Isolation and characterization of a differentially expressed sequence tag from Triticum durum salt-stressed roots

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.

Download Full-text

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

Botany ◽

10.1139/b10-019 ◽

2010 ◽

Vol 88 (5) ◽

pp. 537-543 ◽

Cited By ~ 11

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.

Download Full-text

Isolation and Characterization of Differentially Expressed Transcripts from the Suspension Cells of Oil Palm (Elaeis guineensis Jacq.) in Response to Different Concentration of Auxins

Molecular Biotechnology ◽

10.1007/s12033-010-9262-9 ◽

2010 ◽

Vol 46 (1) ◽

pp. 1-19 ◽

Cited By ~ 20

Author(s):

Siti Habsah Roowi ◽

Chai-Ling Ho ◽

Sharifah Shahrul Rabiah Syed Alwee ◽

Meilina Ong Abdullah ◽

Suhaimi Napis

Keyword(s):

Oil Palm ◽

Elaeis Guineensis ◽

Differentially Expressed ◽

Suspension Cells ◽

Isolation And Characterization ◽

Elaeis Guineensis Jacq

Download Full-text

Isolation and characterization of progesterone receptor-related protein p23 (Pm-p23) differentially expressed during ovarian development of the giant tiger shrimp Penaeus monodon

Aquaculture ◽

10.1016/j.aquaculture.2010.06.037 ◽

2010 ◽

Vol 308 ◽

pp. S75-S82 ◽

Cited By ~ 10

Author(s):

Rachanimuk Preechaphol ◽

Sirawut Klinbunga ◽

Pattareeya Ponza ◽

Piamsak Menasveta

Keyword(s):

Progesterone Receptor ◽

Ovarian Development ◽

Penaeus Monodon ◽

Differentially Expressed ◽

Related Protein ◽

Isolation And Characterization ◽

Tiger Shrimp

Download Full-text

Identification of metalloprotease gene families in sugarcane

Genetics and Molecular Biology ◽

10.1590/s1415-47572001000100037 ◽

2001 ◽

Vol 24 (1-4) ◽

pp. 285-290 ◽

Cited By ~ 12

Author(s):

O.H.P. Ramos ◽

H.S. Selistre-de-Araujo

Keyword(s):

Expressed Sequence Tag ◽

Gene Families ◽

Data Bank ◽

Matrix Metalloproteases ◽

Sequence Motifs ◽

Dna Library ◽

Physiological Processes ◽

Expressed Sequence ◽

Enzyme Class

Metalloproteases play a key role in many physiological processes in mammals such as cell migration, tissue remodeling and processing of growth factors. They have also been identified as important factors in the patho-physiology of a number of human diseases, including cancer and hypertension. Many bacterial pathogens rely on proteases in order to infect the host. Several classes of metalloproteases have been described in humans, bacteria, snake venoms and insects. However, the presence and characterization of plant metalloproteases have rarely been described in the literature. In our research, we searched the sugarcane expressed sequence tag (SUCEST) DNA library in order to identify, by homology with sequences deposited in other databases, metalloprotease gene families expressed under different conditions. Protein sequences from Arabidopsis thaliana and Glycine max were used to search the SUCEST data bank. Conserved regions corresponding to different metalloprotease domains and sequence motifs were identified in the reads to characterize each group of enzymes. At least four classes of sugarcane metalloproteases have been identified, i.e. matrix metalloproteases, zincins, inverzincins, and ATP-dependent metalloproteases. Each enzyme class was analyzed for its expression in different conditions and tissues.

Download Full-text

Expressed sequence tag analysis of developing seed coat and characterization of theRangene in rice

Rice Genetics Collection - Rice Genetics II ◽

10.1142/9789812814319_0178 ◽

2008 ◽

pp. 473-475

Author(s):

M. J. Han ◽

S. H. Jun ◽

S. R. Kim ◽

G. An

Keyword(s):

Seed Coat ◽

Expressed Sequence Tag ◽

Developing Seed ◽

Expressed Sequence Tag Analysis ◽

Expressed Sequence

Download Full-text

Development and characterization of microsatellite markers from tropical forage Stylosanthes species and analysis of genetic variability and cross-species transferability

Genome ◽

10.1139/g11-064 ◽

2011 ◽

Vol 54 (12) ◽

pp. 1016-1028 ◽

Cited By ~ 6

Author(s):

Amaresh Chandra ◽

K.K. Tiwari ◽

D. Nagaich ◽

N. Dubey ◽

S. Kumar ◽

...

Keyword(s):

Genetic Improvement ◽

Expressed Sequence Tag ◽

Intraspecific Diversity ◽

Genomic Libraries ◽

Tropical Forage ◽

Genomic Ssr ◽

Functional Molecular Markers ◽

Expressed Sequence ◽

Simple Sequence

A limited number of functional molecular markers has slowed the desired genetic improvement of Stylosanthes species. Hence, in an attempt to develop simple sequence repeat (SSR) markers, genomic libraries from Stylosanthes seabrana B.L. Maass & ’t Mannetje (2n = 2x = 20) using 5′ anchored degenerate microsatellite primers were constructed. Of the 76 new microsatellites, 21 functional primer pairs were designed. Because of the small number of primer pairs designed, 428 expressed sequence tag (EST) sequences from seven Stylosanthes species were also examined for SSR detection. Approximately 10% of sequences delivered functional primer pairs, and after redundancy elimination, 57 microsatellite repeats were selected. Tetranucleotides followed by trinucleotides were the major repeated sequences in Stylosanthes ESTs. In total, a robust set of 21 genomic–SSR (gSSR) and 20 EST–SSR (eSSR) markers were developed. These markers were analyzed for intraspecific diversity within 20 S. seabrana accessions and for their cross-species transferability. Mean expected (He) and observed (Ho) heterozygosity values with gSSR markers were 0.64 and 0.372, respectively, whereas with eSSR markers these were 0.297 and 0.214, respectively. Dendrograms having moderate bootstrap value (23%–94%) were able to distinguish all accessions of S. seabrana with gSSR markers, whereas eSSR markers showed 100% similarities between few accessions. The set of 21 gSSRs, from S. seabrana, and 20 eSSRs, from selected Stylosanthes species, with their high cross-species transferability (45% with gSSRs, 86% with eSSRs) will facilitate genetic improvement of Stylosanthes species globally.

Download Full-text