Intra and intergeneric transferable gene-derived orthologous microsatellite markers in <i>Eucalyptus</i> and <i>Corymbia</i> species

Kotrappa, Nagabhushana; Hendre, Prasad S.; Rathinavelu, Rajkumar

doi:10.1080/13416979.2016.1262726

Cited by 4 publications

(4 citation statements)

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“…This showed that Eucalyptus sp. and E. urophylla were the highest gene diversity, followed by E. globulus, C. citriodora, E. deglupta, and E. pellita compared to previous studies (Nurtjahjaningsih et al 2013;Kotrappa et al 2017;and Liu et al 2018b). The genetic diversity of E. globulus, C. citriodora, E. deglupta was not significantly high compared to Eucalyptus sp.…”

Section: Discussionmentioning

confidence: 54%

“…This study determined the genetic diversity and population structure of Corymbia and Eucalyptus species using 14 SSR markers. Although the success rate of genomic SSR marker in eucalypt from is transferable, it is relatively low (>50%) compared to cross-species transferability on other eucalypt species (Subashini et al 2014;Kotrappa et al 2017;Liu et al 2018b). Many isolated SSR markers from E. grandis and E. urophylla (EMBRA code) were cross-amplified in different Eucalyptus species such as E. globulus, E. pilularis, E. nitens, E. urophylla, E. pyrocarpa, E. camaldulensis, and E. tereticornis (Bundock et al 2000;Steane et al 2001;Glaubitz et al 2001;Agrama et al 2002;Ottewell et al 2005;Arumugasundaram et al 2011;Subashini et al 2014).…”

Section: Discussionmentioning

confidence: 99%

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Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

et al. 2021

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Abstract. Rahayu, Fatimah, Wiwoho J, Firdaus SU, Pujiyono, Marimin, Arianto DP, Pramono A. 2021. Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia. Biodiversitas 22: 4223-4235. As a repository of a gene pool, eucalypts germplasm enriches biodiversity, maintains ecosystem sustainability, and aids in conservation. Therefore, this study aims to analyze the genetic diversity of eucalypts (Corymbia and Eucalyptus) for the development of germplasm conservation in Forest Area with the Special Purpose (KHDTK) Bromo Forest, Karanganyar, Indonesia. In this study, 14 simple sequence repeat (SSR) markers were used to assess the genetic diversity among 20 accessions (Corymbia and 5 Eucalyptus species) from Central and West Java. Subsequently, the genetic parameters were measured and a phylogenetic tree was constructed. The result showed that the SSR markers have high variability, although they belong to different genera. Furthermore, the genetic diversity showed 49 alleles with an average of 3 alleles per locus, while the polymorphism information content (PIC) values were 0.55. There were 4 SSR markers (EMBRA13, EMBRA8, EMCRC11, and EMBRA2) with high PIC value, while the gene diversity (He) of Corymbia and 5 Eucalyptus showed a low level of genetic diversity. The genetic relationship and population structure were divided into genera Corymbia and Eucalyptus. For further application, the eucalypt cultivated in the KHDTK Bromo Forest can contribute as a reference set and 14 SSR markers as a potential marker in combination with morphological characterization to generate a database for germplasm management and conservation.

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

et al. 2021

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“…The study followed an established procedure for developing and identifying SSR markers (Rosetto, 2003;Selkoe & Toonen, 2006), beginning with a literature review focusing on microsatellite primers developed for taxa closely related to F. amethystina and F. tatrae. This approach is a straightforward and inexpensive method that has already been used in previous studies (Cordeiro et al, 2001;Rosetto, 2003;Saha et al, 2004;Giraldo et al, 2005;Huang et al, 2016;Mansour, Bryngelsson & Garkawa-Gustavvson, 2016;Kotrappa, Hendre & Rathinavelu, 2017).…”

Section: Identifying Accurate Ssr Markersmentioning

confidence: 99%

The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leavedFestucaspecies (Poaceae)

Tomczyk

Kiedrzyński

Jędrzejczyk

et al. 2020

PeerJ

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Background Microsatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina—F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae—as a mountain and narrow endemic species and F. amethystina—a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context. Methods The ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented. Results Flow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them. Conclusions The transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes.

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“…Leaf samples collected from young leaves were powdered using liquid nitrogen and stored in -80° C. Genomic DNA was isolated from the young leaf tissues using the modified CTAB protocol described by Hendre et al (2012). Twelve polymorphic SSR primers were selected for marker analysis by capillary genotyping adopting two-tier PCR system described by Nagabhushana et al (2017).…”

Section: Genotypic Studymentioning

confidence: 99%

Impact of fertility variation on genetic diversity and phenotypic traits in second generation seed production areas and clonal seed orchards of Eucalyptus camaldulensis

et al. 2019

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Fertility and gene diversity were estimated in three second generation (F2) seed stands (SPA 1-3) and two clone trials (CSO 1&2) of Eucalyptus camaldulensis to assess the impact on seed crop. F2 seedlots were evaluated in comparison to native provenances, ten commercial clones and interspecific hybrids at diverse sites. SPA 1&2 were genetic gain trials of five first generation (F1) orchard seedlots, SPA 3 a plantation of one F1 orchard seedlot, and CSOs were clone trials of 21 commercial clones established at two contrasting sites. Fertility variation, as indicated by sibling coefficient, was high (Ψ, 9-14) in the SPAs as only about 26 % trees were fertile compared to 81 % trees in CSOs. Effective population size was higher in SPA 1 and 2 (Ns, 95 and 74, respectively) than SPA 3 (Ns = 39). Fertility was highly skewed in CSO 2 resulting in low effective population size (Ns = 2) compared to CSO 1 (Ns = 11). Constant seed collection enabled 3-fold increase in relative population size and 22 % higher predicted gene diversity in CSO 2. Genetic diversity (He) estimated using SSR markers was higher in SPA 1&2 and native provenances (NAT), compared to SPA 3 and CSO 1, whereas CSO 2 and clones had lower values. There was a high positive correlation between estimated He and predicted gene diversity values of SPAs and CSOs. He was positively correlated to mean field survival and negatively correlated to kraft pulp yield (KPY), evaluated at three years in progeny trials across three locations. Number of alleles per locus was higher in SPAs and native provenances compared to CSOs and clones. Discriminant principal component analysis clustered CSO, NAT and SPA seedlots in different groups while commercial E. camaldulensis clones clustered close to NAT. Multilocus outcrossing rate was generally high (tm, 91-100 %), though selfing was observed in two families of SPA 3 and CSO 2. Selected interspecific hybrid families of commercial E. camaldulensis clones (with E. urophylla and E. pellita) evaluated at two of the sites had higher He and KPY than clones at three years.

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Intra and intergeneric transferable gene-derived orthologous microsatellite markers in Eucalyptus and Corymbia species

Cited by 4 publications

References 16 publications

Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leavedFestucaspecies (Poaceae)

Impact of fertility variation on genetic diversity and phenotypic traits in second generation seed production areas and clonal seed orchards of Eucalyptus camaldulensis

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