Use of Microsatellite Markers in an American Beech (Fagus grandifolia) Population and Paternity Testing

Koch, Jennifer; Carey, David W.; Mason, Mary E.

doi:10.1515/sg-2010-0008

Cited by 7 publications

(6 citation statements)

References 21 publications

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“…Based on SSR of nDNA, the average number of alleles (A) was 21.75 among the 14 F. hayatae populations (Table 1), which was much higher than for any other Koch et al 2009). Our study was in accord with the results of Kung (2012), which also showed an average of 24.33 alleles for populations mainly from Taiwan.…”

Section: Genetic Diversitymentioning

confidence: 82%

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The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

Liu

Zhang

Chiu

et al. 2016

Ecology and Evolution

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The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of R st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G st = 0.712) among populations. A high G st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.

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Section: Genetic Diversitymentioning

confidence: 82%

“…), and Fagus grandifolia ( A = 13.8, Koch et al. ). Our study was in accord with the results of Kung (), which also showed an average of 24.33 alleles for populations mainly from Taiwan.…”

Section: Discussionmentioning

confidence: 99%

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

Liu

Zhang

Chiu

et al. 2016

Ecology and Evolution

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“…Locus‐specific markers, such as microsatellites, can be used not only to determine the level of genetic diversity but also to reveal the genetic structure of the population and to estimate the level of gene flow. They can detect a large number of alleles, with high repeatability and inter‐species transferability, and have mainly been used in the study of bio‐effective populations, genome identification, kinship and other issues, and have even been applied in medical research (Clauss et al, 2002; Turpeinen et al, 2001; Koch et al, 2009; Hiroshi et al, 2007; Zauber et al, 2003). Despite their global applicability, the development of microsatellites requires considerable technical effort to construct the rich microsatellite libraries, which can be expensive or time‐consuming, or the number of different types of useful microsatellite loci that are successfully obtained can be limited (Peakall et al, 1998; Castoe et al, 2010; Zhan et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

Weng

Tao

Liang

2020

Journal of Phytopathology

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The pear‐cypress rust Gymnosporangium asiaticum is one of the most significant causal agents of pear rust in Asian pear, severely affecting the pear industry. Research on the genetic diversity of this widespread pathogen has been hampered due to the absence of molecular markers. In the current study, we developed 16 novel microsatellite markers for G. asiaticum from transcriptome data by combining next‐generation sequencing and PCR screening. These polymorphic markers were tested on 96 individuals from nine provinces in China. The number of alleles for these markers ranged from two to nine, with an average of five at each locus. The polymorphic information content ranged from 0.0411 to 0.7666, with an average of 0.4417. In addition, the observed (HO) and expected (HE) heterozygosities were 0.0312–0.6941 and 0.0417–0.8000, respectively. We also observed low‐to‐moderate levels of genetic differentiation and extremely significant gene flow between the nine provinces. Of these 16 developed simple sequence repeat loci, 11 were transferable to other Gymnosporangium species. These new microsatellite markers can be used in future large‐scale studies of the genetic structure and diversity of G. asiaticum.

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“…In contrast to most proteomics studies conducted on model organisms, our subjects are wild, unrelated, mature trees selected from multiple stands. Like many forest trees, American beech is wind-pollinated and has a low self-pollination rate [52], resulting in high heterozygosity among trees within stands [53]. We selected trees from eight non-contiguous stands, further decreasing any chance of relatedness between trees across the study and likely increasing the number of alleles per locus sampled [54].…”

Section: Discussionmentioning

confidence: 99%

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

et al. 2013

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BackgroundBeech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees.ResultsProteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified.ConclusionsFurther study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services.

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Use of Microsatellite Markers in an American Beech (Fagus grandifolia) Population and Paternity Testing

Cited by 7 publications

References 21 publications

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

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