EST derived PCR-based markers for functional gene homologues in cotton

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 449-462 ◽  
Author(s):  
Peng W Chee ◽  
Junkang Rong ◽  
Dawn Williams-Coplin ◽  
Stefan R Schulze ◽  
Andrew H Paterson
Keyword(s):  
Expressed Sequence Tag ◽  
Sequence Divergence ◽  
Restriction Enzymes ◽  
Orthologous Gene ◽  
Pcr Primers ◽  
Tetraploid Cotton ◽  
Gossypium Arboreum ◽  
Rflp Map ◽  
Amplicon Size ◽  
Expressed Sequence

We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for developing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs amplified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the corresponding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis.Key words: Gossypium arboreum, cotton, expressed sequence tag, PCR, known-function genes.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1114-1121 ◽  
Author(s):  
Shu-Mei Jiang ◽  
Long Zhang ◽  
Jun Hu ◽  
Rui Shi ◽  
Guang-He Zhou ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Expressed Sequence Tag ◽  
Barley Yellow Dwarf Virus ◽  
Differentially Expressed ◽  
Addition Line ◽  
Alien Chromosome ◽  
Thinopyrum Intermedium ◽  
Barley Yellow Dwarf ◽  
Yellow Dwarf Virus ◽  
Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

scholarly journals Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L.

2020 ◽  
Vol 21 (5) ◽  
pp. 1675 ◽  
Author(s):  
Xueying Liu ◽  
Philippe Moncuquet ◽  
Qian-Hao Zhu ◽  
Warwick Stiller ◽  
Zhengsheng Zhang ◽  
...  
Keyword(s):  
Single Cells ◽  
Genetic Identification ◽  
Acceptor Site ◽  
Tetraploid Cotton ◽  
Gossypium Arboreum ◽  
Hub Genes ◽  
Potential Donor ◽  
Cotton Fibres ◽  
Cotton Species ◽  
Final Length

Cotton fibres, as single cells arising from the seed coat, can be classified as lint and fuzz according to their final length. Gossypium arboreum is a cultivated diploid cotton species and a potential donor of the A subgenome of the more widely grown tetraploid cottons. In this study, we performed genetic studies on one lintless and seven fuzzless G. arboreum accessions. Through association and genetic linkage analyses, a recessive locus on Chr06 containing GaHD-1 was found to be the likely gene underlying the lintless trait. GaHD-1 carried a mutation at a splicing acceptor site that resulted in alternative splicing and a deletion of 247 amino acid from the protein. The regions containing GaGIR1 and GaMYB25-like were found to be associated with fuzz development in G. arboreum, with the former being the major contributor. Comparative transcriptome analyses using 0-5 days post-anthesis (dpa) ovules from lintless, fuzzless, and normal fuzzy seed G. arboreum accessions revealed gene modules and hub genes potentially important for lint and fuzz initiation and development. Three significant modules and 26 hub genes associated with lint fibre initiation were detected by weighted gene co-expression network analysis. Similar analyses identified three vital modules and 10 hub genes to be associated with fuzz development. The findings in this study contribute to understanding the complex molecular mechanism(s) regulating fibre initiation and development and indicate that G. arboreum may have fibre developmental pathways different from tetraploid cotton. It also provides candidate genes for further investigation into modifying fibre development in G. arboreum.

Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽  
2010 ◽  
Vol 88 (5) ◽  
pp. 537-543 ◽  
Author(s):  
Yong-Bi Fu ◽  
Gregory W. Peterson
Keyword(s):  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Linum Usitatissimum L ◽  
Evolutionary Studies ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Cultivated Flax

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

scholarly journals Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivumL.)

Genetics ◽  
2004 ◽  
Vol 168 (2) ◽  
pp. 585-593 ◽  
Author(s):  
G. R. Lazo ◽  
S. Chao ◽  
D. D. Hummel ◽  
H. Edwards ◽  
C. C. Crossman ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Expressed Sequence

scholarly journals Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20561 ◽  
Author(s):  
Paul M. Krzyzanowski ◽  
Feodor D. Price ◽  
Enrique M. Muro ◽  
Michael A. Rudnicki ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Expressed Sequence Tag ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rna ◽  
Expressed Sequence

Gene expression profile of rabbit cartilage by expressed sequence tag analysis

Gene ◽  
2008 ◽  
Vol 424 (1-2) ◽  
pp. 147-152 ◽  
Author(s):  
Hyuck Joon Kwon ◽  
Hidetoshi Akimoto ◽  
Yoshihiro Ohmiya ◽  
Kenichi Honma ◽  
Kazunori Yasuda
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Expressed Sequence Tag ◽  
Rabbit Cartilage ◽  
Expressed Sequence Tag Analysis ◽  
Expressed Sequence

scholarly journals Analysis of Expressed Sequence Tag Data and Gene Expression Profiles Involved in Conidial Germination of Fusarium oxysporum

2006 ◽  
Vol 72 (2) ◽  
pp. 1667-1671 ◽  
Author(s):  
Ye Deng ◽  
Haitao Dong ◽  
Qingchao Jin ◽  
Cheng'en Dai ◽  
Yongqi Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Fusarium Oxysporum ◽  
Cdna Library ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Cdna Array ◽  
Gene Expression Profiles ◽  
Conidial Germination ◽  
Expressed Sequence

ABSTRACT We obtained 3,372 tentative unique transcripts (TUTs) from a cDNA library of Fusarium oxysporum. A cDNA array with 3,158 TUTs was produced to analyze gene expression profiles in conidial germination. It seems that ras and other signaling genes, e.g., ccg, cooperatively initiate conidial germination in Fusarium by increasing protein synthesis.

Relationships among blueberry species within the section Cyanococcus of the Vaccinium genus based on EST-PCR markers

2021 ◽  
Author(s):  
Lisa Jeannine Rowland ◽  
Elizabeth L. Ogden ◽  
James R. Ballington
Keyword(s):  
Polymerase Chain Reaction ◽  
Expressed Sequence Tag ◽  
Clustering Methods ◽  
Polyploid Species ◽  
Pcr Markers ◽  
Chain Reaction ◽  
Ploidy Levels ◽  
Commercial Species ◽  
Polymerase Chain ◽  
Expressed Sequence

Commercial blueberry species of North America belong to the Vaccinium genus, section Cyanococcus. Phylogenetic relationships of 50 accessions of different ploidy levels within Cyanococcus were investigated using 249 expressed sequence tag-polymerase chain reaction markers and standard clustering methods. Of the commercial species, tetraploid V. corymbosum grouped most closely with the diploids, V. fuscatum and V. caesariense, followed by the diploid V. elliottii. Tetraploid V. angustifolium grouped with the diploids, V. boreale and V. myrtilloides. Hexaploid V. virgatum grouped most closely with the diploid V. tenellum, thus shedding light on the origins of these polyploid species.

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