Occurrence and inheritance of microsatellites in Pinus radiata

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 977-983 ◽  
Author(s):  
David N. Smith ◽  
Michael E. Devey
Keyword(s):  
Pinus Radiata ◽  
Population Genetic ◽  
Dna Marker ◽  
Genomic Library ◽  
Mendelian Inheritance ◽  
Dinucleotide Repeats ◽  
Sequence Tagged Sites ◽  
Pcr Products ◽  
Conifer Genome ◽  
Highly Repetitive Dna

Microsatellites are an important class of DNA marker because of their abundance and length hypervariability. As part of a project mapping the Pinus radiata genome, we have characterized some of the microsatellites in this species. Southern blots were screened with oligonucleotide probes [(CA)10, (GA)10, (GAA)9, (CAA)8, (CAC)5, (GACA)4] to assess their abundance. CA and GA were the most abundant microsatellites, while GAA was least abundant. A genomic library in lambda ZAP, covering 9 × 104 kb, was screened with a combined poly(CA) + poly(GA) probe and yielded 120 positives, approximately one CA or GA microsatellite every 750 kb of the P. radiata genome. It was found that 25% of the positives were embedded within highly repetitive DNA. Four of the five subclones sequenced contained compound microsatellites, with TA predominating as the additional repeat. Segregation analysis of PCR products for two microsatellites, PR4.6 and PR9.3, in 96 progeny of a controlled out-cross verified simple Mendelian inheritance. Both loci are highly polymorphic with Polymorphism Information Content values of 0.63 and 0.70 for PR4.6 and PR9.3, respectively. These results indicate that microsatellites are abundant in a conifer genome and can be valuable markers for pine mapping, fingerprinting, and population genetic studies.Key words: microsatellites, dinucleotide repeats, conifer genome, sequence tagged sites.

Generation of sequence-tagged sites from Xp22.3 by isolating commonAlu-PCR products of radiation hybrids retaining overlapping human X chromosome fragments

1996 ◽  
Vol 97 (5) ◽  
pp. 604-610 ◽  
Author(s):  
I. A. Glass ◽  
M. Passage ◽  
L. Bernatowicz ◽  
E. C. Salido ◽  
T. Mohandas ◽  
...  
Keyword(s):  
X Chromosome ◽  
Sequence Tagged Sites ◽  
Radiation Hybrids ◽  
Pcr Products ◽  
Chromosome Fragments

Two different thymidylate kinase gene homologues, including one that has catalytic activity, are encoded in the onion yellows phytoplasma genome

Microbiology ◽  
2003 ◽  
Vol 149 (8) ◽  
pp. 2243-2250 ◽  
Author(s):  
Shin-ichi Miyata ◽  
Kenro Oshima ◽  
Shigeyuki Kakizawa ◽  
Hisashi Nishigawa ◽  
Hee-Young Jung ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Genomic Library ◽  
De Novo ◽  
Bacterial Species ◽  
Point Mutations ◽  
Kinase Gene ◽  
Thymidylate Kinase ◽  
Pcr Products ◽  
Multiple Copies ◽  
Salvage Pathways

Thymidylate kinase (TMK) catalyses the phosphorylation of dTMP to form dTDP in both the de novo and salvage pathways of dTTP synthesis in both prokaryotes and eukaryotes. Two homologues of bacterial thymidylate kinase genes were identified in a genomic library of the onion yellows (OY) phytoplasma, a plant pathogen that inhabits both plant phloem and the organs of insects. Southern blotting analysis suggested that the OY genome contained one copy of the tmk-b gene and multiple copies of the tmk-a gene. Sequencing of PCR products generated by amplification of tmk-a enabled identification of three other copies of tmk-a, although the ORF in each of these was interrupted by point mutations. The proteins, TMK-a and TMK-b, encoded by the two intact genes contained conserved motifs for catalytic activity. Both proteins were overexpressed as fusion proteins with a polyhistidine tag in Escherichia coli and purified, and TMK-b was shown to have thymidylate kinase activity. This is believed to be the first report of the catalytic activity of a phytoplasmal protein, and the OY phytoplasma is the first bacterial species to be found to have two intact homologues of tmk in its genome.

scholarly journals Population Genetic Analysis of the Protease Locus of Human Immunodeficiency Virus Type 1 Quasispecies Undergoing Drug Selection, Using a Denaturing Gradient-Heteroduplex Tracking Assay

2001 ◽  
Vol 75 (14) ◽  
pp. 6729-6736 ◽  
Author(s):  
Laurence Doukhan ◽  
Eric Delwart
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Population Genetic ◽  
Protease Gene ◽  
Plasma Viremia ◽  
Viral Quasispecies ◽  
Immunodeficiency Virus ◽  
Pcr Products ◽  
Hiv 1

ABSTRACT Monitoring the evolution of human immunodeficiency virus type 1 (HIV-1) drug resistance requires measuring the frequency of closely related genetic variants making up the complex viral quasispecies found in vivo. In order to resolve both major and minor (≥2%) protease gene variants differing by one or more nucleotide substitutions, we analyzed PCR products derived from plasma viral quasispecies by using a combination of denaturing gradient gel electrophoresis and DNA heteroduplex tracking assays. Correct population sampling of the high level of genetic diversity present within viral quasispecies could be documented by parallel analysis of duplicate, independently generated PCR products. The composition of genetically complex protease gene quasispecies remained constant over short periods of time in the absence of treatment and while plasma viremia fell >100-fold following the initiation of protease inhibitor ritonavir monotherapy. Within a month of initiating therapy, a strong reduction in the genetic diversity of plasma viral populations at the selected protease locus was associated with rising plasma viremia and the emergence of drug resistance. The high levels of protease genetic diversity seen before treatment reemerged only months later. In one patient, reduction in genetic diversity at the protease gene was observed concomitantly with an increase in diversity at the envelope gene (E. L. Delwart, P. Heng, A. Neumann, and M. Markowitz, J. Virol. 72:2416-2421, 1998), indicating that opposite population genetic changes can take place in different HIV-1 loci. The rapid emergence of drug-resistant HIV-1 was therefore associated with a strong, although only transient, reduction in genetic diversity at the selected locus. The denaturing gradient-heteroduplex tracking assay is a simple method for the separation and quantitation of very closely related, low-frequency, genetic variants within complex viral populations.

Low-copy microsatellite markers for Pinus taeda L.

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 550-555 ◽  
Author(s):  
Christine G Elsik ◽  
Virginia T Minihan ◽  
Sarah E Hall ◽  
Ann M Scarpa ◽  
Claire G Williams
Keyword(s):  
Microsatellite Markers ◽  
Pinus Taeda ◽  
Loblolly Pine ◽  
Trinucleotide Repeat ◽  
Polymorphic Information Content ◽  
Mendelian Inheritance ◽  
Multiple Alleles ◽  
Pcr Products ◽  
Pinus Taeda L ◽  
Specific Priming

Eighteen low-copy and genomic microsatellite markers were tested for Mendelian inheritance and then assayed in 41 Pinus taeda L. samples drawn from five regions in the southern United States. The PCR products had multiple alleles, high levels of polymorphism, and little non-specific priming. Fifteen of the 18 markers were informative for a P. taeda three-generation RFLP (restriction fragment length polymorphism) pedigree, and a P. taeda population survey revealed three to 28 alleles per locus. The highest allele numbers and polymorphic information content (PIC) values were associated with complex repeat sequences and (or) with sequences consisting of the longer strings of perfect repeats. The abundance of low- to rare-frequency alleles also accounted for high PIC values in both types of markers. Low-copy microsatellites are useful for the large, complex pine genome, especially in the absence of entire gene sequences in public databases and with the low levels of polymorphism in markers developed from expressed sequence tags (ESTs).Key words: loblolly pine, conifers, gymnosperms, trinucleotide repeat motifs.

Highly polymorphic microsatellite markers in Chamaecyparis obtusa

2001 ◽  
Vol 31 (12) ◽  
pp. 2248-2251 ◽  
Author(s):  
Y Nakao ◽  
H Iwata ◽  
A Matsumoto ◽  
Y Tsumura ◽  
N Tomaru
Keyword(s):  
Microsatellite Loci ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Chamaecyparis Obtusa ◽  
Mendelian Inheritance ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene

Nine microsatellite loci in hinoki, Chamaecyparis obtusa (Sieb. et Zucc.) Endl., were identified and characterized. A genomic library, developed using enrichment with magnetic beads, was screened to identify microsatellite repeats (CT/AG). The microsatellite loci, where the alleles were segregated, displayed codominant Mendelian inheritance. Genetic analysis of 16 plus trees and two unrelated individuals of Chamaecyparis obtusa revealed that all loci were highly polymorphic, with an average of 10.3 alleles per locus, and an average gene diversity of 0.77. The applicability of these microsatellite loci was also tested in other species of the Cupressaceae and in Cryptomeria japonica (L.f.) D. Don (Taxodiaceae, a family closely related to Cupressaceae). Polymerase chain reaction (PCR) amplification was successful for about half of the loci of the species in the genus Chamaecyparis. However, the PCR amplification patterns of the 11 species of Cupressaceae showed no clear correlations with their molecular phylogeny. The highly polymorphic microsatellite loci in Chamaecyparis obtusa, identified here, will be useful in studies of hinoki breeding and population genetics.

Benefit–cost analysis of DNA marker-based selection in progenies of Pinus radiata seed orchard parents

2001 ◽  
Vol 31 (12) ◽  
pp. 2213-2224 ◽  
Author(s):  
P.L. Wilcox ◽  
S.D. Carson ◽  
T.E. Richardson ◽  
R.D. Ball ◽  
G.P. Horgan ◽  
...  
Keyword(s):  
Cost Analysis ◽  
Pinus Radiata ◽  
Dna Marker ◽  
Seed Orchard ◽  
Benefit Cost Analysis ◽  
Benefit Cost

scholarly journals Survey of microsatellite DNA in pine

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 9-17 ◽  
Author(s):  
C. S. Echt ◽  
P. May-Marquardt
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Genomic Library ◽  
Pinus Strobus ◽  
White Pine ◽  
Eastern White Pine ◽  
Dinucleotide Repeats ◽  
Tetranucleotide Repeats ◽  
Nucleotide Repeats ◽  
Simple Sequence

A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC)n and (AG)n, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda) genomic library was also probed with the same set of di- and tri-nucleotide repeats and 11 of the tetranucleotide repeats. The four most abundant microsatellite motifs in both species were (AC)n, (AG)n, (AAT)n, and (ATC)n, which as a group accounted for over half the microsatellite sites investigated. The two dinucleotide repeats were the most abundant microsatellite motifs tested in both species, each at 2–4.5 sites/megabase pair (Mbp), but the two trinucleotide motifs were nearly as abundant and are considered good candidates for pine microsatellite marker development efforts. Eastern white pine had more than twice as many (AC)n as (AG)n loci, in contrast with loblolly pine and most other plant species in which (AG)n is more abundant. In both pine species the minimum estimated genome density for all microsatellites, excluding (AT)n repeats, was 16 sites/Mbp.Key words: Pinus strobus, Pinus taeda, eastern white pine, loblolly pine, simple sequence repeats.

Benefit–cost analysis of DNA marker-based selection in progenies of Pinus radiata seed orchard parents

2001 ◽  
Vol 31 (12) ◽  
pp. 2213-2224
Author(s):  
P L Wilcox ◽  
S D Carson ◽  
T E Richardson ◽  
R D Ball ◽  
G P Horgan ◽  
...  
Keyword(s):  
Pinus Radiata ◽  
Dna Marker ◽  
Seed Orchard ◽  
Qtl Detection ◽  
Family Selection ◽  
Benefit Cost Analysis ◽  
Genetic Gains ◽  
Marginal Costs ◽  
Structural Grade ◽  
Financial Gains

The financial viability of DNA marker-based within-family selection (MBS) compared with full-sib family forestry was evaluated for Pinus radiata Donn. ex D. Don. Two traits were investigated: wood density (WD) and diameter at breast height (DBH, 1.4 m). Assuming 20 biallelic loci of equal additive effect controlling trait variation in 15 unrelated top full-sib families of P. radiata, marginal costs of quantitative trait loci (QTL) detection and selection were estimated based on an average of slightly less than five loci per family. We assumed a program where 10 genotypes per family per year were deployed over a 5-year period, and each replicated 100 000 times via fascicle cuttings methods. Estimated marginal costs were NZ$32 and NZ$72 per 1000 plants for WD and DBH, respectively. Genotyping costs were the single largest component for both traits. Genetic gains were estimated by modifying predicted log volumes (DBH) or proportion of structural-grade timber (WD) with and without pruning. Estimated genetic gains ranged from 3.2 to 3.4%. Net present values (assuming a 9.5% discount rate) ranged from an average of NZ$51 to NZ$621/ha. Results showed that MBS for DBH was more profitable than for WD, despite markedly higher costs of QTL detection. All trait-silviculture combinations showed financial gains with internal rates of return of 9% or greater, even when estimated revenues were decreased 70% from forecast revenues. While this analysis is based on a large number of assumptions, it is robust and the results show that significant financial gains from MBS are possible even when selection is based upon DNA markers linked to a few loci each of relatively small effect.

Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 367-373 ◽  
Author(s):  
Kristina M Sefc ◽  
Ferdinand Regner ◽  
Eva Turetschek ◽  
Josef Glössl ◽  
Herta Steinkellner
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Library ◽  
Mendelian Inheritance ◽  
Null Alleles ◽  
Flanking Sequence ◽  
Vitis Species ◽  
Vitis Riparia ◽  
Expected Heterozygosity ◽  
And Performance ◽  
Simple Sequence

A Vitis riparia genomic library was screened for the presence of (GA)n simple sequence repeats (SSR) and 18 primer pairs yielding amplification products of the expected size were designed. Heterologous amplification with the primer pairs in related species (V. rupestris, V. berlandieri, V. labrusca, V. cinerea, V. aestivalis, V. vinifera, and interspecific hybrids) was successful in most primer-species combinations. Therefore, the new markers are applicable to the genotyping of a range of Vitis species. Variations in the SSR flanking sequence were detected between and within the species. The degree of polymorphism and performance of the markers were determined in up to 120 individuals of V. vinifera. Four of fifteen alleles per locus were detected and expected heterozygosity ranged between 0.37 and 0.88. Null alleles were shown to be present at two loci by a lack of heterozygous individuals and by transmission of the null alleles in a controlled cross. Regular Mendelian inheritance is indicated for all but one loci by a preliminary segregation analysis in 36 offspring. Thirteen of the markers were found suitable for the genotyping of grapevines (V. vinifera).Key words: microsatellites, simple sequence repeats, Vitis.

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