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Identification and characterization of the microRNAs and their targets in Salmo salar 总被引:1,自引:0,他引:1
Barozai MY 《Gene》2012,499(1):163-168
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EST data generated from 14 apple genotypes were downloaded from NCBI and mapped against a reference EST assembly to identify Single Nucleotide Polymorphisms (SNPs). Mapping of these SNPs was undertaken using 90% of sequence similarity and minimum coverage of four reads at each SNP position. In total, 37,807 SNPs were identified with an average of one SNP every 187 bp from a total of 6888 unique EST contigs. Identified SNPs were checked for flanking sequences of ≥ 60 bp along both sides of SNP alleles for reliable design of a custom high-throughput genotyping assay. A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of ≥ 60 bp sequences flanking a SNP position. Of these, 1411 SNPs were validated using four apple genotypes. Based on genotyping assays, it was estimated that 60% of SNPs were valid SNPs, while 26% of SNPs might be derived from paralogous regions. 相似文献
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EVA H. STUKENBROCK S
REN BANKE MARCELLO ZALA BRUCE A. MCDONALD RICHARD P. OLIVER 《Molecular ecology resources》2005,5(4):931-933
Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum. 相似文献
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Gene expression in diplosporous and sexual Eragrostis curvula genotypes with differing ploidy levels
Cervigni GD Paniego N Pessino S Selva JP Díaz M Spangenberg G Echenique V 《Plant molecular biology》2008,67(1-2):11-23
The molecular nature of gene expression during the initiation and progress of diplosporous apomixis is still unknown. Moreover,
the basis of the close correlation between diplospory and polyploidy is not clarified yet. A comparative expression analysis
was performed based on expressed sequence tags (ESTs) sequencing and differential display in an Eragrostis curvula diplosporous tetraploid genotype (T, 4x apo), a sexual diploid derivative obtained from tissue culture (D, 2x sex) and an
artificial sexual tetraploid obtained from the diploid seeds after colchicine treatment (C, 4x sex). From a total of 8,884
unigenes sequenced from inflorescence-derived libraries, 112 (1.26%) showed significant differential expression in individuals
with different ploidy level and/or variable reproductive mode. Independent comparisons between plants with different reproductive
mode (same ploidy) or different ploidy level (same reproductive mode) allowed the identification of genes modulated in response
to diplosporous development or polyploidization, respectively. Surprisingly, a group of genes (Group 3) were differentially
expressed or silenced only in the 4x sex plant, presenting similar levels of expression in the 4x apo and the 2x sex genotypes.
A group of randomly selected differential genes was validated by QR-PCR. Differential display analysis showed that in general
the 4x apo and 4x sex expression profiles were more related and different from the 2x sex one, but confirmed the existence
of Group 3-type genes, in both inflorescences and leaves. The possible biological significance for the occurrence of this
particular group of genes is discussed. In silico mapping onto the rice genome was used to identify candidates mapping to
the region syntenic to the diplospory locus.
Gerardo D. L. Cervigni, Norma Paniego and Silvina Pessino contributed equally to the work. 相似文献
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Madjid Delghandi Jørgen Stenvik Frank Nilsen Mette Serine Wesmajervi Kjersti Turid Fjalestad Børge Damsgård 《Conservation Genetics》2008,9(3):747-749
Nine polymorphic microsatellite markers were identified by screening of 2464 ESTs derived from a cDNA library of Atlantic
cod (Gadus morhua L.). About 35 novel microsatellite loci were selected and characterised in 96 individual cod. Nine markers were successfully
amplified with number of alleles from 3 to 18 per locus and the average heterozygosity was 0.57 in the panel examined (range
0.29–0.86). All loci followed the Hardy–Weinberg expectation and no significant linkage disequilibrium was found in a test
including all pairwise combinations. The gene identity was determined at four of the loci, confirming the associated microsatellites
as Type I markers. 相似文献
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A simple procedure was developed to convertLathyrus sativus defence-related expressed sequence tags (ESTs) into mappable genetic markers by using PCR. Twenty-nine STS primer pairs were
generated on the basis of sequence information from anL. sativus cDNA library. These primers were used to screen for polymorphisms between 2L. sativus accessions, ATC 80878 and ATC 80407, resistant and susceptible, respectively, toMycosphaerella pinodes infection. All 29 primer pairs amplified PCR products in both accessions, 11 of which amplified multiple RAPD-like products.
The remaining 18 primer pairs amplified single monomorphic products. Following cloning, sequencing, and database searches,
17 of 18 PCR products were confirmed to have amplified the targeted genome region. Ten of these 17 STS primer pairs revealed
polymorphisms between ATC 80878 and ATC 80407 when PCR products were digested with a range of restriction endonucleases. These
results suggest that the STS-based PCR analysis will be useful for generating informative molecular markers inL. sativus for future genome mapping experiments. 相似文献
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MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in both plants and animals. A large number of
miRNAs has been identified from various animals and model plant species such as Arabidopsis thaliana and rice (Oryza sativa); however, characteristics of wheat (Triticum aestivum) miRNAs are poorly understood. Here, computational identification of miRNAs from wheat EST sequences was preformed by using
the in-house program GenomicSVM, a prediction model for miRNAs. This study resulted in the discovery of 79 miRNA candidates.
Nine out of 22 miRNA representatives randomly selected from the 79 candidates were experimentally validated with Northern
blotting, indicating that prediction accuracy is about 40%. For the 9 validated miRNAs, 59 wheat ESTs were predicted as their
putative targets.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Weibo Jin and Nannan Li contributed equally to the work. 相似文献
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