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  • 1
    ISSN: 1432-2242
    Keywords: Key words Zea mays L. ; AFLP® ; Methylation AFLP® ; Genetic map ; DNA methylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  This study demonstrates the relative ease of generating high-density linkage maps using the AFLP® technology. Two high-density AFLP linkage maps of Zea mays L. were generated based on: (1) a B73 × Mo17 recombinant inbred population and (2) a D32 × D145 immortalized F2 population. Although AFLP technology is in essence a mono-allelic marker system, markers can be scored quantitatively and used to deduce zygosity. AFLP markers were generated using the enzyme combinations EcoRI/MseI and PstI/MseI. A total of 1539 and 1355 AFLP markers have been mapped in the two populations, respectively. Among the mapped PstI/MseIAFLP markers we have included fragments bounded by a methylated PstI site (mAFLP markers). Mapping these mAFLP markers shows that the presence of C-methylation segregates in perfect accordance with the primary target sequence, leading to Mendelian inheritance. Simultaneous mapping of PstI/MseIAFLP and PstI/MseI mAFLP markers allowed us to identify a number of epi-alleles, showing allelic variation in the CpNpG methylation only. However, their frequency in maize is low. Map comparison shows that, despite some rearrangements, most of the AFLP markers that are common in both populations, map at similar positions. This would indicate that AFLP markers are predominantly single-locus markers. Changes in map order occur mainly in marker-dense regions. These marker-dense regions, representing clusters of mainly EcoRI/MseI AFLP and PstI/MseI mAFLP markers, co- localize well with the putative centromeric regions of the maize chromosomes. In contrast, PstI/MseImarkers are more uniformly distributed over the genome.
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  • 2
    ISSN: 1432-2242
    Keywords: Key words Zea mays L ; AFLP ; RFLP ; Testcross mean ; Testcross variance ; Genetic distance ; Midparent heterosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base populations. In this study, we investigated whether the testcross (TC) means and variances of F3 progenies from F1 crosses in European maize can be predicted from the TC means of their parents and F1 crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLPTM 1 markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P1−P2∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent germplasm and the six possible F1 crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random F3 plants per F1 cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17 and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F1 crosses, and F3 populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett’s test revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in five sets for dry matter content. Correlations among the TC means of the parents, F1 crosses, and F3 populations were highly significant and positive for all traits. Estimates of the TC variance among F3 progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits. The results demonstrated that for our material, the TC means of the parents or the parental F1 cross can be used as predictors for the TC means of F3 populations. However, the prediction of the TC variance remains an unsolved problem.
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  • 3
    ISSN: 1432-2242
    Keywords: Key words Amplified fragment length polymorphism (AFLP) ; Simple-sequence length polymorphism (SSLP) ; Restriction fragment length polymorphism (RFLP) ; Rice (Oryza sativa L.) ; Molecular map
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A molecular map of rice consisting of 231 amplified fragment length polymorphisms (AFLPs), 212 restriction fragment length polymorphisms (RFLPs), 86 simple-sequence length polymorphisms (SSLPs), five isozyme loci, and two morphological mutant loci [phenol staining of grain (Ph), semi-dwarf habit (sd-1)] has been constructed using an F11 recombinant inbred (RI) population. The mapping population consisted of 164 RI lines and was developed via single-seed descent from an intercross between the genetically divergent parents Milyang 23 (M) (tongil type) and Gihobyeo (G) ( japonica type). A subset of previously mapped RFLP and SSLP markers were used to construct the map framework. The AFLP markers were derived from ten EcoRI(+2) and MseI(+3) primer combinations. All marker types were well distributed throughout the 12 chromosomes. The integrated map covered 1814 cM, with an average interval size of 3.4 cM. The MG map is a cornerstone of the Korean Rice Genome Research Program (KRGRP) and is being continuously refined through the addition of partially sequenced cDNA markers derived from an immature-seed cDNA library developed in Korea, and microsatellite markers developed at Cornell. The population is also being used for quantitative trait locus (QTL) analysis and as the basis for marker-assisted variety development.
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  • 4
    ISSN: 1432-2242
    Keywords: Key words DNA polymorphisms ; Genetic distances ; Molecular markers ; Yield prediction ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The challenge to maize breeders is to identify inbred lines that produce highly heterotic hybrids. In the present study we surveyed genetic divergence among 13 inbred lines of maize using DNA markers and assessed the relationship between genetic distance and hybrid performance in a diallel set of crosses between them. The parental lines were assayed for DNA polymorphism using 135 restriction fragment length polymorphisms (RFLPs) and 209 amplified-fragment polymorphisms (AFLPs). Considerable variation among inbreds was detected with RFLP and AFLP markers. Moreover AFLPs detect polymorphisms more efficiently in comparison to RFLPs, due to the larger number of loci assayed in a single PCR reaction. Genetic distances (GDs), calculated from RFLP and AFLP data, were greater among lines belonging to different heterotic groups compared to those calculated from lines of the same heterotic group. Cluster analysis based on GDs revealed associations among lines which agree with expectations based on pedigree information. The GD values of the 78 F1 crosses were partioned into general (GGD) and specific (SGD) components. Correlations of GD with F1 performance for grain yield were positive but too small to be of predictive value. The correlations of SGDs, particularly those based on AFLP data, with specific combining-ability effects for yield may have a practical utility in predicting hybrid performance.
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  • 5
    ISSN: 1572-9788
    Keywords: AFLP® ; genetic diversity ; methylation AFLP® ; polymorphism information content ; maize
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract AFLP® markers generated by CNG methylation sensitive (PstI/MseI) and CNG methylation insensitive (EcoRI/MseI) enzyme combinations and AFLP markers collected from hypomethylated (PstI/MseI) and hypermethylated (m PstI/MseI) regions were compared for their polymorphism information content, sampling variance and patterns of genetic diversity in a representative sample of 33 inbred lines of maize (Zea mays L.). We demonstrate that the mean polymorphism information content generated by sets of PstI/MseI and m PstI/MseI markers (0.38) is significantly higher than by sets ofEcoRI/MseI markers (0.33). Also the sampling variance highlighted the distinctive nature of the (m) PstI/MseI markers: to achieve a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds, the PstI/MseI and m PstI/MseI marker sets (135 and 129 markers, respectively) are clearly smaller than the EcoRI/MseI marker set (173 markers). A further minimizing of the sampling variance of AFLP data in the estimation of genetic similarities was obtained by reducing marker information redundancy by selecting markers evenly distributed over each chromosome: a set of only 106 AFLP markers, sampled conditionally on their genetic map position, was required for a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds.
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  • 6
  • 7
    Publication Date: 2013-09-20
    Description: : Gene regulatory network assembly and analysis requires high-quality knowledge sources that cover functional aspects of the various components of the gene regulatory machinery. A multiplicity of resources exists with information about mammalian transcription factors (TFs); yet, only few of these provide sufficiently accurate classifications of the functional roles of individual TFs, or standardized evidence that would justify the information on which these functional classifications are based. We compiled the list of all putative TFs from nine different resources, ignored factors such as general TFs, mediator complexes and chromatin modifiers, and for the remaining factors checked the available literature for references that support their function as a true sequence-specific DNA-binding RNA polymerase II TF (DbTF). The results are available in the TFcheckpoint database, an exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. TFcheckpoint.org provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies. Availability: The TFcheckpoint database is freely available at www.tfcheckpoint.org Contact: martin.kuiper@ntnu.no Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2005-03-30
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2015-02-18
    Description: β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2014-02-26
    Description: Motivation: The comparison of genes and gene products across species depends on high-quality tools to determine the relationships between gene or protein sequences from various species. Although some excellent applications are available and widely used, their performance leaves room for improvement. Results: We developed orthAgogue: a multithreaded C application for high-speed estimation of homology relations in massive datasets, operated via a flexible and easy command-line interface. Availability: The orthAgogue software is distributed under the GNU license. The source code and binaries compiled for Linux are available at https://code.google.com/p/orthagogue/ . Contact: orthagogue-issue-tracker@googlegroups.com
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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