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G A Tuskan

Publications and source records attributed to G A Tuskan.

8 recordsLinked to original sources
PubMed2006

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Arabidopsis↗
PubMed2004

Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map.

We report the most complete genetic map to have been constructed for the genus Populus. This map includes 544 markers mapped onto 19 linkage groups, equivalent to the Populus chromosome number, with all markers displaying internally consistent linkage patterns. We estimate the genome length to be between 2,300 and 2,500 cM, based both on the observed number of crossovers in the maternal haplotypes, as well as the total observed map length. Genome coverage was estimated to be greater than 99.9% at 20 cM per marker. We did not detect obvious recombination repression in the maternal tree (a hybrid of Populus trichocarpa Hooker x P. deltoides Marsh.) compared to the paternal tree (pure P. deltoides). Finally, most markers exhibiting segregation distortion were derived from the donor parent in this backcross, and generally occurred in large contiguous blocks on two linkage groups. We hypothesize that divergent selection has occurred on chromosomal scales among the parental species used to create this pedigree, and explore the evolutionary implications of this observation. This genetic linkage map provides the most comprehensive view of the Populus genome reported to date and will prove invaluable for future inquiries into the structural and functional genomics, evolutionary biology, and genetic improvement of this ecologically important model species.

Chromosome Mapping↗
PubMed2003

Highly variable SSR markers in Douglas-fir: Mendelian inheritance and map locations.

Twenty-two highly variable SSR markers were developed in Douglas-fir [ Pseudotsuga menziesii (Mirb.) Franco] from five SSR-enriched genomic libraries. Fifteen PCR primer pairs amplified a single codominant locus, while seven primer pairs occasionally amplified two loci. The Mendelian inheritance of all 22 SSRs was confirmed via segregation analyses in several Douglas-fir families. The mean observed heterozygosity and the mean number of alleles per locus were 0.855 (SE=0.020) and 23 (SE=1.6), respectively. Twenty markers were used in genetic linkage analysis and mapped to ten known linkage groups. Because of their high polymorphism and unambiguous phenotypes, 15 single-locus markers were selected as the most suitable for DNA fingerprinting and parentage analysis. Only three SSRs were sufficient to achieve an average probability of exclusion from paternity of 0.998 in a Douglas-fir seed orchard block consisting of 59 parents.

Base Sequence↗
PubMed2002

Genomics and the tree physiologist.

During the last decade, a strong case has been made for viewing trees as model systems in plant biology. More recently, forest biologists have argued for the sequencing of the genome of a forest tree. Now, the United States Department of Energy has announced plans for sequencing the genome of the Populus trichocarpa clone, "Nisqually-1." Thus, forest biology is poised to enter an exciting period of scientific discovery. Embracing new technology and new research paradigms, however, is never easy. It is, therefore, timely to ask how tree physiologists will take advantage of the Populus genome data. We contend that the most attractive opportunities will arise through genome-wide research designed to: (1). examine the differences between trees and herbaceous annuals; (2). explore questions relating to the temporal and spatial scales that characterize the life histories and growth of trees; and (3). investigate cause-and-effect relationships that are intractable to conventional research methodologies. To highlight the potential applications of genomics in tree physiology, we briefly discuss each of these approaches.

Genome, Plant↗
PubMedDate not supplied

Poplar genomics is getting popular: the impact of the poplar genome project on tree research.

Trees, due to their long life-span, have characteristics that distinguish them from annual, herbaceous plants. It is likely that many of these properties are based on a tree-specific genetic foundation. The U.S. Department of Energy initiated a genome-sequencing project for Populus, a model perennial plant. Through international collaboration and input to the sequencing effort, the annotated whole genome sequence of Populus trichocarpa will be released to the public in early 2004. This genomic resource will, for the first time, allow comparison between a perennial and an annual plant on a whole genome basis and therefore provide clues for molecular research on tree-specific questions like dormancy, development of a secondary cambium, juvenile-mature phase change, or long-term host-pest interactions. The approximately 520 Mbp of annotated genomic sequence will complement and expand the knowledge provided so far by the 125,000 ESTs from poplar that are available in public databases. This article introduces the international poplar research programmes and points out the significance of the poplar genome project for plant research.

Databases, Genetic↗
PubMedDate not supplied

The development of two flanking SCAR markers linked to a sex determination locus in Salix viminalis L.

Most studies of sex determination systems in plants involve dioecious annuals that have known sex chromosomes. Despite the absence of such structures in the majority of dioecious plants, gender seems to be under relatively strict genetic control in some species. Genetic markers linked to a female sex-determination locus in Salix viminalis L. have been discovered through bulked segregant analysis of three full-sib families using approximately 1,000 arbitrary primers. Two RAPD markers that were present in the common female parent as well as in predominantly female progeny of these families were subsequently sequenced and converted to sequence characterized amplified region (SCAR) markers. The two SCAR markers are correlated with gender in the three full-sib families and are present in 96.4% of the female progeny and 2.2% of the males, providing evidence of linkage to a putative female-specific locus associated with gender determination in S. viminalis. Estimates of recombination suggest that the two markers are flanking a putative sex determination locus, SDL-II, in certain families of S. viminalis.

Genetic Markers↗