Isolation and characterization of SSR sequences from the genome and TAC clones of common wheat using the PCR technique

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 432-444 ◽  
Author(s):  
Michiya Koike ◽  
Kanako Kawaura ◽  
Yasunari Ogihara ◽  
Atsushi Torada
Keyword(s):  
Ssr Markers ◽  
Common Wheat ◽  
Genomic Dna ◽  
Genomic Library ◽  
Artificial Chromosome ◽  
Triticum Aestivum L ◽  
Pcr Screening ◽  
Artificial Chromosomes ◽  
Isolation And Characterization ◽  
Simple Sequence

We have developed the 2-step PCR method, a kind of suppression PCR procedure, to isolate simple sequence repeats (SSRs) from common wheat (Triticum aestivum L.) in a more convenient manner. This system requires neither genomic library screening nor the SSR-enrichment procedure. As a result, we designed 131 primer pairs based on isolated SSRs from not only genomic DNA, but also transformation-competent artificial chromosome (TAC) clones. It has been demonstrated that 34 of the 131 SSR markers developed were polymorphic among 8 wheat lines. Four of 34 polymorphic SSR markers were derived from TAC clones, indicating that this method could be applied to the targeted development of unique SSR markers in large genomic DNA libraries such as those composed of bacterial artificial chromosomes (BACs). A considerable number of isolated SSR clones had similarities with part of several long terminal repeats of retrotransposons (LTR-RTs) identified in various Triticeae genome sequences. Most of those SSRs showed smear amplification profiles, suggesting that a considerable number of dysfunctional SSRs originating from repetitive DNA components, especially LTR-RTs, might exist in the common wheat genome.Key words: common wheat, simple sequence repeat (SSR), PCR screening, LTR-retrotransposon, TAC clone.

scholarly journals Genetic Diversity Analysis between Different Varieties of Chickpea (Cicer arietinum L.) Using SSR Markers

2019 ◽  
Vol 7 (2) ◽  
pp. 236-242
Author(s):  
Summy Yadav ◽  
Vaidehi Shah ◽  
Bhavya Mod
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genomic Dna ◽  
Physiological Data ◽  
Diversity Analysis ◽  
Hierarchical Tree ◽  
Cicer Arietinum L ◽  
Equal Distance ◽  
Genomic Regions ◽  
Simple Sequence

The paper aims at evaluating genetic diversity among genomes of chickpea comprising of 5 different varieties with the help of simple sequence repeats (SSR) molecular markers. Genomic DNA isolated from all varieties was checked with 15 different SSR markers specific for ENDPOINT PCR using PCR based techniques. Amplification bands with different markers enabled identification of the genomic regions responsible for Drought Tolerance in chickpea. All 15 SSR markers chosen gave monomorphic bands.  A hierarchical tree was also constructed using UPGMA Dendogram for figuring out the exact genetic distance of cultivars using band amplification data. It depicted GUJ-1 and GUJ-2 are closest of all cultivars. GUJ-5 is at the center having GUJ-3 and UJJAVAL at an almost equal distance but GUJ-5 and GUJ-3 are more related. Physiological data also supported this genetic evidence. Int. J. Appl. Sci. Biotechnol. Vol 7(2): 236-242

scholarly journals MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 01-06 ◽  
Author(s):  
A. K. M. Khorsheduzzaman ◽  
M. Z. Alam ◽  
M. M. Rahman ◽  
M. A. K. Mian ◽  
M. I. H. Mian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Banding Pattern ◽  
Genomic Dna ◽  
Molecular Level ◽  
Narrow Range ◽  
Solanum Melongena ◽  
Pcr Amplification ◽  
Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccard’s coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 805-818 ◽  
Author(s):  
Ju-Kyung Yu ◽  
Trevor M Dake ◽  
Sukhwinder Singh ◽  
David Benscher ◽  
Wanlong Li ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Hexaploid Wheat ◽  
Sequence Similarity ◽  
Triticum Aestivum L ◽  
Grass Species ◽  
Multiple Loci ◽  
Polymorphic Gene ◽  
Sequence Similarity Analysis ◽  
Expressed Sequence ◽  
Simple Sequence

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.

scholarly journals Development of Novel Coconut Ssr Markers Derived From Genome-Wide Bioinformatics Prediction

2021 ◽  
Author(s):  
Reina Esther S. Caro ◽  
Jesmar Cagayan ◽  
Roanne R. Gardoce ◽  
Anand Noel C. Manohar ◽  
Alma O. Canama-Salinas ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Assembly ◽  
Artificial Chromosome ◽  
West African ◽  
Size Exclusion ◽  
Bioinformatics Pipeline ◽  
Product Size ◽  
Online Databases ◽  
Genome Wide ◽  
Simple Sequence

Abstract In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSR markers are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers. A total of 7,139 novel SSR markers were derived from the genome assembly of coconut ‘Catigan Green Dwarf’ (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. OligoAnalyzer-tool was also employed using the following desired parameters: %GC: 40–60%; minimum ΔG value for hairpin loop: -0.3 kcal/mol; minimum ΔG value for self-dimer: -0.9 kcal/mol; and minimum ΔG value for hetero-dimer: -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using ‘Catigan Green Dwarf’ (CATD), ‘Laguna Tall’ (LAGT), ‘West African Tall’ (WAT), and SYNVAR (LAGT x WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes. The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.

scholarly journals Isolation and Characterization of New Polymorphic Simple Sequence Repeat Loci in Chrysopogon aciculatus (Retz.) Trin.

HortScience ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 232-235 ◽  
Author(s):  
Xinyi Zhang ◽  
Li Liao ◽  
Yang Liu ◽  
Zhiyong Wang ◽  
Jianxiu Liu
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Magnetic Bead ◽  
Group Method ◽  
Amplification Efficiency ◽  
Sequence Repeat ◽  
Arithmetic Means ◽  
Pair Group ◽  
Isolation And Characterization ◽  
Simple Sequence

Chrysopogon aciculatus (Retz.) Trin. is a perennial turfgrass for its low management and resistance. To develop simple sequence repeat (SSR) markers for C. aciculatus, we used four Roche 454 pyrosequencing, combined with the magnetic bead enrichment method FIASCO (fast isolation by amplified fragment length polymorphism of sequences containing repeats) to isolate from the C. aciculatus. A total of 66,198 raw sequencing reads were obtained with 4289 sequences (6.48%) were fit for primer pair design. One hundred microsatellite loci were selected to test the primer amplification efficiency in 20 accessions, and out of these, 11 loci were polymorphic. The amount of observed alleles ranged from three to six, with an average of 3.64. Nei’s genetic diversity values ranged from 0.085 to 0.493, with an average of 0.293. Shannon’s information index values ranged from 0.141 to 0.686, with an average of 0.428. Twenty accessions were clustered into three groups by unweighted pair-group method with arithmetic means (UPGMA). These SSR markers will provide an ideal marker system to assist with gene targeting, cultivar variety or species identification, and marker-assisted selection in C. aciculatus species.

Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthio camelus) genome

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 833-840 ◽  
Author(s):  
Bo Tang ◽  
Yin Hua Huang ◽  
Li Lin ◽  
Xiao Xiang Hu ◽  
Ji Dong Feng ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genomic Library ◽  
Enriched Library ◽  
Genetic Studies ◽  
Pcr Screening ◽  
Struthio Camelus ◽  
Parentage Testing ◽  
Isolation And Characterization ◽  
Length Polymorphisms

Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.

Isolation and characterization of TaQsd1 genes for period of dormancy in common wheat (Triticum aestivum L.)

2019 ◽  
Vol 39 (10-11) ◽  
Author(s):  
Wenxin Wei ◽  
Xiaoyu Min ◽  
Siyao Shan ◽  
Hao Jiang ◽  
Jiajia Cao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Common Wheat ◽  
Triticum Aestivum L ◽  
Isolation And Characterization

Isolation and characterization of a developmentally regulated homeobox sequence in the Mexican axolotl Ambystoma mexicanum

1990 ◽  
Vol 68 (3) ◽  
pp. 622-629 ◽  
Author(s):  
Mary Whiteley ◽  
John B. Armstrong
Keyword(s):  
Genomic Dna ◽  
Genomic Library ◽  
Ambystoma Mexicanum ◽  
Tail Bud ◽  
Developmentally Regulated ◽  
Mexican Axolotl ◽  
Isolation And Characterization ◽  
Partial Genomic Library ◽  
Homeobox Sequence

A homeobox-containing genomic DNA fragment was isolated from the Mexican axolotl. This clone was obtained from a partial genomic library enriched for sequences that cross-hybridized with the Drosophila Antp homeobox under low stringency hybridization conditions. DNA sequence analysis revealed that this sequence (Ahox1) was 66% homologous to the Antp homeobox sequence and was most closely related to the mouse Hox-1.6 (84% identity) and Drosophila lab (79% identity) homeobox sequences. Several cross-hybridizing fragments to Ahox1 were detected in both mouse and axolotl genomic DNA. This sequence was also shown to be conserved in other Ambystoma species. Northern blot analysis revealed that genes containing this sequence are developmentally regulated. Transcripts hybridizing to the Ahox1 homeobox probe were detected during the neurula and tail bud stages of development.Key words: axolotl, homeobox, mouse, Drosophila, gene expression.

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