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Jean Bousquet - One of the best experts on this subject based on the ideXlab platform.
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cross species amplification of mitochondrial dna Sequence Tagged Site markers in conifers the nature of polymorphism and variation within and among species in picea
Theoretical and Applied Genetics, 2003Co-Authors: Juan P Jaramillocorrea, Nathalie Isabel, Jean Bousquet, Martin Perron, Jean Beaulieu, Marie BouilleAbstract:Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect Sequence-Tagged-Site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others (nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L-orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L-orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.
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genetic diversity and mating system of post fire and post harvest black spruce an investigation using codominant Sequence Tagged Site sts markers
Canadian Journal of Forest Research, 2001Co-Authors: Daniel J Perry, Jean BousquetAbstract:cDNA-based Sequence-Tagged-Site (STS) markers were used to examine the genetic composition of three mature, layer-origin populations of black spruce (Picea mariana (Mill.) BSP), which were the resu...
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evidence from Sequence Tagged Site markers of a recent progenitor derivative species pair in conifers
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Martin Perron, Daniel J Perry, Christophe Andalo, Jean BousquetAbstract:Abstract Black spruce (Picea mariana [B.S.P.] Mill.) and red spruce (Picea rubens Sarg.) are two conifer species known to hybridize naturally in northeastern North America. We hypothesized that there is a progenitor-derivative relationship between these two taxa and conducted a genetic investigation by using Sequence-Tagged-Site markers of expressed genes. Based on the 26 Sequence-Tagged-Site loci assayed in this study, the unbiased genetic identity between the two taxa was quite high with a value of 0.920. The mean number of polymorphic loci, the mean number of alleles per polymorphic locus, and the average observed heterozygosity were lower in red spruce (P = 35%, AP = 2.1, Ho = 0.069) than in black spruce (P = 54%, AP = 2.9, Ho = 0.103). No unique alleles were found in red spruce, and the observed patterns of allele distribution indicated that the genetic diversity of red spruce was essentially a subset of that found in black spruce. When considered in combination with ecological evidence and simulation results, these observations clearly support the existence of a progenitor-derivative relationship and suggest that the reduced level of genetic diversity in red spruce may result from allopatric speciation through glaciation-induced isolation of a preexisting black spruce population during the Pleistocene era. Our observations signal a need for a thorough reexamination of several conifer species complexes in which natural hybridization is known to occur.
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Sequence Tagged Site sts markers of arbitrary genes the amount and nature of variation revealed in norway spruce
Heredity, 1999Co-Authors: Daniel J Perry, Nathalie Isabel, Jean BousquetAbstract:We examined the amount and nature of variation revealed by cDNA-based Sequence-Tagged-Site (STS) markers in Norway spruce (Picea abies (L.) Karst.) using 39 pairs of heterologous primers that were based upon arbitrary genes in black spruce (Picea mariana (Mill.) B.S.P.). A panel of 22 diverse Norway spruce genotypes was screened for variation that could be observed directly using standard agarose gel electrophoresis, without additional manipulation of amplification products. Examination of marker segregation among haploid megagametophytes revealed that nine markers behaved in a codominant manner, two markers had codominant length polymorphisms and null alleles, and four others had dominant length polymorphisms. DNA sequencing of codominant alleles at seven loci indicated that most insertions/deletions (indels) were in noncoding regions and that alleles often differed by the presence or absence of direct repeats that ranged in size from three to 23 bp. The nine markers that showed exclusively codominant polymorphisms in Norway spruce had an average observed heterozygosity of 0.30 and an average of 2.9 alleles in the panel of 22 trees. These levels of variation are similar to those previously found for similar sets of markers in other spruces, and appear to be at least as high as those revealed by polymorphic allozyme markers in Norway spruce. Polymorphisms at one STS locus suggested a higher affinity between Norway spruce and white spruce (Picea glauca (Moench) Voss) than between either of these spruces and black spruce. The STS markers described in this report should be useful in a variety of applications in Norway spruce, including population studies and genome mapping.
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Sequence Tagged Site sts markers of arbitrary genes the utility of black spruce derived sts primers in other conifers
Theoretical and Applied Genetics, 1998Co-Authors: Daniel J Perry, Jean BousquetAbstract:Sequence-Tagged-Site primers, previously developed based upon black spruce (Picea mariana) cDNA Sequences, were tested for their ability to direct specific amplification in two individuals of each of 12 additional conifer species. Nearly all (95–97%) of the primers functioned well in congeneric trials, while a lower proportion (21–33%) scored positively in other Pinaceae genera. Outside of the Pinaceae, amplification of homologous products was not achieved. Products from the various species often differed in size from their homologs in black spruce. In one case a large difference in size was due to the lack of an intron in a jack pine product while in several other cases the differences were due to the presence or absence of large direct repeats in the DNA Sequences. Length polymorphism was occasionally evident between the two individuals examined of a given species. We investigated marker polymorphism in detail in a panel of 15 white spruce (Picea glauca) trees. Allelic segregation among haploid megagametophytes was revealed directly at 16 loci by standard agarose-gel electrophoresis without any additional manipulation of amplification products. Polymorphisms observed at 12 of these loci were exclusively co-dominant. For this subset of 12 loci, the average number of alleles was 3.2 and the average observed heterozygosity was 0.37.
Daniel J Perry - One of the best experts on this subject based on the ideXlab platform.
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genetic diversity and mating system of post fire and post harvest black spruce an investigation using codominant Sequence Tagged Site sts markers
Canadian Journal of Forest Research, 2001Co-Authors: Daniel J Perry, Jean BousquetAbstract:cDNA-based Sequence-Tagged-Site (STS) markers were used to examine the genetic composition of three mature, layer-origin populations of black spruce (Picea mariana (Mill.) BSP), which were the resu...
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evidence from Sequence Tagged Site markers of a recent progenitor derivative species pair in conifers
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Martin Perron, Daniel J Perry, Christophe Andalo, Jean BousquetAbstract:Abstract Black spruce (Picea mariana [B.S.P.] Mill.) and red spruce (Picea rubens Sarg.) are two conifer species known to hybridize naturally in northeastern North America. We hypothesized that there is a progenitor-derivative relationship between these two taxa and conducted a genetic investigation by using Sequence-Tagged-Site markers of expressed genes. Based on the 26 Sequence-Tagged-Site loci assayed in this study, the unbiased genetic identity between the two taxa was quite high with a value of 0.920. The mean number of polymorphic loci, the mean number of alleles per polymorphic locus, and the average observed heterozygosity were lower in red spruce (P = 35%, AP = 2.1, Ho = 0.069) than in black spruce (P = 54%, AP = 2.9, Ho = 0.103). No unique alleles were found in red spruce, and the observed patterns of allele distribution indicated that the genetic diversity of red spruce was essentially a subset of that found in black spruce. When considered in combination with ecological evidence and simulation results, these observations clearly support the existence of a progenitor-derivative relationship and suggest that the reduced level of genetic diversity in red spruce may result from allopatric speciation through glaciation-induced isolation of a preexisting black spruce population during the Pleistocene era. Our observations signal a need for a thorough reexamination of several conifer species complexes in which natural hybridization is known to occur.
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Sequence Tagged Site sts markers of arbitrary genes the amount and nature of variation revealed in norway spruce
Heredity, 1999Co-Authors: Daniel J Perry, Nathalie Isabel, Jean BousquetAbstract:We examined the amount and nature of variation revealed by cDNA-based Sequence-Tagged-Site (STS) markers in Norway spruce (Picea abies (L.) Karst.) using 39 pairs of heterologous primers that were based upon arbitrary genes in black spruce (Picea mariana (Mill.) B.S.P.). A panel of 22 diverse Norway spruce genotypes was screened for variation that could be observed directly using standard agarose gel electrophoresis, without additional manipulation of amplification products. Examination of marker segregation among haploid megagametophytes revealed that nine markers behaved in a codominant manner, two markers had codominant length polymorphisms and null alleles, and four others had dominant length polymorphisms. DNA sequencing of codominant alleles at seven loci indicated that most insertions/deletions (indels) were in noncoding regions and that alleles often differed by the presence or absence of direct repeats that ranged in size from three to 23 bp. The nine markers that showed exclusively codominant polymorphisms in Norway spruce had an average observed heterozygosity of 0.30 and an average of 2.9 alleles in the panel of 22 trees. These levels of variation are similar to those previously found for similar sets of markers in other spruces, and appear to be at least as high as those revealed by polymorphic allozyme markers in Norway spruce. Polymorphisms at one STS locus suggested a higher affinity between Norway spruce and white spruce (Picea glauca (Moench) Voss) than between either of these spruces and black spruce. The STS markers described in this report should be useful in a variety of applications in Norway spruce, including population studies and genome mapping.
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Sequence Tagged Site sts markers of arbitrary genes the utility of black spruce derived sts primers in other conifers
Theoretical and Applied Genetics, 1998Co-Authors: Daniel J Perry, Jean BousquetAbstract:Sequence-Tagged-Site primers, previously developed based upon black spruce (Picea mariana) cDNA Sequences, were tested for their ability to direct specific amplification in two individuals of each of 12 additional conifer species. Nearly all (95–97%) of the primers functioned well in congeneric trials, while a lower proportion (21–33%) scored positively in other Pinaceae genera. Outside of the Pinaceae, amplification of homologous products was not achieved. Products from the various species often differed in size from their homologs in black spruce. In one case a large difference in size was due to the lack of an intron in a jack pine product while in several other cases the differences were due to the presence or absence of large direct repeats in the DNA Sequences. Length polymorphism was occasionally evident between the two individuals examined of a given species. We investigated marker polymorphism in detail in a panel of 15 white spruce (Picea glauca) trees. Allelic segregation among haploid megagametophytes was revealed directly at 16 loci by standard agarose-gel electrophoresis without any additional manipulation of amplification products. Polymorphisms observed at 12 of these loci were exclusively co-dominant. For this subset of 12 loci, the average number of alleles was 3.2 and the average observed heterozygosity was 0.37.
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Sequence Tagged Site sts markers of arbitrary genes development characterization and analysis of linkage in black spruce
Genetics, 1998Co-Authors: Daniel J Perry, Jean BousquetAbstract:Sequence-Tagged-Site (STS) markers of arbitrary genes were investigated in black spruce [Picea mariana (Mill.) B.S.P.]. Thirty-nine pairs of PCR primers were used to screen diverse panels of haploid and diploid DNAs for variation that could be detected by standard agarose gel electrophoresis without further manipulation of amplification products. Codominant length polymorphisms were revealed at 15 loci. Three of these loci also had null amplification alleles as did 3 other loci that had no apparent product-length variation. Dominant length polymorphisms were observed at 2 other loci. Alleles of codominant markers differed in size by as little as 1 bp to as much as an estimated 175 bp with nearly all insertions/deletions found in noncoding regions. Polymorphisms at 3 loci involved large (33 bp to at least 114 bp) direct repeats and similar repeats were found in 7 of 51 cDNAs Sequenced. Allelic segregation was in accordance with Mendelian inheritance and linkage was detected for 5 of 63 pairwise combinations of loci tested. Codominant STS markers of 12 loci revealed an average heterozygosity of 0.26 and an average of 2.8 alleles in a range-wide sample of 22 trees.
Alison Goate - One of the best experts on this subject based on the ideXlab platform.
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a yeast artificial chromosome contig from human chromosome 14q24 spanning the alzheimer s disease locus ad3
Human Molecular Genetics, 1995Co-Authors: Robert F Clark, Marc Cruts, Kevin M Korenblat, Conover C Talbot, C Van Broeckhoven, Alison GoateAbstract:Familial Alzheimer's disease has been previously linked to three genetic loci on chromosomes 21, 19 and 14. The AD3 locus on chromosome 14 has not been cloned and the molecular defect in chromosome 14-linked AD3 families has yet to be identified. Genetic linkage analysis has placed the AD3 locus in band 14q24 between the dinucleotide markers D14S61 and D14S289, a genetic distance of approximately 6.4 cM. We have constructed a yeast artificial chromosome (YAC) contig that covers the entire minimal region, encompassing all genetic markers that are non-recombinant for the disease in AD3-linked families. This contig, constructed by using a combination of YAC end Sequence walking and Sequence-Tagged Site (STS) mapping, consists of 63 YACs from three different libraries. The AD3 contig contains 12 polymorphic dinucleotide repeat markers from D14S61 to D14S251, as well as an additional 43 non-polymorphic STSs. This contiguous physical map of the region will allow the physical distances between the markers to be determined, as well as providing a framework for the identification of candidate genes.
Nathalie Isabel - One of the best experts on this subject based on the ideXlab platform.
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cross species amplification of mitochondrial dna Sequence Tagged Site markers in conifers the nature of polymorphism and variation within and among species in picea
Theoretical and Applied Genetics, 2003Co-Authors: Juan P Jaramillocorrea, Nathalie Isabel, Jean Bousquet, Martin Perron, Jean Beaulieu, Marie BouilleAbstract:Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect Sequence-Tagged-Site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others (nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L-orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L-orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.
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Sequence Tagged Site sts markers of arbitrary genes the amount and nature of variation revealed in norway spruce
Heredity, 1999Co-Authors: Daniel J Perry, Nathalie Isabel, Jean BousquetAbstract:We examined the amount and nature of variation revealed by cDNA-based Sequence-Tagged-Site (STS) markers in Norway spruce (Picea abies (L.) Karst.) using 39 pairs of heterologous primers that were based upon arbitrary genes in black spruce (Picea mariana (Mill.) B.S.P.). A panel of 22 diverse Norway spruce genotypes was screened for variation that could be observed directly using standard agarose gel electrophoresis, without additional manipulation of amplification products. Examination of marker segregation among haploid megagametophytes revealed that nine markers behaved in a codominant manner, two markers had codominant length polymorphisms and null alleles, and four others had dominant length polymorphisms. DNA sequencing of codominant alleles at seven loci indicated that most insertions/deletions (indels) were in noncoding regions and that alleles often differed by the presence or absence of direct repeats that ranged in size from three to 23 bp. The nine markers that showed exclusively codominant polymorphisms in Norway spruce had an average observed heterozygosity of 0.30 and an average of 2.9 alleles in the panel of 22 trees. These levels of variation are similar to those previously found for similar sets of markers in other spruces, and appear to be at least as high as those revealed by polymorphic allozyme markers in Norway spruce. Polymorphisms at one STS locus suggested a higher affinity between Norway spruce and white spruce (Picea glauca (Moench) Voss) than between either of these spruces and black spruce. The STS markers described in this report should be useful in a variety of applications in Norway spruce, including population studies and genome mapping.
Alain Bernheim - One of the best experts on this subject based on the ideXlab platform.
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construction of a yeast artificial chromosome contig spanning the pseudoautosomal region and isolation of 25 new Sequence Tagged Sites
Genomics, 1993Co-Authors: Rima Slim, Susan J Donohue, Liat Mintz, Jacqueline Levilliers, Sylvie Compain, Denis Le Paslier, David C Klein, P Ougen, Alain Billault, Alain BernheimAbstract:Thirty-one yeast artificial chromosomes (YACs) from the human pseudoautosomal region were identified by a combination of Sequence-Tagged Site (STS) screenings and colony hybridizations, using a subtelomeric interspersed repetitive element mapping predominantly to the pseudoautosomal region. Twenty-five new pseudoautosomal STSs were generated, of which 4 detected restriction fragment length polymorphisms. A total of 33 STSs were used to assemble the 31 YACs into a single contiguous set of overlapping DNA fragments spanning at least 2.3 megabases of the pseudoautosomal region. In addition, four pseudoautosomal genes including hydroxyindole O-methyltransferase have been positioned on this set of fragments. 48 refs., 1 fig., 3 tabs.
