Journal articles: 'EST clustering'

1

Wang, J. P. Z., B. G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W. C. Miller, and C. W. dePamphilis. "EST clustering error evaluation and correction." Bioinformatics 20, no. 17 (June 9, 2004): 2973–84. http://dx.doi.org/10.1093/bioinformatics/bth342.

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Hazelhurst, Scott, Winston Hide, Zsuzsanna Lipták, Ramon Nogueira, and Richard Starfield. "An overview of the wcd EST clustering tool." Bioinformatics 24, no. 13 (May 14, 2008): 1542–46. http://dx.doi.org/10.1093/bioinformatics/btn203.

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Mudhireddy, R., F. Ercal, and R. Frank. "Parallel Hash-Based EST Clustering Algorithm for Gene Sequencing." DNA and Cell Biology 23, no. 10 (October 2004): 615–23. http://dx.doi.org/10.1089/dna.2004.23.615.

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Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, et al. "TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets." Bioinformatics 19, no. 5 (March 22, 2003): 651–52. http://dx.doi.org/10.1093/bioinformatics/btg034.

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Kalyanaraman, A. "Efficient clustering of large EST data sets on parallel computers." Nucleic Acids Research 31, no. 11 (June 1, 2003): 2963–74. http://dx.doi.org/10.1093/nar/gkg379.

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Telles, Guilherme P., Marília D. V. Braga, Zanoni Dias, Lin Tzy-Li, José A. A. Quitzau, Felipe R. da Silva, and João Meidanis. "Bioinformatics of the sugarcane EST project." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 9–15. http://dx.doi.org/10.1590/s1415-47572001000100003.

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The Sugarcane EST project (SUCEST) produced 291,904 expressed sequence tags (ESTs) in a consortium that involved 74 sequencing and data mining laboratories. We created a web site for this project that served as a ‘meeting point’ for receiving, processing, analyzing, and providing services to help explore the sequence data. In this paper we describe the information pathway that we implemented to support this project and a brief explanation of the clustering procedure, which resulted in 43,141 clusters.

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Perseguini, Juliana Morini Küpper Cardoso, Lineu Roberto de Castro Romão, Boris Briñez, Erivaldo José Scaloppi Junior, Paulo de Souza Gonçalves, and Luciana Lasry Benchimol. "Genetic diversity of cultivated accessions and wild species of rubber tree using EST‑SSR markers." Pesquisa Agropecuária Brasileira 47, no. 8 (August 2012): 1087–94. http://dx.doi.org/10.1590/s0100-204x2012000800008.

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The objective of this work was to evaluate the efficiency of EST‑SSR markers in the assessment of the genetic diversity of rubber tree genotypes (Hevea brasiliensis) and to verify the transferability of these markers for wild species of Hevea. Forty‑five rubber tree accessions from the Instituto Agronômico (Campinas, SP, Brazil) and six wild species were used. Information provided by modified Roger's genetic distance were used to analyze EST‑SSR data. UPGMA clustering divided the samples into two major groups with high genetic differentiation, while the software Structure distributed the 51 clones into eight groups. A parallel could be established between both clustering analyses. The 30 polymorphic EST‑SSRs showed from two to ten alleles and were efficient in amplifying the six wild species. Functional EST‑SSR microsatellites are efficient in evaluating the genetic diversity among rubber tree clones and can be used to translate the genetic differences among cultivars and to fingerprint closely related materials. The accessions from the Instituto Agronômico show high genetic diversity. The EST‑SSR markers, developed from Hevea brasiliensis, show transferability and are able to amplify other species of Hevea.

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Lijoi, Antonio, Ramsés H. Mena, and Igor Prünster. "A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries." Journal of Computational Biology 15, no. 10 (December 2008): 1315–27. http://dx.doi.org/10.1089/cmb.2008.0043.

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Kim, N. "ECgene: Genome-based EST clustering and gene modeling for alternative splicing." Genome Research 15, no. 4 (March 21, 2005): 566–76. http://dx.doi.org/10.1101/gr.3030405.

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Kalyanaraman, A., S. Aluru, V. Brendel, and S. Kothari. "Space and time efficient parallel algorithms and software for EST clustering." IEEE Transactions on Parallel and Distributed Systems 14, no. 12 (December 2003): 1209–21. http://dx.doi.org/10.1109/tpds.2003.1255634.

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Lambais, Marcio R. "In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 103–11. http://dx.doi.org/10.1590/s1415-47572001000100015.

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The expression patterns of 277 sugarcane expressed sequence tags (EST)-contigs encoding putative defense-related (DR) proteins were evaluated using the Sugarcane EST database. The DR proteins evaluated included chitinases, beta-1,3-glucanases, phenylalanine ammonia-lyases, chalcone synthases, chalcone isomerases, isoflavone reductases, hydroxyproline-rich glycoproteins, proline-rich glycoproteins, peroxidases, catalases, superoxide dismutases, WRKY-like transcription factors and proteins involved in cell death control. Putative sugarcane WRKY proteins were compared and their phylogenetic relationships determined. A hierarchical clustering approach was used to identify DR ESTs with similar expression profiles in representative cDNA libraries. To identify DR ESTs differentially expressed in sugarcane tissues infected with Gluconacetobacter diazotrophicus or Herbaspirillum rubrisubalbicans, 179 putative DR EST-contigs expressed in non-infected tissues (leaves and roots) and/or infected tissues were selected and arrayed by similarity of their expression profiles. Changes in the expression levels of 124 putative DR EST-contigs, expressed in non-infected tissues, were evaluated in infected tissues. Approximately 42% of these EST-contigs showed no expression in infected tissues, whereas 15% and 3% showed more than 2-fold suppression in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. Approximately 14 and 8% of the DR EST-contigs evaluated showed more than 2-fold induction in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. The differential expression of clusters of DR genes may be important in the establishment of a compatible interaction between sugarcane and diazotrophic endophytes. It is suggested that the hierarchical clustering approach can be used on a genome-wide scale to identify genes likely involved in controlling plant-microorganism interactions.

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Gautheret, Daniel, Olivier Poirot, Fabrice Lopez, Stéphane Audic, and Jean-Michel Claverie. "Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering." Genome Research 8, no. 5 (May 1, 1998): 524–30. http://dx.doi.org/10.1101/gr.8.5.524.

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Burke, J. "d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences." Genome Research 9, no. 11 (November 1, 1999): 1135–42. http://dx.doi.org/10.1101/gr.9.11.1135.

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Watanabe, Hajime, Norihisa Tatarazako, Shigeto Oda, Hiroyo Nishide, Ikuo Uchiyama, Masatoshi Morita, and Taisen Iguchi. "Analysis of expressed sequence tags of the water flea Daphnia magna." Genome 48, no. 4 (August 1, 2005): 606–9. http://dx.doi.org/10.1139/g05-038.

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To study gene expression in the water flea Daphnia magna we constructed a cDNA library and characterized the expressed sequence tags (ESTs) of 7210 clones. The EST sequences clustered into 2958 nonredundant groups. BLAST analyses of both protein and DNA databases showed that 1218 (41%) of the unique sequences shared significant similarities to known nucleotide or amino acid sequences, whereas the remaining 1740 (59%) showed no significant similarities to other genes. Clustering analysis revealed particularly high expression of genes related to ATP synthesis, structural proteins, and proteases. The cDNA clones and EST sequence information should be useful for future functional analysis of daphnid biology and investigation of the links between ecology and genomics.Key words: Daphnia magna, EST, classification, ATP synthesis.

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Sim, Sung-Chur, Ju-Kyung Yu, Young-ki Jo, Mark E. Sorrells, and Geunhwa Jung. "Transferability of cereal EST-SSR markers to ryegrass." Genome 52, no. 5 (May 2009): 431–37. http://dx.doi.org/10.1139/g09-019.

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A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass ( Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37 EST-SSRs were mapped on an existing ryegrass genetic map. The mapped loci were uniformly distributed across all seven linkage groups without significant clustering at the distal regions of linkage groups. Sequences of ryegrass amplicons generated by randomly selected 16 EST-SSRs were aligned with reference sequences of cereal EST-SSRs. The SSR motifs and repeat lengths of the cereal EST-SSR markers were different from the majority of ryegrass amplicons. Furthermore, a majority of EST-SSRs amplified different flanking sequences of SSRs in ryegrass than the original cereal sequences. Our results suggest that the high degree of cereal EST-SSR transferability to ryegrass can be a useful enhancement to the molecular database of PCR-based markers but sequence analysis is essential before transferring genetic information using comparative mapping.

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Gailing, Oliver, and C. Dana Nelson. "Genetic variation patterns of American chestnut populations at EST-SSRs." Botany 95, no. 8 (August 2017): 799–807. http://dx.doi.org/10.1139/cjb-2016-0323.

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The objective of this study is to analyze patterns of genetic variation at genic expressed sequence tag – simple sequence repeats (EST-SSRs) and at chloroplast DNA markers in populations of American chestnut (Castanea dentata Borkh.) to assist in conservation and breeding efforts. Allelic diversity at EST-SSRs decreased significantly from southwest to northeast along the Appalachian range, suggesting repeated founder events during postglacial migration. Comparatively high allelic diversity in Ontario, northwest of the Appalachian range, suggested more recent long-distance dispersal. Clinal variation of allele frequencies along the Appalachian axis was also in accordance with postglacial colonization from one refugium southwest of the Appalachian range. We observed clustering of the northwestern population from Ontario with southwestern populations and sharing of a rare chloroplast haplotype among western populations across the whole latitudinal range. This pattern is consistent with a divergence of postglacial migration routes and higher levels of more recent potentially human-mediated gene exchange between populations west of the Appalachian range. Population pairs east and west of the Appalachian axis showed pronounced allele frequency differences over a small geographic range. These patterns of genetic variation should be considered when sampling reproductive material for conservation and breeding.

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Bhatt, Dhrumit S., and Samir C. Debnath. "Genetic Diversity of Blueberry Genotypes Estimated by Antioxidant Properties and Molecular Markers." Antioxidants 10, no. 3 (March 15, 2021): 458. http://dx.doi.org/10.3390/antiox10030458.

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Blueberries (Vaccinium spp.) have gained much attention worldwide because of their potential health benefits and economic importance. Genetic diversity was estimated in blueberry hybrids, wild clones and cultivars by their antioxidant efficacy, total phenolic and flavonoid contents, and express sequence tag–simple sequence repeat (SSR) (EST–SSR), genomic (G)–SSR and express sequence tag–polymerase chain reaction (EST–PCR) markers. Wide diversity existed among the genotypes for antioxidant properties, with the highest variation for DPPH radical scavenging activity (20-fold), followed by the contents of total flavonoids (16-fold) and phenolics (3.8-fold). Although a group of 11 hybrids generated the maximum diversity for antioxidant activity (15-fold), wild clones collected from Quebec, Canada, had the maximum variation for total phenolic (2.8-fold) and flavonoid contents (6.9-fold). Extensive genetic diversity was evident from Shannon’s index (0.34 for EST–SSRs, 0.29 for G–SSR, 0.26 for EST–PCR) and expected heterozygosity (0.23 for EST–SSR, 0.19 for G–SSR, 0.16 for EST–PCR). STRUCTURE analysis separated the genotypes into three groups, which were in agreement with principal coordinate and neighbour-joining analyses. Molecular variance suggested 19% variation among groups and 81% among genotypes within the groups. Clustering based on biochemical data and molecular analysis did not coincide, indicating a random distribution of loci in the blueberry genome, conferring antioxidant properties. However, the stepwise multiple regression analysis (SMRA) revealed that 17 EST–SSR, G–SSR and EST–PCR markers were associated with antioxidant properties. The study is valuable to breeding and germplasm conservation programs.

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Ding, Maomao, Ke Wang, Wenting Wang, Miaojin Chen, Dajun Wu, Changjie Xu, and Kunsong Chen. "Development of High Quality EST-SSR Markers Without Stutter Bands in Peach and Their Application in Cultivar Discrimination and Hybrid Authentication." HortScience 52, no. 1 (January 2017): 24–30. http://dx.doi.org/10.21273/hortsci11314-16.

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Peach (Prunus persica) is an important fruit crop worldwide with several thousand cultivars. Cultivar discrimination and hybrid authentication are often required in peach breeding and can be achieved by applying various molecular markers including simple sequence repeat (SSR). In this study a total of 2146 expressed sequence tag (EST)–SSR loci were detected with the 10,737 EST sequences retrieved from the NCBI. A total of 49 EST-SSR markers, including 24 simple ones with a motif comprising of tri-, tetra-, penta-, hexanucleotides, and 25 compound ones, were selected and then primers were designed. Following conventional polymerase chain reaction (PCR) specificity control and sequence authentication, as well as fluorescence-based PCR product size and stutter band evaluation, 37 EST-SSR markers with correct amplification and without stutter band interference were validated. Among them, 14 were polymorphic in 18 closely related peach accessions, with polymorphism information content (PIC) ranging from 0.0994 to 0.3750. The 18 peach accessions can be distinguished using nine polymorphic markers, with the exception of ‘Shangshandayulu’ and ‘Xipu 1’, both being bud sports from ‘Yulu’. The clustering of the accessions as well as the fingerprint profiles supported the authentication of the hybrids. These EST-SSR markers are useful for peach breeding research.

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Stavridou, Evangelia, Georgios Lagiotis, Parthena Kalaitzidou, Ioannis Grigoriadis, Irini Bosmali, Eleni Tsaliki, Stiliani Tsiotsiou, Apostolos Kalivas, Ioannis Ganopoulos, and Panagiotis Madesis. "Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis." Plants 10, no. 4 (March 30, 2021): 656. http://dx.doi.org/10.3390/plants10040656.

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A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

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Yu, Ju-Kyung, Qi Sun, Mauricio La Rota, Hugh Edwards, Hailu Tefera, and Mark E. Sorrells. "Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter)." Genome 49, no. 4 (April 1, 2006): 365–72. http://dx.doi.org/10.1139/g05-118.

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Tef (Eragrostis tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA libraries: seedling leaf, seedling root, and inflorescence of E. tef and seedling leaf of Eragrostis pilosa, a wild relative of E. tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 tef unigenes. Ap prox imately 3/4 of tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68% of the putative tef genes with gene ontology categories. Identification of the translated unigenes for conserved protein domains revealed 389 protein family domains (Pfam), the most frequent of which was protein kinase. A total of 170 ESTs containing simple sequence repeats (EST-SSRs) were identified and 80 EST-SSR markers were developed. In addition, 19 single-nucleotide polymorphism (SNP) and (or) insertion–deletion (indel) and 34 intron frag ment length polymorphism (IFLP) markers were developed. The EST database and molecular markers generated in this study will be valuable resources for further tef genetic research.Key words: tef, Ethiopian cereal crop, EST, molecular markers.

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Davison, D. B., and J. F. Burke. "Brute force estimation of the number of human genes using EST clustering as a measure." IBM Journal of Research and Development 45, no. 3.4 (May 2001): 439–47. http://dx.doi.org/10.1147/rd.453.0439.

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Bragg, L. M., and G. Stone. "k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage." Bioinformatics 25, no. 18 (July 1, 2009): 2302–8. http://dx.doi.org/10.1093/bioinformatics/btp410.

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Belaj, Angjelina, Antònia Ninot, Francisco J. Gómez-Gálvez, Milad El Riachy, Melek Gurbuz-Veral, Mariela Torres, Adhurim Lazaj, et al. "Utility of EST-SNP Markers for Improving Management and Use of Olive Genetic Resources: A Case Study at the Worldwide Olive Germplasm Bank of Córdoba." Plants 11, no. 7 (March 29, 2022): 921. http://dx.doi.org/10.3390/plants11070921.

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Olive, the emblematic Mediterranean fruit crop, owns a great varietal diversity, which is maintained in ex situ field collections, such as the World Olive Germplasm Bank of Córdoba (WOGBC), Spain. Accurate identification of WOGBC, one of the world’s largest collections, is essential for efficient management and use of olive germplasm. The present study is the first report of the use of a core set of 96 EST-SNP markers for the fingerprinting of 1273 accessions from 29 countries, including both field and new acquired accessions. The EST-SNP fingerprinting made possible the accurate identification of 668 different genotypes, including 148 detected among the new acquired accessions. Despite the overall high genetic diversity found at WOGBC, the EST-SNPs also revealed the presence of remarkable redundant germplasm mostly represented by synonymy cases within and between countries. This finding, together with the presence of homonymy cases, may reflect a continuous interchange of olive cultivars, as well as a common and general approach for their naming. The structure analysis revealed a certain geographic clustering of the analysed germplasm. The EST-SNP panel under study provides a powerful and accurate genotyping tool, allowing for the foundation of a common strategy for efficient safeguarding and management of olive genetic resources.

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Kim, Changsoo, Cheol Seong Jang, Terry L. Kamps, Jon S. Robertson, Frank A. Feltus, and Andrew H. Paterson. "Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cDNA library." Functional Plant Biology 35, no. 7 (2008): 585. http://dx.doi.org/10.1071/fp08133.

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A normalised cDNA library was constructed from Bermudagrass to gain insight into the transcriptome of Cynodon dactylon L. A total of 15 588 high-quality expressed sequence tags (ESTs) from the cDNA library were subjected to The Institute for Genomic Research Gene Indices clustering tools to produce a unigene set. A total of 9414 unigenes were obtained from the high-quality ESTs and only 39.6% of the high-quality ESTs were redundant, indicating that the normalisation procedure was effective. A large-scale comparative genomic analysis of the unigenes was carried out using publicly available tools, such as BLAST, InterProScan and Gene Ontology. The unigenes were also subjected to a search for EST-derived simple sequence repeats (EST-SSRs) and conserved-intron scanning primers (CISPs), which are useful as DNA markers. Although the candidate EST-SSRs and CISPs found in the present study need to be empirically tested, they are expected to be useful as DNA markers for many purposes, including comparative genomic studies of grass species, by virtue of their significant similarities to EST sequences from other grasses. Thus, knowledge of Cynodon ESTs will empower turfgrass research by providing homologues for genes that are thought to confer important functions in other plants.

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Ghazy, Abdelhalim I., Talal K. Al-Ateeq, Eid I. Ibrahim, Hussein M. Migdadi, Kotb A. Attia, Muhammad Javed, Muhammad Altaf Khan, Ibrahim Al-Ashkar, and Abdullah Al-Doss. "Phylogenetic Analysis of Ryegrass (Lolium rigidum) Populations and the Proliferation of ALS Resistance in Saudi Arabia." Agriculture 12, no. 2 (February 17, 2022): 290. http://dx.doi.org/10.3390/agriculture12020290.

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Morphological and simple sequence repeat (SSR) approaches were used to determine the genetic diversity of 29 ryegrass (Lolium rigidum) genotypes belonging to eight populations collected from several regions in Saudi Arabia. In this study, 50 in Silico-developed SSR markers derived from genomic and expressed sequence tag (EST) microsatellites were examined. Analysis of variance showed highly significant differences in all studied traits. Cluster analysis based on the morphological data of the 29 Lolium genotypes and using PAST (paleontological statistics) software was performed. According to the results, clustering was based mostly on genotype location. The sensitive genotypes for herbicide were clustered in one group. In addition, using EST-SSR markers, we observed the existence of a considerable number of genetic variations among Lolium genotypes. From these markers, only 31 produced reasonable amplification products. The results showed that 23 SSR markers revealed that 74.19% were polymorphic. The number of alleles detected per primer ranged from one to five in the primer LTC SSR1. The tested primers amplified 1434 bands across eight populations, with an average of 46.26 bands per primer. The polymorphism information content (PIC) values ranged from 0.11 to 0.76 for the primers LT EST-SSR5 and LTC SSR1. The unweighted pair group method with arithmetic average (UPGMA) clustering of the 29 genotypes representing eight populations was based essentially on their locations and herbicide-tolerance levels. Most of the populations formed into four clusters, together representing genotypes. Moreover, the tolerant populations were distinguished from the sensitive ones. The relationship between the genetic diversity and geographical source of Lolium rigidum populations of Saudi Arabia was revealed through this study. The results showed that the efficiency of developed SSR markers are transferable across species. They have been helpful to assess the genetic diversity of the ryegrass population as this could be applied to differentiate between tolerant and sensitive populations of ryegrass.

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Lee, Y. "The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes." Nucleic Acids Research 33, Database issue (December 17, 2004): D71—D74. http://dx.doi.org/10.1093/nar/gki064.

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Gil-Ariza, David Jesús, Iraida Amaya, José Manuel López-Aranda, José Federico Sánchez-Sevilla, Miguel Ángel Botella, and Victoriano Valpuesta. "Impact of Plant Breeding on the Genetic Diversity of Cultivated Strawberry as Revealed by Expressed Sequence Tag-derived Simple Sequence Repeat Markers." Journal of the American Society for Horticultural Science 134, no. 3 (May 2009): 337–47. http://dx.doi.org/10.21273/jashs.134.3.337.

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Unlike other important crops analyzed so far for genetic diversity and population structure, the brief history and particularities of the genetics of the cultivated strawberry (Fragaria ×ananassa Duchesne) have limited its genetic characterization. The genomic composition and the pattern of inheritance have not been fully elucidated, although a number of studies have suggested a highly diploidized genome. In this study, the similarity relationships and structure of 92 selected strawberry cultivars with widely diverse origins have been established using simple sequence repeat (SSR) markers derived from expressed sequence tags (EST-SSR markers). Genetic analysis performed by the unweighted pair group method with arithmetic mean clustering revealed a distribution according to both date of cultivar release and breeding for a specific climatic adaptation. Additionally, a model-based clustering approach identified three populations among the strawberry cultivars with an overall FST value of 0.15 to 0.16. Both analyses support a limited differentiation of modern cultivars, most probably as a consequence of the methodology of strawberry breeding. Interestingly, the collection of strawberry cultivars here analyzed showed comparable genetic differentiation to that observed in natural populations of Fragaria chiloensis (L.) Mill., one of its wild ancestors. Our results suggest that breeding has produced a small but significant reduction on the genetic diversity of F. ×ananassa. The panel of 10 EST-SSRs described in this work provided an extremely low probability of confusion (less than 10−11), offering an efficient and accurate method for cultivar identification.

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Wang, Xiben, Guus Bakkeren, and Brent McCallum. "Virulence and molecular polymorphisms of the wheat leaf rust fungus Puccinia triticina in Canada from 1997 to 2007." Botany 88, no. 6 (June 2010): 575–89. http://dx.doi.org/10.1139/b10-034.

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Populations of Puccinia triticina , one of the casual agents of wheat leaf rust disease, in the pacific (British Columbia and Alberta), prairie (Manitoba and Saskatchewan), and eastern regions (Quebec and Ontario) of Canada from 1997 to 2007 were analyzed for virulence and genetic diversity by revealing expressed sequence tag derived simple sequence repeat (EST-SSR) polymorphisms. Since 1997, a significant shift in the virulence of P. triticina occurred across Canada. The diversity of P. triticina virulence phenotypes in Manitoba and Saskatchewan, as measured by Shannon and Simpson indexes, decreased due to the directional selection toward predominant virulence phenotypes, whereas it remained relatively constant in Quebec and Ontario. The clustering of P. triticina virulence phenotypes from 1997 to 2007 was similar to that found in previous years, and was correlated with virulence to leaf rust resistance genes Lr2a, Lr2c, and Lr17a. Distinct EST-SSR profiles were found in different groups of P. triticina virulence phenotypes based on virulence to Lr2a, Lr2c, and Lr17a. In addition, the population of P. triticina in Manitoba and Saskatchewan was different from that in Quebec and Ontario from 1997 to 2007, based on both virulence characteristics and EST-SSR genotypes.

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Zhang, Xi, Xiu Hong, Jiang Yang Duan, Lu Lu Han, Zi Yang Hong, Peng Jiang, Zhong Quan Wang, and Jing Cui. "Development of EST-derived microsatellite markers to investigate the population structure of sparganum — the causative agent of zoonotic sparganosis." Parasitology 146, no. 07 (March 12, 2019): 947–55. http://dx.doi.org/10.1017/s0031182019000222.

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AbstractThe plerocercoid (sparganum) of Spirometra erinaceieuropaei is the main aetiological agent of human sparganosis. To improve the current knowledge on S. erinaceieuropaei evolution, we performed multi-locus microsatellite typing of sparganum isolates from China for the first time. All available expressed sequence tag (EST) sequences for the Spirometra were downloaded from the GenBank. The identification and localization of microsatellites in ESTs was accomplished by MISA. Based on the selected microsatellites, the genetic structure of 64 sparganum isolates collected from 11 geographical locations in southwest China were investigated through principal component analysis, STRUCTURE analysis and neighbour-joining clustering. A total of 522 non-redundant ESTs containing 915 simple sequence repeats were identified from 12 481 ESTs screened. Five primer pairs were finally selected. Using these loci, a total of 12 alleles were detected in 64 sparganum isolates. Little variability was observed within each of geographical population, especially among isolates derived from Kunming of Yunnan (YN-KM) province. Both STRUCTURE analysis and the clustering analysis supported that two genotypes existed among the sparganum isolates from southwest China. In conclusion, five microsatellite markers were successfully developed, and sparganum population was observed to harbour low genetic variation, further investigation with deeper sampling was needed to elucidate the population structure.

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Cordonnier-Pratt, Marie-Michèle, Chun Liang, Haiming Wang, Dmitri S. Kolychev, Feng Sun, Robert Freeman, Robert Sullivan, and Lee H. Pratt. "MAGIC Database and Interfaces: An Integrated Package for Gene Discovery and Expression." Comparative and Functional Genomics 5, no. 3 (2004): 268–75. http://dx.doi.org/10.1002/cfg.399.

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The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

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Mian, M. A. Rouf, Malay C. Saha, Andrew A. Hopkins, and Zeng-Yu Wang. "Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses." Genome 48, no. 4 (August 1, 2005): 637–47. http://dx.doi.org/10.1139/g05-029.

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Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

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Izzah, Nur Kholilatul, Reflinur Reflinur, and Tae-Jin Yang. "DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES." Indonesian Journal of Agricultural Science 17, no. 1 (January 30, 2017): 17. http://dx.doi.org/10.21082/ijas.v17n1.2016.p17-26.

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<p>Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.</p>

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Li, Jin, Changbing Zhang, Shiyong Chen, Keke Jiang, Hao Guan, and Wenhui Liu. "Characterization and Application of EST-SSR Markers Developed from Transcriptome Sequences in Elymus breviaristatus (Poaceae: Triticeae)." Genes 14, no. 2 (January 23, 2023): 302. http://dx.doi.org/10.3390/genes14020302.

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Background: Elymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures. Results: We obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2–98.3%. UPGMA analysis generally grouped species with similar genome types together. Conclusions: Here, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

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Liu, Yang, Xiaomei Fang, Tian Tang, Yudong Wang, Yinhuan Wu, Jinyu Luo, Haotian Wu, et al. "Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)." Plants 11, no. 6 (March 10, 2022): 742. http://dx.doi.org/10.3390/plants11060742.

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Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.

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Jayashree, B., Manindra S. Hanspal, Rajgopal Srinivasan, R. Vigneshwaran, Rajeev K. Varshney, N. Spurthi, K. Eshwar, N. Ramesh, S. Chandra, and David A. Hoisington. "An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms." Comparative and Functional Genomics 2007 (2007): 1–7. http://dx.doi.org/10.1155/2007/35604.

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The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

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MEDOUKALI, Imane, Ines BELLIL, and Douadi KHELIFI. "Morphological and Isozyme Variation in Natural Populations of the Genus Medicago L. Prospected in Northern Algeria." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 43, no. 1 (May 13, 2015): 86–95. http://dx.doi.org/10.15835/nbha4319676.

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As part of the evaluation and enhancement of genetic resources, morphological and isozyme variability within and among 169 accessions, representing 14 species of the genus Medicago L. collected in northern Algeria, was assessed using twelve quantitative traits and two enzymatic systems. Phenotype frequencies were scored in six enzyme zones to determine isozyme variability within and among populations. The data analysis resolved a high level of genetic diversity. Ten morphometric characteristics contributed to the discrimination of the species. The relationship between the collection site environment and phenotypic characteristics was also studied. Esterase (EST) enzyme system was more polymorphic than glutamate oxaloacetate transaminase (GOT) system. Were scored 2 zones with 10 bands and 21 phenotypes for GOT (glutamate oxaloacetate transaminase) and 4 zones with 22 bands and 71 phenotypes for EST (esterase) Polymorphism index and Jaccardâ€™s genetic distances revealed the existence of a high genetic diversity within and among the studied populations. The annual species M. polymorpha presented an intraspecific polymorphism index of 0.57, which was higher than all other species indices. Clustering of the species based on isozyme markers was in agreement with taxonomic criteria and showed no significant correlation with morphological characteristics. Conservation programs should take into account the level of genetic diversity within and between populations revealed by isozyme markers.

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Graham, Michelle A., Mario Ramírez, Oswaldo Valdés-López, Miguel Lara, Mesfin Tesfaye, Carroll P. Vance, and Georgina Hernandez. "Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris through clustering analysis across several plant species." Functional Plant Biology 33, no. 8 (2006): 789. http://dx.doi.org/10.1071/fp06101.

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Common bean (Phaseolus vulgaris L.) is the world’s most important grain legume for direct human consumption. However, the soils in which common bean predominate are frequently limited by the availability of phosphorus (P). Improving bean yield and quality requires an understanding of the genes controlling P acquisition and use, ultimately utilising these genes for crop improvement. Here we report an in silico approach for the identification of genes involved in adaptation of P. vulgaris and other legumes to P-deficiency. Some 22 groups of genes from four legume species and Arabidopsis thaliana, encoding diverse functions, were identified as statistically over-represented in EST contigs from P-stressed tissues. By combining bioinformatics analysis with available micro / macroarray technologies and clustering results across five species, we identified 52 P. vulgaris candidate genes belonging to 19 categories as induced by P-stress response. Transport-related, stress (defence and regulation) signal transduction genes are abundantly represented. Manipulating these genes through traditional breeding methodologies and / or biotechnology approaches may allow us to improve crop P-nutrition.

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Guo, Baozhu, Xiaoping Chen, Yanbin Hong, Xuanqiang Liang, Phat Dang, Tim Brenneman, Corley Holbrook, and Albert Culbreath. "Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery." International Journal of Plant Genomics 2009 (June 24, 2009): 1–14. http://dx.doi.org/10.1155/2009/715605.

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Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453.

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Pranavi, B., G. Sitaram, K. N. Yamini, and V. Dinesh Kumar. "Development of EST–SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids." Genome 54, no. 8 (August 2011): 684–91. http://dx.doi.org/10.1139/g11-033.

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Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST–SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.

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Ould Med Mahmoud, M. A., and S. Hamza. "Genetic diversity in local barley accessions collected from different geographical regions of Tunisia." Plant Genetic Resources 7, no. 02 (July 3, 2009): 169–76. http://dx.doi.org/10.1017/s1479262108162086.

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To assess the genetic diversity among Tunisian local barley, a set of 120 barley accessions representing five distinct geographical regions (North-West, Littoral, South, Jerba and Kerkennah Islands) was characterized with 20 simple sequence repeats (SSR) and 8 expressed sequence tag (EST)-SSR markers. The 28 loci revealed a total of 98 alleles, with an average of 3.76 alleles per locus (range 2–10). Gene diversity averaged 0.50 (range 0.09–0.84). Partitioning analysis of genetic diversity showed that about 95% of the total variation was within regions and no geographical differentiation could be found except for the North-West population. Similarly, neighbour joining clustering of the genotypes did not indicate any clear pattern of division among the barley accessions based on geographical origin. These results may reflect the impact of seed exchange between farmers which is likely to limit highlighting favourable alleles due to local adaptation.

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Vásquez-Mayorga, Marcela, Eric J. Fuchs, Eduardo J. Hernández, Franklin Herrera, Jesús Hernández, Ileana Moreira, Elizabeth Arnáez, and Natalia M. Barboza. "Molecular characterization and genetic diversity ofJatropha curcasL. in Costa Rica." PeerJ 5 (February 9, 2017): e2931. http://dx.doi.org/10.7717/peerj.2931.

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We estimated the genetic diversity of 50Jatropha curcassamples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values forJ. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of theJatropha curcasgermplasm bank in Costa Rica.

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SINGH, A., H. K. DIKSHIT, D. SINGH, N. JAIN, M. ASKI, A. SARKER, and T. R. SHARMA. "Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species." Journal of Agricultural Science 154, no. 7 (January 14, 2016): 1254–69. http://dx.doi.org/10.1017/s0021859615001252.

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SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to analyse genetic diversity among three Lens species. The SSR loci amplified successfully in wild species, with 94·82% transferability in Lens culinaris subsp. orientalis, 95·4% in Lens nigricans, 98·81% in L. culinaris subsp. odemensis, 94·82% in L. culinaris subsp. tomentosus and 96·55% in Lens ervoides. Ninety-nine alleles (average 3·41 alleles/locus) were detected by 29 SSR markers. Based on the unweighted pair group method with arithmetic mean cluster analysis, all the genotypes were grouped into three clusters at a similarity level of 0·30. The diversity analysis indicated no species-specific clustering of the wild and cultivated species. Wild species L. nigricans and L. culinaris subsp. odemensis, L. culinaris subsp. orientalis and L. ervoides were grouped in Cluster I, whereas the Mediterranean land races of L. culinaris subsp. culinaris and L. culinaris subsp. tomentosus formed a separate group in Cluster II A. Cluster II B comprised L. ervoides, L. culinaris subsp. orientalis and L. culinaris subsp. culinaris. Clusters II C, II D and II F included cultivated Indian lentil genotypes. Cluster II E comprised Indian and Mediterranean germplasm lines. Cluster II F included three early maturing germplasm lines, whereas Cluster III included only two germplasm lines. The functional annotation of SSR-containing unigenes revealed that a majority of genes were involved in an important transport-related function or were a component of metabolic pathways. A high level of polymorphism of EST-SSRs and their transferability to related wild species indicated that these markers could be used for molecular screening, map construction, comparative genomic studies and marker-assisted selection.

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Yao, Saraka Didier Martial, Eric-Blanchard Zadjéhi Koffi, Wentia Alimata Marie-Pierre Daramcoum, Koffi Yoboue, Jean-Louis Konan Konan, Nafan Diarrassouba, Roland Bourdeix, and Raoul Sylvère Sie. "Apport des descripteurs qualitatifs dans l’identification des accessions de cocotier Grand pour les programmes de régénération des collections au champ." International Journal of Biological and Chemical Sciences 14, no. 2 (October 5, 2020): 580–99. http://dx.doi.org/10.4314/ijbcs.v14i2.22.

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Les descripteurs qualitatifs ont été toujours négligés dans les études de caractérisation du cocotier surtout chez les écotypes de type Grand. Cet article se propose de mettre en évidence la contribution de six caractères morphologiques de type qualitatif dans la description et la typologie de 18 populations de cocotier Grand plantées dans la collection internationale de Côte d’Ivoire. Pour y arriver les stipes, les inflorescences, les fleurs femelles et les fruits ont été observés. Compte tenu à la fois de leurs fortes valeurs d’indice de diversité de Shannon normalisé (H’ variant entre 0,93 et 0,99) et faibles valeurs d’indice de diversité de Simpson (D variant entre 0,24 et 0,28), les caractères formes du fruit et de la noix débourrée ont été les plus discriminants. Les résultats de la classification des populations de cocotier Grand de la collection de Côte d’Ivoire utilisant les caractères qualitatifs sont en désaccord avec la structuration admise et fournie antérieurement à partir des marqueurs morphologiques quantitatifs et moléculaires microsatellites (SSRs). Bien que longtemps marginalisé dans l’étude de la diversité génétique des écotypes Grand de cocotier, l’apport des caractères qualitatifs dans l’identification de ces accessions de la collection de Côte d’Ivoire est discuté. Aussi, l’intérêt du recours aux descripteurs qualitatifs comme alternative aux marqueurs moléculaires pour le suivi de la pureté des accessions de cocotier au champ pendant les cycles de régénération est souligné.© 2020 International Formulae Group. All rights reserved. English abstract Qualitative morphological descriptors have always been neglected in coconut population’s characterization, especially in Tall coconut varieties. This paper proposes the contribution of six qualitative traits in the description and typology of 18 Tall coconut populations planted at the international field genebank of Côte d'Ivoire. Relatively to high values of standardized index of Shannon Weaver diversity H' (0.93 to 0.99) and low values of Simpson diversity index D (0.24 to 0.28), the two qualitative traits that are fruit and husked nut shapes were more discriminating. The results about clustering of the Tall coconut populations in Côte d'Ivoire genebank using all studied qualitative characters were in disagreement with the clustering assumed and provided before from quantitative traits and SSRs molecular markers. Although a long time marginalized in the genetic diversity studies, the contribution of the qualitative traits in the identification of Tall coconut populations in international field genebank of Côte d’Ivoire has been discussed. Also, the interest of recourse of the qualitative descriptors as alternative to the molecular markers for purity follow-up of the coconut accession during the cycles of field genebank regeneration is clearly underlined.

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Kouame, Yao Francis, Atolé Brice Bienvenu Kedi, Seka Simplice Kouassi, N’Guessan Jimmy Aristide Konan, Egomli Stanislas Assohoun, Ossey Bernard Yapo, and Théophile Gnagne. "Caractéristiques physico-chimiques des eaux de forages à usage domestique dans la ville de Daloa (centre-ouest de la Côte d’Ivoire)." International Journal of Biological and Chemical Sciences 15, no. 2 (June 23, 2021): 835–45. http://dx.doi.org/10.4314/ijbcs.v15i2.33.

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Les populations de la ville de Daloa en Côte d’Ivoire consomment majoritairement les eaux de forages au détriment de l’eau fournie par la société agréée. Ainsi, cette étude des eaux de forages a pour objectif l’évaluation de ses caractéristiques physico-chimiques. Elle a permis de mesurer au niveau de quinze forages les paramètres tels que le pH, la conductivité électrique, la température, le nitrite, le nitrate, l’ammonium, le sulfate, le bicarbonate, le calcium, le magnésium et le potassium. Les valeurs moyennes sont comparées aux normes relatives à la qualité de l’eau de boisson. L’analyse statistique multivariée dont l’Analyse en Composantes Principales (ACP) et la Classification Hiérarchique Ascendante (CHA) a été également appliquée à l’ensemble des paramètres mesurés. Il ressort des résultats que l’eau des forages est légèrement acide avec un pH moyen de 6,0 ± 0,5. Elle est faiblement minéralisée avec une conductivité électrique moyenne de 246,2 ± 162,6 μS/cm. Une forte corrélation est signalée entre la conductivité électrique et les paramètres suivants : nitrate, ammonium, bicarbonate, calcium, magnésium, sodium et potassium. La classification des forages est gouvernée par les valeurs de conductivité et de pH qui permettent de regrouper les forages selon leur qualité physico-chimique. Les eaux des forages de Daloa sont conformes aux directives de l’OMS.Mots clés : Daloa, eau de forage, norme, paramètres physico-chimique, qualité de l’eau. English title: Physicochemical characteristic of ground water for domestic use in the town of Daloa (Midwest, Ivory Coast) The population of Daloa (third largest city in Côte d’Ivoire) mainly consume borehole water to the detriment of water provided by approved company. Thus, the quality of borehole water is evaluated from their physicochemical characteristics in this study. The study carried out in various districts of the city made it possible to measure for fifteen boreholes the physicochemical parameters such as pH, electric conductivity, temperature, nitrite, nitrate, ammonium, sulphate, bicarbonate, calcium, magnesium and potassium. The average values are compared with the standards relating to drinking water quality. The Multivariate statistical analysis whose Principal Components Analysis (PCA) and hierarchical clustering (HC) were also applied to the whole of the measured parameters. The results show that the borehole water is slightly acid with an average pH of 6,0 ± 0,5. It is slightly mineral-bearing with an average electric conductivity of 246,2 ± 162,6 μS/cm. A strong correlation is announced between electric conductivity and the following parameters: nitrate, ammonium, bicarbonate, calcium, magnesium, sodium and potassium. The classification of borehole controlled by this value of conductivity and pH which makes it possible to gather borehole according to their physicochemical quality. The physicochemical parameters of borehole water from Daloa are in conformity with the directives of WHO.Keywords: Daloa, borehole water, standard, physicochemical parameters, water quality.

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Pei-Qing, Liu, Wu Min-Liang, Li Ben-Jin, Lan Cheng-Zhong, Weng Qi-Yong, and Chen Qing-He. "Development of Expressed Sequence Tag-Drived Simple Sequence Repeat Markers and Diversity Analysis of Phytophthora capsici in China." International Journal of Phytopathology 2, no. 3 (December 30, 2013): 137–46. http://dx.doi.org/10.33687/phytopath.002.03.0410.

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Phytophthora capsici is a highly dynamic and destructive pathogen of vegetable and great interests on the genetic structure of P. capsici have grown in the world. However, there is little genetic information about P. capsici based on the EST-SSR markers. In this study, 193 SSR markers were developed and 33 selected markers were successfully detected and they were polymorphic with the number of alleles per locus ranging from 2 to 7. 4 SSR markers were further selected for genetic diversity analysis and Nei’s genetic diversity values of 15 populations ranged from 0.38 to 0.66, with an average of 0.53. The higher polymorphism and greater transport ability of these markers among P. capsici species were proved by the expected heterozygosity (He =0.64) and Shannon’s index of diversity (I =1.14), indicating that they maintained a substantial level of genetic diversity. Additionally, the genetic differentiation among the 4 markers (Fst =0.15) was moderate and the gene flow among groups was consequent (Nm =1.69). Clustering analyses revealed that 15 populations are made of two differentiated genetic clusters and are similar regarding genetic diversity composition. Our results suggest that there are considerable evolutionary potential of P. capsici in China and useful management strategies should be adapt to it.

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Ramiandrisoa, Botovao A., Cyrille Maharombaka, and Hery L. T. Ranarijaona. "Inventaire et typologie floristique des milieux lentiques dans le district de Vohipeno." Madagascar Conservation & Development 16, no. 2s (February 11, 2022): 48–51. http://dx.doi.org/10.4314/mcd.wetlands.7.

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L’écologie des macrophytes (plantes aquatiques visibles à l’œil nu) est peu étudiée à Madagascar. L’écosystème aquatique du district de Vohipeno (Région Vatovavy Fitovinany) n’a fait l’objet d’étude que pendant la période coloniale de 1921 à 1936. Les objectifs de cette étude sont d’améliorer la connaissance sur les macrophytes et d’établir une typologie floristique des zones humides malgaches. Au total, 43 espèces réparties entre 34 genres et 19 familles ont été recensées. Les valeurs de l’indice de Shannon Weaver ont montré une faible diversité mais une distribution hétérogène. L’analyse du coefficient de similarité de Sorensen a révélé une ressemblance entre certains sites. L’Analyse Factorielle des Correspondances (AFC) met en exergue quatre groupements de végétaux appuyés par la Classification Ascendante Hiérarchique (CAH). The ecology of macrophytes (aquatic plants) has not been extensively studied in Madagascar. The aquatic ecosystem of the district of Vohipeno (Vatovavy Fitovinany) was last studied during the colonial period 1921 to 1936. The objectives of this study were to improve the knowledge on macrophytes and to make a floristic typology of Malagasy wetlands. In total 43 species distributed between 34 genera and 19 families were recorded. The Shannon Weaver index showed low diversity but a heterogeneous distribution. The Sorensen coefficient analysis revealed resemblances between certain sites. Correspondence Analysis (CA) highlighted four vegetation groups and was supported by Hierarchical Clustering (HCPC).

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Liu, Guosheng, Xiaoyan Sheng, David L. Greenshields, Adam Ogieglo, Susan Kaminskyj, Gopalan Selvaraj, and Yangdou Wei. "Profiling of Wheat Class III Peroxidase Genes Derived from Powdery Mildew-Attacked Epidermis Reveals Distinct Sequence-Associated Expression Patterns." Molecular Plant-Microbe Interactions® 18, no. 7 (July 2005): 730–41. http://dx.doi.org/10.1094/mpmi-18-0730.

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A cDNA library was constructed from leaf epidermis of diploid wheat (Triticum monococcum) infected with the powdery mildew fungus (Blumeria graminis f. sp. tritici) and was screened for genes encoding peroxidases. From 2,500 expressed sequence tags (ESTs), 36 cDNAs representing 10 peroxidase genes (designated TmPRX1 to TmPRX10) were isolated and further characterized. Alignment of the deduced amino acid sequences and phylogenetic clustering with peroxidases from other plant species demonstrated that these peroxidases fall into four distinct groups. Differential expression and tissue-specific localization among the members were observed during the B. graminis f. sp. tritici attack using Northern blots and reverse-transcriptase polymerase chain reaction analyses. Consistent with its abundance in the EST collection, TmPRX1 expression showed the highest induction during pathogen attack and fluctuated in response to the fungal parasitic stages. TmPRX1 to TmPRX6 were expressed predominantly in mesophyll cells, whereas TmPRX7 to TmPRX10, which feature a putative C-terminal propeptide, were detectable mainly in epidermal cells. Using TmPRX8 as a representative, we demonstrated that its C-terminal propeptide was sufficient to target a green fluorescent protein fusion protein to the vacuoles in onion cells. Finally, differential expression profiles of the TmPRXs after abiotic stresses and signal molecule treatments were used to dissect the potential role of these peroxidases in multiple stress and defense pathways.

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George, Suja, Gayatri Venkataraman, and Ajay Parida. "Identification of stress-induced genes from the drought-tolerant plant Prosopis juliflora (Swartz) DC. through analysis of expressed sequence tags." Genome 50, no. 5 (May 2007): 470–78. http://dx.doi.org/10.1139/g07-014.

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Abiotic stresses such as cold, salinity, drought, wounding, and heavy metal contamination adversely affect crop productivity throughout the world. Prosopis juliflora is a phreatophyte that can tolerate severe adverse environmental conditions such as drought, salinity, and heavy metal contamination. As a first step towards the characterization of genes that contribute to combating abiotic stress, construction and analysis of a cDNA library of P. juliflora genes is reported here. Random expressed sequence tag (EST) sequencing of 1750 clones produced 1467 high-quality reads. These clones were classified into functional categories, and BLAST comparisons revealed that 114 clones were homologous to genes implicated in stress response(s) and included heat shock proteins, metallothioneins, lipid transfer proteins, and late embryogenesis abundant proteins. Of the ESTs analyzed, 26% showed homology to previously uncharacterized genes in the databases. Fifty-two clones from this category were selected for reverse Northern analysis: 21 were shown to be upregulated and 16 downregulated. The results obtained by reverse Northern analysis were confirmed by Northern analysis. Clustering of the 1467 ESTs produced a total of 295 contigs encompassing 790 ESTs, resulting in a 54.2% redundancy. Two of the abundant genes coding for a nonspecific lipid transfer protein and late embryogenesis abundant protein were sequenced completely. Northern analysis (after polyethylene glycol stress) of the 2 genes was carried out. The implications of the analyzed genes in abiotic stress tolerance are also discussed.

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Jin, L., H. Wang, T. Narita, R. Kikuno, O. Ohara, N. Shihara, T. Nishigori, Y. Horikawa, and J. Takeda. "Expression profile of mRNAs from human pancreatic islet tumors." Journal of Molecular Endocrinology 31, no. 3 (December 1, 2003): 519–28. http://dx.doi.org/10.1677/jme.0.0310519.

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In order to understand the tIssue specificity of the endocrine pancreas, it is important to clarify the expression profile of mRNAs in various states of the tIssue. A total of approximately 9000 non-redundant expressed genes from human pancreatic islets and insulinoma have so far been determined as expressed sequence tags (ESTs) and deposited in public databases. In the present study towards the identification of a complete set of genes expressed in human pancreatic islets, we have determined 3'-ESTs of 21267 clones randomly selected from a cDNA library of human pancreatic islet tumors. Clustering analysis generated 6157 non-redundant sequences comprising 2323 groups and 3834 singletons. Nucleotide and peptide database searches show that 3103 of them represent known human sequences or homologs of genes identified in other species and 58 are new members of structurally related families. The sequences were classified on the basis of the putative protein functions encoded, and were assigned to the respective chromosome by database analysis. The sequences were also compared with the EST databases (dbEST and EPConDB) including ESTs from normal pancreatic islet, insulinoma, and fetal pancreas. Since 3384 genes were newly found to be expressed in human pancreatic islets and 587 of them were unique to the islets, this study has considerably expanded the catalog of genes expressed in the endocrine pancreas. The larger collection of pancreatic islet-related ESTs should provide a better genome source for molecular studies of differentiation, tIssue-specific functions, and tumorigenesis of the endocrine pancreas as well as for genetic studies of diabetes mellitus.

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Saboori, Somayeh, Masoud Sheidai, Zahra Noourmohammadi, Seyed Samih Marashi, and Fahimeh Koohdar. "Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates." Caryologia 74, no. 3 (December 21, 2021): 151–68. http://dx.doi.org/10.36253/caryologia-1089.

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Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st (Nei) = 0.673, P = 0.001; G’st (Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological and agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

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Journal articles on the topic 'EST clustering'

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