Development and Characterization of Three Highly Informative EST-SSR Multiplexes for Pinus halepensis mill. and their Transferability to Other Mediterranean Pines

Leonarduzzi, Cristina; Spanu, Ilaria; Labriola, Mariaceleste; González‐Martínez, Santiago C.; Piotti, Andrea; Vendramin, G. G.

doi:10.1007/s11105-016-0980-4

Cited by 14 publications

(11 citation statements)

References 69 publications

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“…Expected heterozygosity (H e ) values were also high, with an average value above 0.7, and similar to the values observed for this species (Pluess, 2011) and for the related L. kaempferi (Isoda and Watanabe, 2006), providing further evidence of the utility and highly informative nature of the SSRs used. As observed in L. decidua (Pluess, 2011;Wagner et al, 2012;Nardin et al, 2015) and in other conifer species (Mosca et al, 2012;Leonarduzzi et al, 2016), H o and H e values were quite similar, revealing a high degree of allogamy and low genetic isolation in the materials evaluated, as observed with RAPD markers in these same populations (Vilcan et al, 2017). As a result, the fixation index (F is ) values for the SSR markers were low and, as occurs in both Larix (Nardin et al, 2015;Vilcan et al, 2017) and other conifers (Leonarduzzi et al, 2016), in some cases negative, revealing an excess of heterozygotes over those predicted by the Hardy-Weinberg equilibrium for these markers (Wright, 1965).…”

Section: Discussionsupporting

confidence: 64%

“…As observed in L. decidua (Pluess, 2011;Wagner et al, 2012;Nardin et al, 2015) and in other conifer species (Mosca et al, 2012;Leonarduzzi et al, 2016), H o and H e values were quite similar, revealing a high degree of allogamy and low genetic isolation in the materials evaluated, as observed with RAPD markers in these same populations (Vilcan et al, 2017). As a result, the fixation index (F is ) values for the SSR markers were low and, as occurs in both Larix (Nardin et al, 2015;Vilcan et al, 2017) and other conifers (Leonarduzzi et al, 2016), in some cases negative, revealing an excess of heterozygotes over those predicted by the Hardy-Weinberg equilibrium for these markers (Wright, 1965). Overall, because of their codominant nature, high degree of amplification, efficient multiplexing, robustness, reduced rate of missing data, high polymorphism, and high informativeness, the markers used here, which were developed by Isoda and Watanabe (2006) and Wagner et al (2012), are of great utility for evaluating the diversity and genetic structure of L. decidua populations.…”

Section: Discussionsupporting

confidence: 64%

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Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larixdecidua) populations from Romania

Gramazio¹,

Plesa²,

Truță³

et al. 2018

Turk J Agric For

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European larch (Larix decidua) is naturally distributed at high elevations in Central Europe. Romanian populations of L. decidua are scattered in different areas of the country. In this study, we used 12 highly informative genomic simple sequence repeat (SSR) markers for genotyping seven populations from different areas of Romania. The SSR markers were highly variable, with up to 11 alleles per SSR locus and an average polymorphic information content of 0.713. High values of observed (H o = 0.542) and expected (H e = 0.738) heterozygosities were observed. Cluster analysis of populations did not group them according to geographical distance, but some clusters contained populations from a similar altitudinal range. The partition of genetic variation revealed that two-thirds of the genetic variation was found within individuals (due to high H o levels), while only one-sixth of the total genetic variation corresponded to variation among populations. A population structure analysis identified four genetic clusters, and in most cases individuals from a single population were assigned to several genetic clusters. Multivariate principal coordinates analysis confirmed the population structure analysis. SSR markers are a powerful tool for evaluating diversity, relationships, and the genetic structure of Romanian L. decidua populations, which have high levels of diversity and low genetic structuration.

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Section: Discussionsupporting

confidence: 64%

Section: Discussionsupporting

confidence: 64%

Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larixdecidua) populations from Romania

Gramazio¹,

Plesa²,

Truță³

et al. 2018

Turk J Agric For

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“…Compared to the ten best-ranked di-nucleotide SSRs (Baldoni et al 2009), the ten most informative OLEST-SSRs showed a lower variability and a higher frequency of null alleles, probably because EST-derived SSRs are associated with transcribed regions, thus reflecting a lower genetic variability then genomic, neutral, and randomly selected markers as di-nucleotide SSRs (Hu et al 2011;Leonarduzzi et al 2016). However, both kinds of markers are well suitable to characterize the olive variability and their combined application could efficiently contribute to explore the olive germplasm and resolve variety identification problems arising from the use of di-nucleotide markers.…”

Section: Discussionmentioning

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

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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.

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“…) make it ideal for genetic study where genotyping errors may strongly affect final estimates (Leonarduzzi et al . ). The EST‐SSR primers were obtained by the H. compressa 's transcriptome sequence development from our group's previous study (Huang et al .…”

Section: Introductionmentioning

confidence: 97%

“…Compared with SSR markers, EST-SSR markers reflect the coding portion of the gene, detect genetic differences between varieties more accurately, and directly obtain information on gene expression, providing "absolute" markers for functional genes. Meanwhile, the labor-and cost-effective (Sorrells 2005) features of EST-SSR being more reproducible and less prone to null alleles (Kim et al 2008;Sullivan et al 2013) make it ideal for genetic study where genotyping errors may strongly affect final estimates (Leonarduzzi et al 2016). The EST-SSR primers were obtained by the H. compressa's transcriptome sequence development from our group's previous study (Huang et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Influence of radiation on Hemarthria compressa's genetic variations

Yan

Yang

et al. 2018

Grassland Science

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Using the material of Hemarthria compressa (L.F.) R.Br. cv. YA’AN, we carried out this research to study the influence of radiation on the genetic variation of plants. Genetic difference was analyzed with expressed sequence tag‐simple sequence repeat (EST‐SSR) molecular marker through the comparison of 60Co‐γ radiation on H. compressa seed stems and original variety. By using 20 primer pairs, 176 polymerase chain reaction (PCR)‐amplifications with clear and consistent bands were obtained. The results showed that 155 of 176 bands were polymorphic, which indicating an 88.07% polymorphism rate, and each pair of primers had 8.8 amplified bands on average; the amplitude of polymorphism information content was 0.4709–0.6952 with an average value 0.6081. The genetic similarity coefficient of H. compressa and its mutants ranged from 0.4318 to 0.8239 with an average of 0.6671. As a consequence, existence of genetic differences between the mutants and the basic material was proved.

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Development and Characterization of Three Highly Informative EST-SSR Multiplexes for Pinus halepensis mill. and their Transferability to Other Mediterranean Pines

Cited by 14 publications

References 69 publications

Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larixdecidua) populations from Romania

Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larixdecidua) populations from Romania

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

Influence of radiation on Hemarthria compressa's genetic variations

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