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991.
Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust 总被引:7,自引:7,他引:0
Vales MI Schön CC Capettini F Chen XM Corey AE Mather DE Mundt CC Richardson KL Sandoval-Islas JS Utz HF Hayes PM 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(7):1260-1270
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation
of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust
pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n=409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population
was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions.
BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles.
The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods—resampling,
selective genotyping, and selective phenotyping—to evaluate the effect of population size on the estimation of QTL parameters.
In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small
populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective
phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large
populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
992.
The availability of large amounts of genomic DNA is of critical importance for many of the molecular biology assays used in the analysis of human disease. However, since the amount of patient tissue available is often limited and as particular foci of interest may consist of only a few hundred cells, the yield of DNA is often insufficient for extensive analysis. To address this problem, several whole genome amplification (WGA) methodologies have been developed. Initial WGA approaches were based on the polymerase chain reaction (PCR). However, recent reports have described the use of non-PCR-based linear amplification protocols for WGA. Using these methods, it is possible to generate microgram quantities of DNA starting with as little as 1mg of genomic DNA. This review will provide an overview of WGA approaches and summarize some of the uses for amplified DNA in various high-throughput genetic applications. 相似文献
993.
Lee KF Kwok KL Chung MK Lee YL Chow JF Yeung WS 《Journal of cellular biochemistry》2005,95(4):740-749
In mammal, fertilization and early preimplantation embryo development occurs in the oviduct. Evidence is accumulating that the oviductal epithelia secrete various biomolecules to the lumen during the secretory phase of the estrus cycle to enhance embryo development. This secretory activity of the oviduct is under the regulation of steroid hormones. Observations also suggested that the gametes and embryos modulate the physiology and gene-expressing pattern of the oviduct. However, the underlying molecular changes remain elusive. We hypothesize that the developing embryos interact with the surrounding environment and affect the gene expression patterns of the oviduct, thereby modulating the oviductal secretory activity conducive to the preimplantation embryo development. To test this hypothesis, suppression subtractive hybridization (SSH) was used to compare the gene expressions in mouse oviduct containing transferred in vitro cultured preimplantation embryos with that of oviduct containing oocytes during the preimplantation period. We reported here the identification and characterization of phospholipids transfer protein (PLTP), which is highly expressed in the embryo-containing oviduct and localized at the oviductal epithelium by in situ hybridization. PLTP contains signal peptide putative for secretory function. More importantly, PLTP mRNA increases in the oviductal epithelia of pregnant, but not pseudo-pregnant mice when assayed by real-time PCR. Taken together, our data suggested that PLTP may play important role(s) during in vivo preimplantation embryo development. This molecule would be a target to delineate the mechanisms and the roles of oviductal secretory proteins on early embryonic development. 相似文献
994.
Lopez C Soto M Restrepo S Piégu B Cooke R Delseny M Tohme J Verdier V 《Plant molecular biology》2005,57(3):393-410
A cassava cDNA microarray based on a large cassava EST database was constructed and used to study the incompatible interaction between cassava and Xanthomonas axonopodis pv. manihotis (Xam) strain CIO151. For microarray construction, 5700 clones from the cassava unigene set were amplified by polymerase chain reaction (PCR) and printed on glass slides. Microarray hybridization was performed using cDNA from cassava plants (resistant variety MBra685) collected at 12, 24, 48 h and 7 and 15 days post-infection as treatment and cDNA from mock-inoculated plants as control. A total of 199 genes were found to be differentially expressed (126 up-regulated and 73 down-regulated). A greater proportion of differentially-expressed genes was observed at 7 days after inoculation. Expression profiling and cluster analyses indicate that, in response to inoculation with Xam, cassava induces dozens of genes, including principally those involved in oxidative burst, protein degradation and pathogenesis-related (PR) genes. In contrast, genes encoding proteins that are involved in photosynthesis and metabolism were down regulated. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. Quantitative real time PCR experiments confirmed the reliability of our microarray data. In addition we showed that some genes are induced more rapidly in the resistant than in the susceptible cultivar.These authors made equal contributions to this work. 相似文献
995.
996.
This paper describes an approach for preparing unimolecular double-stranded DNA (uni-dsDNA) microarray chip. In this method, the various target oligonucleotides containing a reverse complementary sequence at 5' end were firstly annealed to a same universal oligonucleotide with amino group at 5' end and immobilized on aldehyde-derivatized glass slide. An on-chip DNA polymerization reaction was then performed to elongate the universal oligonucleotides. After a denaturation and a followed intra-strand annealing, a hairpin structure was formed at the free 3' end of the immobilized oligonucleotides. Finally, another on-chip DNA polymerization was done to synthesize the uni-dsDNA microarray. Combining with a PCR amplification of chemically synthesized target oligonucleotides, this method was much cost-effective for production of the uni-dsDNA microarray. The uni-dsDNA microarray was verified applicable for detecting the presence and monitoring the DNA-binding activity of the sequence-specific DNA-binding proteins. 相似文献
997.
Ligation-mediated suppression PCR (LMS-PCR) is a powerful tool for walking in unknown genomic DNA regions from known adjacent sequences. This approach has made it feasible to obtain promoter sequences and to enable researchers to identify full-length gene sequences or isoforms of multigene families. However, the advantages of LMS-PCR can be obviated by the presence of incomplete base modifications on the suppression adapters. We propose here that a 'partial-complementary adapter' is a more reliable suppression adapter, demanding only 5'-end phosphorylation. We also describe a simplified procedure for the easier preparation of PCR templates with very small quantities of DNA and a fast and direct characterization of the suppression-PCR products. A set of practical guidelines is proposed for pre-checking the efficiency of the adapter modification using two model systems: bacteriophage lambda (lambda) and Arabidopsis. 相似文献
998.
Haider MZ Habeeb Y Al-Nakkas E Al-Anzi H Zaki M Al-Tawari A Al-Bloushi M 《Journal of biomedical science》2005,12(5):815-818
Summary Idiopathic generalized epilepsies (IGEs) are the most common types of epilepsy in childhood and adolescence. A variety of
data suggest that IGEs have a predominant genetic etiology. Recently, a number of gene mutations have been found to be associated
with various types of epilepsy in mainly the Caucasian populations. The objective of this study was to investigate the association
of three different candidate genes with IGE in Kuwaiti Arab children. This study includes 123 Kuwaiti patients with a confirmed
diagnosis of epilepsy. Most of the patients have had a diagnostic EEG with generalized spike-wave discharges (GSWs). All patients
were evaluated by using a validated seizure questionnaire. The clinical type of epilepsy was determined by a trained neurologist/pediatrician.
The study also include 100 controls, the control subjects were children which did not have any history of neurological disorders.
Blood samples were collected from all patients and control subjects after taking informed consent. DNA was isolated and analyzed
by molecular methods. A FokI polymorphism in neuronal nicotinic acetylcholine receptor alpha-4 subunit (CHRNA4) gene was detected by PCR-RFLP method.
A missense mutation (Ser248Phe) in CHRNA4 gene was analyzed by PCR-RFLP using HpaII. A C121W mutation in sodium-channel beta-1 subunit (SCN1B) gene was screened by a PCR-RFLP method using HinPI. A 2-bp deletion in Cystatin B gene was detected by PCR-RFLP using XcmI. The incidence of three FokI polymorphism genotypes in Kuwaiti IGE patients was 1,1 (85%), 1,2 (14%) and 2,2 (1%) respectively. The missense mutation
Ser248Phe of CHRNA4 gene was not detected at all in Kuwaiti IGE patients. The C387G transversion resulting in C121W change
in third exon of the SCN1B gene was detected in 3/123 patients (2%). The patients carrying this mutation also exhibited febrile
seizures. The incidence of 2 bp deletion in the cystatin B gene was found to be 4% (5/123 IGE patients). The data obtained
from molecular analysis show a lack of association between three candidate genes and clinical expression of IGE in Kuwaiti
Arab children. This is completely different from the findings reported from Caucasian populations of France, Australia and
USA in which case a strong association has been reported between IGE and these genes.
To whom corresspondence should be addressed. Tel: +965-5319486; Fax: +965-5338940; E-mail: haider@hsc.edu.kw 相似文献
999.
Echevarría-Machado I Sánchez-Cach LA Hernández-Zepeda C Rivera-Madrid R Moreno-Valenzuela OA 《Molecular biotechnology》2005,31(2):129-135
A protocol is described for rapid DNA isolation from Malvaceae plant species and different tissues of Bixaceae that contain
large amounts of polysaccharides, polyphenols, and pigments that interfere with DNA extractions. The method is a modification
of Dellaporta et al. The current protocol is simple, and no phenolchloroform extraction, ethanol, or isopropranol precipitation
is required. The method is based in the incubation of soluble DNA with silica, mix in batch during the extraction. The procedure
can be completed in 2 h and many samples can be processed at the same time. DNA of excellent quality was recovered and used
for polymerase chain reaction (PCR) amplification, restriction enzyme digestion, and Southern blot analysis. The method was
used with healthy Bixa orellana and virus-infected Malvaceae plants. 相似文献
1000.