, reduce reagent costs, and are ideal for repetitive genotyping applications where common sets of SSR marker loci are required or advantageous.
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Simple Sequence Repeat map of the sunflower genome
Theoretical and Applied Genetics, 2002Co-Authors: Shunxue Tang, Mary B Slabaugh, David K Shintani, Steven J. KnappAbstract:Several independent molecular genetic linkage maps of varying density and completeness have been constructed for cultivated sunflower (Helianthus annuus L.). Because of the dearth of Sequence and probe-specific DNA markers in the public domain, the various genetic maps of sunflower have not been integrated and a single reference map has not emerged. Moreover, comparisons between maps have been confounded by multiple linkage group nomenclatures and the lack of common DNA markers. The goal of the present research was to construct a dense molecular genetic linkage map for sunflower using Simple Sequence Repeat (SSR) markers. First, 879 SSR markers were developed by identifying 1,093 unique SSR Sequences in the DNA Sequences of 2,033 clones isolated from genomic DNA libraries enriched for (AC)n or (AG)n and screening 1,000 SSR primer pairs; 579 of the newly developed SSR markers (65.9% of the total) were polymorphic among four elite inbred lines (RHA280, RHA801, PHA and PHB). The genetic map was constructed using 94 RHA280 × RHA801 F7 recombinant inbred lines (RILs) and 408 polymorphic SSR markers (462 SSR marker loci segregated in the mapping population). Of the latter, 459 coalesced into 17 linkage groups presumably corresponding to the 17 chromosomes in the haploid sunflower genome (x = 17). The map was 1,368.3-cM long and had a mean density of 3.1 cM per locus. The SSR markers described herein supply a critical mass of DNA markers for constructing genetic maps of sunflower and create the basis for unifying and cross-referencing the multitude of genetic maps developed for wild and cultivated sunflowers.
Mahinur S. Akkaya - One of the best experts on this subject based on the ideXlab platform.
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integration of Simple Sequence Repeat dna markers into a soybean linkage map
Crop Science, 1995Co-Authors: Mahinur S. Akkaya, Arvind A. Bhagwat, Randy C Shoemaker, James E Specht, Perry B. CreganAbstract:A total of 40 Simple Sequence Repeat (SSR) or microsatellite DNA markers were mapped in a soybean [Glycine max (L.) Merrill] mapping population that consisted of 60 F 2 plants from a cross between near isogenic lines of the cultivars Clark and Harosoy. The first objective of study was to determine the map location of SSR loci in relation to 13 classical loci controlling pigmentation and morphological traits, seven isozyme loci, and a total of 118 RFLP and RAPD markers. The second objective was to determine if the microsatellite loci were randomly distributed in the soybean genome. Linkage analysis with MAPMAKER 3.0b yielded 29 linkage groups with a total map length of 1486 centimorgans (cM). This compares with a map length of 1056 cM if the SSR markers were removed from the data set. Thirty-four of the microsatellite loci were placed in linkage groups. SSR loci were linked to loci controlling nine of the 13 classical traits, and two of seven isozyme loci. Eighteen of the 29 linkage groups contained at least one SSR locus. While this result suggested that the microsatellite loci were randomly distributed throughout the soybean genome, two clusters of five and four SSR loci, spanning 23.4 and 33.6 cM, respectively, were detected. These results indicated a relatively limited amount of clustering of soybean SSR loci, and demonstrated that microsatellite genetic markers should provide an excellent complement to RFLP and RAPD markers for use in soybean molecular biology, genetics, and breeding research. Because SSR markers detect only single genetic loci and are highly polymorphic, they can be extremely informative in pedigree tracing studies, in the analysis of progeny from multiparent matings, in a wide range of mapping applications, and in genotype identification.
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Methodology of generation and characteristics of Simple Sequence Repeat DNA markers in avocado (Persea americana M.)
Euphytica, 1994Co-Authors: Uri Lavi, Mahinur S. Akkaya, Arvind A. Bhagwat, E. Lahav, Perry B. CreganAbstract:Generation of Simple Sequence Repeat (SSR) DNA markers was based on the construction of genomic DNA library of avocado (Persea americana M.). The library was screened with the four dinucleotide probes (AG), (AT), (GC) and (CA). Positive clones were Sequenced to validate the presence of Simple Sequence Repeats (SSR) and to generate polymerase chain reaction (PCR) primers based on the Sequences flanking the Simple Sequence Repeat. Twenty six different pairs of primers which yield a PCR product in the initial screening were synthesized. The SSR A1E11 was found to have eleven alleles while A3F8 has eight alleles. The SSRs in avocado were found to be inherited in a Mendelian fashion.
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length polymorphisms of Simple Sequence Repeat dna in soybean
Genetics, 1992Co-Authors: Mahinur S. Akkaya, Arvind A. Bhagwat, Perry B. CreganAbstract: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.
