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  • 1
    Electronic Resource
    Electronic Resource
    Characterization and application of soybean YACs to molecular cytogenetics (1996)
    Springer
    Molecular genetics and genomics 252 (1996), S. 483-488 
    Details
    ISSN: 1617-4623
    Keywords: Degenerate oligonucleotide-primed PCR (DOP-PCR) ; Fluorescence in situ hybridization ; Glycine max ; Yeast artificial chromosomes ; Soybean
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Yeast artificial chromosomes (YACs) are widely used in the physical analysis of complex genomes. In addition to their value in chromosome walking for map-based cloning, YACs represent excellent probes for chromosome mapping using fluorescence in situ hybridization (FISH). We have screened such a library for low-copy-number clones by hybridization to total genomic DNA. Four clones were chosen for chromosome tagging based upon their low or moderate signal. By using degenerate oligonucleotide-primed PCR (DOP-PCR), we were able to use relatively small amounts of soybean YAC DNA, isolated directly by preparative pulsed-field gel electrophoresis, as FISH probes for both metaphase chromosome spreads and interphase nuclei. FISH chromosomal analysis using the three of the clones as probes resulted in relatively simple hybridization patterns consistent with a single homologous locus or two homoeologous loci. The fourth YAC probe resulted in a diffuse hybridization pattern with signal on all metaphase chromosomes. We conclude that YACs represent a valuable source of probes for chromosomal analysis in soybean.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02173014
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  • 2
    Electronic Resource
    Electronic Resource
    Characterization and application of soybean YACs to molecular cytogenetics (1996)
    Springer
    Molecular genetics and genomics 252 (1996), S. 483-488 
    Details
    ISSN: 1617-4623
    Keywords: Key words Degenerate oligonucleotide-primed PCR(DOP-PCR) ; Fluorescence in situ hybridization ; Glycine max ; Yeast artificial chromosomes ; Soybean
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Yeast artificial chromosomes (YACs) are widely used in the physical analysis of complex genomes. In addition to their value in chromosome walking for map-based cloning, YACs represent excellent probes for chromosome mapping using fluorescence in situ hybridization (FISH). We have screened such a library for low-copy-number clones by hybridization to total genomic DNA. Four clones were chosen for chromosome tagging based upon their low or moderate signal. By using degenerate oligonucleotide-primed PCR (DOP-PCR), we were able to use relatively small amounts of soybean YAC DNA, isolated directly by preparative pulsed-field gel electrophoresis, as FISH probes for both metaphase chromosome spreads and interphase nuclei. FISH chromosomal analysis using the three of the clones as probes resulted in relatively simple hybridization patterns consistent with a single homologous locus or two homoeologous loci. The fourth YAC probe resulted in a diffuse hybridization pattern with signal on all metaphase chromosomes. We conclude that YACs represent a valuable source of probes for chromosomal analysis in soybean.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02173014
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  • 3
    Electronic Resource
    Electronic Resource
    A single nuclear locus phylogeny of soybean based on DNA sequence (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 991-999 
    Details
    ISSN: 1432-2242
    Keywords: Glycininae ; Soybean ; Phylogeny ; DNA sequence ; Genomic donors ; Glycine ; Phaseoleae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222912
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  • 4
    Electronic Resource
    Electronic Resource
    Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides (2000)
    Springer
    Genetica 110 (2000), S. 219-226 
    Details
    ISSN: 1573-6857
    Keywords: birds ; sequence tagged sites ; single nucleotide polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1012772831699
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  • 5
    Electronic Resource
    Electronic Resource
    Comparative DNA sequence analysis of genetic variation in the African grey parrot, Psittacus erythacus (2000)
    Springer
    Genetica 110 (2000), S. 227-230 
    Details
    ISSN: 1573-6857
    Keywords: African grey parrot ; sequence tagged sites ; single nucleotide polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Comparative genome analysis promises to provide an insight into avian species that have been very little studied. To test the feasibility of this approach, we investigated the use of heterologous primers to generate single nucleotide polymorphisms (SNP) in the African grey parrot, Psittacus erythacus, using primers specific for chicken and turkey DNA fragments. Three of the primers were specific for three expressed sequence tagged sites in the turkey and the fourth for a chicken proteoglycan core protein-like DNA sequence. A total of about 2200 bp of the parrot genome was evaluated for DNA sequence variation. Seven SNPs were identified and confirmed by Mendelian segregation. The frequency distribution of the most common nucleotide at each SNP locus in an unrelated group of parrots ranged from 0.84 to 0.97. The percent similarity of each parrot sequence to the reference sequence was inconsistent and ranged from zero to 100%. The primers as well as the nucleotide variants described represent valuable resources for genetic analysis in the parrot.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1012738632608
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