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A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae).

Narayan L, Dodd RS, O'Hara KL - Appl Plant Sci (2015)

Bottom Line: The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees.Data from simulations showed that our protocol allowed us to accurately identify clonal lineages.The techniques used in this paper can be applied to studies of other clonal organisms as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720-3114 USA.

ABSTRACT

Premise of the study: Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens).

Methods: Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees.

Results: Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average.

Discussion: The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well.

No MeSH data available.


Plot of pairwise Bruvo distances for (A) Big Basin Redwoods State Park 1, (B) Big Basin Redwoods State Park 2, (C) Humboldt Redwoods State Park 1, (D) Humboldt Redwoods State Park 2, (E) Redwood National Park, and (F) Prairie Creek Redwoods State Park.
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fig1: Plot of pairwise Bruvo distances for (A) Big Basin Redwoods State Park 1, (B) Big Basin Redwoods State Park 2, (C) Humboldt Redwoods State Park 1, (D) Humboldt Redwoods State Park 2, (E) Redwood National Park, and (F) Prairie Creek Redwoods State Park.

Mentions: We plotted histograms of pairwise genetic distances for each 1-ha plot, which generally showed one peak around 0.6 and a second peak close to zero. The second peak likely resulted from scoring errors or somatic mutations causing slight variation between the genotype of clones (Fig. 1). The histograms consistently showed a trough around 0.2, so we set this as our genetic distance cutoff for clonal assignment. Using this criterion, 449 clones were identified in the 770 trees genotyped.


A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae).

Narayan L, Dodd RS, O'Hara KL - Appl Plant Sci (2015)

Plot of pairwise Bruvo distances for (A) Big Basin Redwoods State Park 1, (B) Big Basin Redwoods State Park 2, (C) Humboldt Redwoods State Park 1, (D) Humboldt Redwoods State Park 2, (E) Redwood National Park, and (F) Prairie Creek Redwoods State Park.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356318&req=5

fig1: Plot of pairwise Bruvo distances for (A) Big Basin Redwoods State Park 1, (B) Big Basin Redwoods State Park 2, (C) Humboldt Redwoods State Park 1, (D) Humboldt Redwoods State Park 2, (E) Redwood National Park, and (F) Prairie Creek Redwoods State Park.
Mentions: We plotted histograms of pairwise genetic distances for each 1-ha plot, which generally showed one peak around 0.6 and a second peak close to zero. The second peak likely resulted from scoring errors or somatic mutations causing slight variation between the genotype of clones (Fig. 1). The histograms consistently showed a trough around 0.2, so we set this as our genetic distance cutoff for clonal assignment. Using this criterion, 449 clones were identified in the 770 trees genotyped.

Bottom Line: The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees.Data from simulations showed that our protocol allowed us to accurately identify clonal lineages.The techniques used in this paper can be applied to studies of other clonal organisms as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720-3114 USA.

ABSTRACT

Premise of the study: Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens).

Methods: Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees.

Results: Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average.

Discussion: The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well.

No MeSH data available.