Population dynamics of Pinus taeda L. based on nuclear microsatellites

Alrababah, Mohammad A.; Williams, Claire G.

doi:10.1016/s0378-1127(01)00584-9

Cited by 64 publications

(47 citation statements)

References 14 publications

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“…Indeed, using putatively neutral markers (21 nuSSRs) evenly distributed along most P. taeda linkage groups, we did not find any evidence of population structure, which confirms previous reports showing absence of population genetic structure within the eastern Mississippi Valley range of P. taeda (see, for instance, Al-Rabab'ah and Williams 2002). Despite the moderate level of LD and its rapid decay within genes, the use of htSNPs would reduce SNP genotyping effort by 30-40%, 50-100 SNPs being enough to represent common allelic variants in the sequenced candidate gene loci.…”

Section: Discussionsupporting

confidence: 90%

“…variation in forest trees is normally found within populations (see, for instance, Hamrick et al 1992). The extensive sampling of Florida, which is considered a putative Pleistocene glacial refugium of the species (Schmidtling et al 1999;Al-Rabab'ah and Williams 2002), resulted in only slightly higher nucleotide variation estimates than those in previous studies of the species ½average of 0.00604 vs. 0.00580, based on five gene fragments from our study, ccoaomt-1, pal-1, sams-2, ug_2-498, and lp3-1, that we also sequenced in Brown et al's (2004) set of samples, the difference not being significant (P ¼ 0.281) as shown by a pairwise signed rank test (n ¼ 5). Bottlenecks, as those that might have occurred in forest trees during Pleistocene range shifts, can generate substantial LD due to a reduction in population size with accompanying genetic drift (Flint-García et al 2003;Rafalski and Morgante 2004).…”

Section: Discussionmentioning

confidence: 99%

“…In this article, we used a data set of 21 nuclear microsatellites for detecting population structure and demographic processes that might cause spurious associations in association studies and bias neutrality tests, and sequenced all or portions of 18 candidate genes for drought-stress response in P. taeda, an important tree crop. Our sample covered the southeastern native range of P. taeda, including Florida, a putative Pleistocene glacial refugium of this species (Schmidtling et al 1999;Al-Rabab'ah and Williams 2002), which was not extensively sampled in our previous studies (see Brown et al 2004). We have used DNA sequences to estimate levels of nucleotide diversity and linkage disequilibrium, to identify candidate genes under selection (by means of neutrality tests), and to select haplotypetagging single-nucleotide polymorphisms (htSNPs) for our current genetic association studies.…”

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confidence: 99%

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DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.

et al. 2006

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Genetic association studies are rapidly becoming the experimental approach of choice to dissect complex traits, including tolerance to drought stress, which is the most common cause of mortality and yield losses in forest trees. Optimization of association mapping requires knowledge of the patterns of nucleotide diversity and linkage disequilibrium and the selection of suitable polymorphisms for genotyping. Moreover, standard neutrality tests applied to DNA sequence variation data can be used to select candidate genes or amino acid sites that are putatively under selection for association mapping. In this article, we study the pattern of polymorphism of 18 candidate genes for drought-stress response in Pinus taeda L., an important tree crop. Data analyses based on a set of 21 putatively neutral nuclear microsatellites did not show population genetic structure or genomewide departures from neutrality. Candidate genes had moderate average nucleotide diversity at silent sites (p sil ¼ 0.00853), varying 100-fold among single genes. The level of within-gene LD was low, with an average pairwise r 2 of 0.30, decaying rapidly from 0.50 to 0.20 at 800 bp. No apparent LD among genes was found. A selective sweep may have occurred at the early-response-to-drought-3 (erd3) gene, although population expansion can also explain our results and evidence for selection was not conclusive. One other gene, ccoaomt-1, a methylating enzyme involved in lignification, showed dimorphism (i.e., two highly divergent haplotype lineages at equal frequency), which is commonly associated with the long-term action of balancing selection. Finally, a set of haplotype-tagging SNPs (htSNPs) was selected. Using htSNPs, a reduction of genotyping effort of 30-40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought tolerance in pine.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.

et al. 2006

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“…This value was the minimal value of K at which the log probability of the data leveled, and membership coefficients (i.e., q-values) illustrated geographical trends for most clusters (Eckert et al 2010). Membership coefficients for these clusters were also in agreement with previous research, which identified significant structure (F ST ¼ 0.02-0.04) between samples spanning the Mississippi River Valley (Schmidtling 1999;Al-Rabab'ah and Williams 2002). These data were used to construct the X (structure) matrix described below.…”

Section: Methodssupporting

confidence: 87%

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

Quesada¹,

Gopal²,

Cumbie

et al. 2010

Genetics

101

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Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants.Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes (''tails''). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response.

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“…In this study, we identified single nucleotide polymorphisms (SNPs) in Ϸ18 kb of DNA distributed across 19 loci from 32 alleles of the long-lived gymnosperm loblolly pine (Pinus taeda L.). Pertinent attributes of the species include a highly outcrossed mating system with extensive wind dispersal of pollen (13), a 50-million-acre distribution in the southeastern United States (14), abundant allozyme and microsatellite polymorphism with only weak population differentiation across its range (15,16), and a very recent domestication history. Thus, natural, undisturbed stands of loblolly pine may be a good approximation to an idealized random mating population.…”

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Nucleotide diversity and linkage disequilibrium in loblolly pine

Brown

Gill

Kuntz

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

284

216

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Outbreeding species with large, stable population sizes, such as widely distributed conifers, are expected to harbor relatively more DNA sequence polymorphism. Under the neutral theory of molecular evolution, the expected heterozygosity is a function of the product 4N e, where Ne is the effective population size and is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4N er, where r is the per-generation recombination rate between adjacent sites. These parameters were estimated in the long-lived, outcrossing gymnosperm loblolly pine (Pinus taeda L.) from a survey of single nucleotide polymorphisms across Ϸ18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4Ne at silent and nonsynonymous sites were 0.00658 and 0.00108, respectively, and both were statistically heterogeneous among loci. By Tajima's D statistic, the site frequency spectrum of no locus was observed to deviate from that predicted by neutral theory. Substantial recombination in the history of the sampled alleles was observed and linkage disequilibrium declined within several kilobases. The composite likelihood estimate of 4N er based on all two-site sample configurations equaled 0.00175. When geological dating, an assumed generation time (25 years), and an estimated divergence from Pinus pinaster Ait. are used, the effective population size of loblolly pine should be 5.6 ؋ 10 5 . The emerging narrow range of estimated silent site heterozygosities (relative to the vast range of population sizes) for humans, Drosophila, maize, and pine parallels the paradox described earlier for allozyme polymorphism and challenges simple equilibrium models of molecular evolution. N ew genetic variation within a species arises solely by the process of mutation. A new neutral variant may be lost rapidly from a population at the rate of one minus its initial frequency. If the new variant is not lost, genetic, demographic, and evolutionary processes, in addition to random genetic drift, determine its population frequency and its nonrandom association with adjacent sites (linkage disequilibrium, LD) along the segment of DNA on which it arose. Recombination is the primary genetic process that erodes LD over time. Therefore, two key parameters in simple population genetic models that govern the amount and distribution of intraspecific sequence variation are the population mutation parameter, ϭ 4N e , and the population recombination parameter, ϭ 4N e r, where N e is the effective population size, is the per-generation, per-base pair mutation rate, and r is the per-generation recombination rate between adjacent sites.Estimates of 4N e can be readily calculated from DNA sequences obtained from population samples, even with relatively small data sets. Watterson's estimate of 4N e as W (1) is based on the number of polymorphic sites in a sample of sequences drawn at random from a population. A second estimate of 4N e is nucleotide diversity, or (2), which is the average number of pairwise n...

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Population dynamics of Pinus taeda L. based on nuclear microsatellites

Cited by 64 publications

References 14 publications

DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.

DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

Nucleotide diversity and linkage disequilibrium in loblolly pine

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