Transpecific microsatellites for hard pines

Theoretical and Applied Genetics, 2004

Biologia, 2013

Background: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results: The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions: Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda.

Genome, 1997

2001

The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold. Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10-25 million of years. Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (FST = 0.02). O...

PLOS ONE, 2018

Tree Genetics & Genomes, 2011

Canadian Journal of Forest Research, 1999

Analysis, 2023

Our gender identity is our sense of ourselves as a woman, a man, as genderqueer, or as another gender. Our gender is the property we have of being a woman, being a man, being non-binary, or being another gender. What is the relationship between our gender identity and our gender? Recently, much work has been done on ameliorative accounts of the gender concepts that we should accept and on the metaphysics of gender properties. From this work 4 views of the relationship between having gender identity G (e.g. having a female gender identity) and being a gender G (e.g. being a woman) have emerged. A first, the no connection view, says that gender identity and gender are entirely distinct; Sally Haslanger’s ameliorative account of gender, as well as Theodore Bach’s account of gender properties, are instances of this view. A second, the gender-identity-first view, says that all there is to our gender is our gender identity; this view is at least similar to views that Talia Bettcher and R.A. Briggs and B.R. George have argued for. A third, contextualist view, says that in some contexts and relative to certain standards, our gender identity determines our gender, and that in others it does not; Ásta and Robin Dembroff have proposed and defended views along these lines. A fourth view, the two gender properties view, says that there are two properties that can make it the case that one is gender G (in any context), one’s having gender identity G and one’s being socially classed as a G; Katharine Jenkins and Elizabeth Barnes have proposed views along these lines. This article explains these 4 different views and spells out their prospects, and the problems they face, as both ameliorative and as metaphysical views.