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Biomedical subjects

P B Cregan

Publications and source records attributed to P B Cregan.

7 recordsLinked to original sources
PubMed2003

Assignment of molecular linkage groups to soybean chromosomes by primary trisomics.

Gene-linkage groups (classical linkage groups, CLGs; molecular linkage groups, MLGs) and chromosome relationship in soybean [ Glycine max (L.) Merr., 2n = 40] is not yet established. However, primary trisomics provide an invaluable cytogenetic tool to associate genes and linkage groups to specific chromosomes. We have assigned 11 MLGs to soybean chromosomes by using primary trisomics (2 x + 1 = 41) and SSR markers. Primary trisomics were hybridized with Glycine soja Sieb. and Zucc. (2n = 40) in the greenhouse, F(1) plants with 2n = 40 and 41 were identified cytologically and 41 chromosome plants were selfed. A deviation from the 1:2:1 ratio in the F(2) population suggests a marker is associated with a chromosome. Of the possible 220 combinations involving 20 MLGs and 11 primary trisomics, 151 combinations were examined. The relationships between soybean chromosomes and MLGs are: 1 = D1a+q, 3 = N, 5 = A1, 8 = A2, 9 = K, 13 = F, 14 = C1, 17 = D2, 18 = G, 19 = L and 20 = I. This study sets the stage to establish relationship between nine remaining MLGs with the other genetically unidentified nine primary trisomics. The association of CLGs with the soybean chromosomes will be discussed.

Chromosomes, Plant↗
PubMed2003

Single-nucleotide polymorphisms in soybean.

Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

DNA Primers↗
PubMed1995

The analysis of simple sequence repeat DNA in soybean by Capillary Gel Electrophoresis.

The objective of this work is to examine the presence of simple sequence repeat (SSR) DNA in soybean plant genotypes by Capillary Gel Electrophoresis (CGE). The SSR DNA length polymorphism in soybean determines the variation in polymerase chain reaction (PCR) product lengths. Loci were chosen where amplification produced one PCR product per genotype (M.S. Akkaya et al., 1992). The F1 hybrids of parents carrying different alleles produced two PCR products identical to the two parents. The CGE system used a 3%T,3%C polyacrylamide gel capillary with an effective length of 40 cm. The PCR products with lengths of 150 to 200 base pairs were monitored at 260 nm. The analysis time was under 50 minutes. CGE is capable of separating these PCR products by base pair number the same as conventional sequencing gel techniques. CGE offers an automated, high speed, high resolution analytical method for determining soybean SSR allele sizes as compared with the traditional methodologies.

Autoanalysis↗
PubMed1992

Length polymorphisms of simple sequence repeat DNA in soybean.

The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.

Base Sequence↗
PubMed1992

Hyperreiterated DNA regions are conserved among Bradyrhizobium japonicum serocluster 123 strains.

We have identified and cloned two DNA regions which are highly reiterated in Bradyrhizobium japonicum serocluster 123 strains. While one of the reiterated DNA regions, pFR2503, is closely linked to the B. japonicum common and genotype-specific nodulation genes in strain USDA 424, the other, pMAP9, is located next to a Tn5 insertion site in a host-range extension mutant of B. japonicum USDA 438. The DNA cloned in pFR2503 and pMAP9 are reiterated 18 to 21 times, respectively, in the genomes of B. japonicum serocluster 123 strains. Gene probes from the reiterated regions share sequence homology, failed to hybridize (or hybridized poorly) to genomic DNA from other B. japonicum and Bradyrhizobium spp. strains, and did not hybridize to DNA from Rhizobium meliloti, Rhizobium fredii, Rhizobium leguminosarum biovars trifolii, phaseoli, and viceae, or Agrobacterium tumefacians. The restriction fragment length polymorphism hybridization profiles obtained by using these gene probes are useful for discriminating among serologically related B. japonicum serocluster 123 strains.

Chromosome Mapping↗
PubMed1991

The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans.

Several soybean genotypes have been identified which specifically exclude nodulation by members of Bradyrhizobium japonicum serocluster 123. We have identified and sequenced a DNA region from B. japonicum strain USDA 110 which is involved in genotype-specific nodulation of soybeans. This 2.3-kilobase region, cloned in pMJS12, allows B. japonicum serocluster 123 isolates to form nodules on plants of serogroup 123-restricting genotypes. The nodules, however, were ineffective for symbiotic nitrogen fixation. The nodulation-complementing region is located approximately 590 base pairs transcriptionally downstream from nodD2. The 5' end of pMJS12 contains a putative open reading frame (ORF) of 710 base pairs, termed nolA. Transposon Tn3-HoHo mutations only within the ORF abolished nodulation complementation. The N terminus of the predicted nolA gene product has strong similarity with the N terminus of MerR, the regulator of mercury resistance genes. Translational lacZ fusion experiments indicated that nolA was moderately induced by soybean seed extract and the isoflavone genistein. Restriction fragments that hybridize to pMJS12 were detected in genomic DNAs from both nodulation-restricted and -unrestricted strains.

Amino Acid Sequence↗