Microsatellite primers for the Pacific Northwest endemic conifer<i>Chamaecyparis lawsoniana</i>(Cupressaceae)

Jennings, Tara; Knaus, Brian J.; Kolpak, Scott E.; Cronn, Richard

doi:10.3732/ajb.1100317

Cited by 5 publications

(4 citation statements)

References 9 publications

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“…Initially hampered by short read lengths, the development of paired end sequencing and the increase in sequence lengths have opened the Illumina platform to inexpensive, high throughput SSR discovery. This has been successfully demonstrated with both microsatellite-enriched libraries [ 20 , 21 ] and unenriched genomic DNA [ 13 , 22 ]. Such large volumes of data are produced in a single lane of Illumina sequencing that multiple individuals and species may be surveyed simultaneously through multiplexing, i.e.…”

Section: Introductionmentioning

confidence: 99%

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

et al. 2015

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Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

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Section: Introductionmentioning

confidence: 99%

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

et al. 2015

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“…This is approximately one-fifth the success rate of SSRs developed in Chamaecyparis lawsoniana (A. Murray) Parl. using these same methods [ 60 ]. This conversion rate is extremely low for species of genus Pinus , which have already been characterized by low conversion rates, attributed to the complexity of their genomes (> 20Gbp) and the presence of large numbers of paralogous SSR families [ 76 ], [ 77 ], [ 78 ].…”

Section: Discussionmentioning

confidence: 99%

“…To develop novel microsatellite loci for P . albicaulis , we identified di- and tri-nucleotide repeats using the procedure outlined in Jennings et al [ 60 ], a strategy that was designed to identify very short (< 80bp) paired-end sequence data from early-generation Illumina sequencers. Genomic DNA from diploid needle tissue from a single tree (Custer Gallatin National Forest, Montana; 45.443°N, -110.005°W, 2,470 m a.s.l.)…”

Section: Methodsmentioning

confidence: 99%

Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern

Lea¹,

Syring²,

Jennings³

et al. 2018

PLoS ONE

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Pinus albicaulis (whitebark pine) is a widely-distributed but rapidly declining high elevation western North American tree and a candidate for listing under the U.S. Endangered Species Act. Our objectives were to develop reliable nuclear microsatellite markers that can be used to assess within-population genetic diversity as well as seed and pollen migration dynamics, and to validate markers using two geographically proximal P. albicaulis populations. We identified 1,667 microsatellite-containing sequences from shotgun DNA libraries of P. albicaulis. Primer pairs were designed for 308 unique microsatellite-containing loci, and these were evaluated for PCR amplification success and segregation in a panel of diploid needle tissue. DNA was extracted with an SDS protocol, and primers were screened through gel electrophoresis. Microsatellites were genotyped through fluorescent primer fragment analysis. Ten novel and 13 transferred loci were found to be reproducible in analyses based on 20 foliage samples from each of two locations: Henderson Mountain, Custer Gallatin National Forest, Montana, and Mt. Washburn, Yellowstone National Park, Wyoming (USA). Transferred loci had higher numbers of alleles and expected heterozygosities than novel loci, but also revealed evidence for a higher frequency of null alleles. Eight of the 13 transferred loci deviated significantly from Hardy-Weinberg Equilibrium, and showed large positive FIS values that were likely inflated by null alleles. Mantel’s tests of transferred and novel markers showed no correlation between genetic and geographic distances within or among the two sampled populations. AMOVA suggests that 91% of genetic variability occurs within populations and 9% between the two populations. Studies assessing genetic diversity using these microsatellite loci can help guide future management and restoration activities for P. albicaulis.

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“…The field trials will also be used to examine genetic variation in adaptive traits within POC, serve as sentinel plantings with known genetic constitution, and provide in situ genetic conservation (Harrington et al 2012;Sniezko et al 2012aSniezko et al , 2012b. More recently, DNA-based genetic markers have been developed through a USDA FS Special Technology Development grant (Jennings et al 2011) to help assist the operational breeding program and evaluate patterns of genetic variation throughout the range of National seed collection and gene conservation programs have expanded in recent years, especially in response to pressure from non-native pests such as the emerald ash borer (Agrilus planipennis). Since 2008, we have been working with the U.S. Department of Agriculture Agricultural Research Service (USDA ARS) and USDA Forest Service (USDA FS) leading seed collection efforts in the genus Fraxinus chiefly in Minnesota and North Dakota with smaller collections in Wisconsin and Iowa.…”

Section: Genetic Conservationmentioning

confidence: 99%

Gene conservation of tree species—banking on the future. Proceedings of a workshop.

Sniezko¹,

Man²,

Hipkins³

et al. 2017

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Microsatellite primers for the Pacific Northwest endemic coniferChamaecyparis lawsoniana(Cupressaceae)

Abstract: These microsatellite primers show high polymorphism and should provide a high level of individual discrimination for paternity analysis in defined pedigrees, and routine screening of wild variation in Chamaecyparis lawsoniana.

Cited by 5 publications

References 9 publications

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern

Gene conservation of tree species—banking on the future. Proceedings of a workshop.

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