Development and characterization of a new set of 164 polymorphic <scp>EST</scp>‐<scp>SSR</scp> markers for diversity and breeding studies in rubber tree (<i><scp>H</scp>evea brasiliensis </i><scp>M</scp>üll. <scp>A</scp>rg.)

Cubry, Philippe; Pujade-Renaud, Valérie; García, Dominique; Espeout, Sandra; Guen, Vincent Le; Granet, Françoise; Séguin, Marc

doi:10.1111/pbr.12158

Cited by 25 publications

(16 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in the preliminary analysis in the present study, the goodness‐of‐fit of the model with a mean value of μ = 5 × 10 –4 was poor. Furthermore, the mutation rate for EST‐SSR is generally lower than that for genomic SSR (Cubry et al, 2014). Therefore, we used 1 × 10 –4 as the mean value of μ .…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

et al. 2020

View full text Add to dashboard Cite

Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population diversity and structure across old and young islands, to assess potential differences in population demography with island age, and to collect any evidence of migration between old and young islands. We found that the genetic diversity of expressed sequence tag (EST)–based microsatellite (SSR) markers, the nucleotide diversity of nuclear DNA sequences, and the haplotype diversity of chloroplast DNA on young islands were lower than those on old islands. Clustering analyses of EST‐SSR indicated that populations on old islands were strongly diverged from those on young islands. Approximate Bayesian computation analysis of EST‐SSR suggested that population expansion occurred on old islands while population reduction occurred on young islands. We also found evidence of migration among old islands (mostly from south to north), while it appears that there have been very few migration events between old and young islands. These differences could be due to the fact that young islands tend to be geographically isolated and support smaller populations that began a shorter time ago from limited founders. The P. boninensis populations on the Volcano Islands are interesting from an evolutionary perspective as they constitute a classic example of the early stages of progressive colonization on oceanic islands with small effective population sizes and low genetic diversity.

show abstract

Section: Methodsmentioning

confidence: 99%

Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

et al. 2020

View full text Add to dashboard Cite

show abstract

“…A high frequency of trinucleotide repeats is reported in exons that contain almost no tetranucleotide repeats (Toth et al 2000;Varshney et al 2005), whereas mutability tests showed that the allelic variability of exon SSRs is lower than that of intronic repeats (Li et al 2011). Massive EST and genomic sequence data have made available information on repeat region abundance and position, and bioinformatic analyses have significantly accelerated the process of identification and selection, reducing the time for their application (Acuna et al 2012;Li et al 2012;Shiferaw et al 2012;Yang et al 2012;Duran et al 2013;Cubry et al 2014).…”

Section: Communicated By G G Vendraminmentioning

confidence: 99%

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

Mariotti

Cultrera

Mousavi

et al. 2016

Tree Genetics & Genomes

View full text Add to dashboard Cite

Rapid and effective genotyping is an important goal to discriminate among the numerous olive cultivars and their wild related forms. The largely used di-nucleotide simple sequence repeat (SSR) markers show a high level of polymorphism and have strongly contributed to solve many inconsistencies in varietal identity, but many problems related to difficult discrimination of neighboring alleles and low comparability of data among different labs severely reduce their applicability for large-scale screening. The availability of numerous transcriptome libraries, which were developed from different tissues of several olive varieties, has allowed their intensive screening to search for polynucleotide microsatellite regions with long core repeats, potentially polymorphic among varieties. An accurate screening of all these polymorphisms has allowed to select a set of 25 trinucleotide and one tetranucleotide SSRs, showing a good level of discrimination power with a high allele pattern resolution and repeatability. They were preliminarily tested on a group of cultivated varieties then validated on a wider group of cultivated and wild plants, and related species and subspecies, demonstrating a good transferability within the entire Olea taxon. Furthermore, an in silico functional prediction has allowed to assign each transcribed sequence to their gene functions and biological process categories, highlighting their potential application of these new EST-SSRs as functional markers.

show abstract

“…Molecular markers have been used to assess genetic diversity through indices such as expected and observed heterozygosity and fixation index, among others. Some studies have quantified the genetic diversity of rubber trees using these markers (CUBRY et al, 2014;PERSEGUINI et al, 2012;PETHIN et al, 2015), offering significant potential for genetic studies involving the species (SOUZA et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure in ex situ conserved populations of Hevea brasiliensis

Silva¹,

Cambuim²,

Kubota³

et al. 2019

Sci. For.

View full text Add to dashboard Cite

Development and characterization of a new set of 164 polymorphic EST‐SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.)

Cited by 25 publications

References 26 publications

Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

Genetic diversity and structure in ex situ conserved populations of Hevea brasiliensis

Contact Info

Product

Resources

About