Development of 240 novel EST-SSRs in Eucalyptus L’Hérit

Zhou, Changpin; He, Xiaoling; Li, Fagen; Weng, Qijie; Yu, Xiaoli; Wang, Yu; Li, Mei; Shi, Jisen; Shen, Gan

doi:10.1007/s11032-013-9923-z

Cited by 28 publications

(21 citation statements)

References 21 publications

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“…Furthermore, average values of number of alleles 508 C. V. Acuña et al / Forest Systems (2014) (Table 2). These values are similar to the polymorphic patterns described in an study of ESTSSRs in E. urophylla and E. tereticornis and other in E. grandis (Zhou et al, 2013). However, the values found in the present study are lower than those described by Faria et al, (2010), also in E. grandis.…”

Section: Resultssupporting

confidence: 87%

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Transferability of microsatellite markers located in candidate genes for wood properties between Eucalyptus species

et al. 2014

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Aim of study: To analyze the feasibility of extrapolating conclusions on wood quality genetic control between different Eucalyptus species, particularly from species with better genomic information, to those less characterized. For this purpose, the first step is to analyze the conservation and cross-transferability of microsatellites markers (SSRs) located in candidate genes.Area of study: Eucalyptus species implanted in Argentina coming from different Australian origins.Materials and methods: Twelve validated and polymorphic SSRs in candidate genes (SSR-CGs) for wood quality in E. globulus were selected for cross species amplification in six species: E. grandis, E. saligna, E. dunnii, E. viminalis, E. camaldulensis and E. tereticornis.Main results: High cross-species transferability (92% to 100%) was found for the 12 polymorphic SSRs detected in E. globulus. These markers revealed allelic diversity in nine important candidate genes: cinnamoyl CoA reductase (CCR), cellulose synthase 3 (CesA3), the transcription factor LIM1, homocysteine S-methyltransferase (HMT), shikimate kinase (SK), xyloglucan endotransglycosylase 2 (XTH2), glutathione S-transferase (GST), glutamate decarboxylase (GAD) and peroxidase (PER).Research highlights: The markers described are potentially suitable for comparative QTL mapping, molecular marker assisted breeding (MAB) and for population genetic studies across different species within the subgenus Symphyomyrtus.Keywords: validation; cross-transferability; SSR; functional markers; eucalypts; Symphyomyrtus.

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Section: Resultssupporting

confidence: 87%

“…As the primers were designed from genic regions, it is reasonable that they have a high potential for cross-transferability in related species. In fact, in a recent study, similar cross-species transferability of SSR markers was already reported for species of the subgenus Symphyomyrtus (Zhou et al, 2013).…”

Section: Resultssupporting

confidence: 83%

Transferability of microsatellite markers located in candidate genes for wood properties between Eucalyptus species

et al. 2014

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“…SSR variations in the coding regions should be subjected to much stronger selective pressure than variations in the 5 0 -UTR (untranslated regions) and 3 0 -UTR (Zhou et al, 2014). In the present study, 204 EST-SSR variations were all found in the coding regions.…”

Section: Resultsmentioning

confidence: 43%

“…EST-SSRs always exhibit lower levels of polymorphism than the genomic sequence-based SSRs. However, they are predicted to possess advantages like easy access, presence in gene-rich regions and high level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies (Zhou et al, 2014). Despite the growing availability of single nucleotide polymorphism (SNP) markers, SSRs are still the most used molecular markers by many breeders that might not have access to expensive SNP-genotyping platforms for their species (Tyrka et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa

Zhou

Chen

Wang

et al. 2014

Biochemical Systematics and Ecology

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“…During cross transfer, it is essential to verify the allele variations by sequencing the PCR fragments, wherein the structural variants in the form type of repeats, insertion or deletion generated by the SSRs are accurately detected. In eucalypts, 240 EST-SSRs were confi rmed for their sequence homology with the original EST sequences, however, no information on repeat size variations were reported (Zhou et al 2014). Recently, it was emphasized that the sequence verifi cation of SSR alleles is critical for interpretation of the SSR polymorphism for genetic analysis (Barthe et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite allele length variations in inter-specific hybrids of Eucalyptus

Sumathi¹,

Yasodha²

2017

Acta Botanica Croatica

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-The genus Eucalyptus encompasses several species of industrial importance. Many of these species have been subjected to genetic characterization using different kinds of DNA markers. More than 1000 microsatellites have been identifi ed from the genome of eucalypts and they are highly amenable for cross species transferability. During cross amplifi cation of microsatellites, homoplasy is reported in many species in which although the allele size might be the same, the sequences are not. Thus, it is essential to ascertain the DNA sequence homology with source and target microsatellite repeats. Accordingly, fifty five alleles from six microsatellite loci (ECc1, ECc2, Eg61, Embra100, Embra1468 and Embra2002) were amplifi ed in two inter-specifi c hybrid populations (Eucalyptus tereticornis × E. grandis and E. tereticornis × E. camaldulensis) and sequenced. The results showed that all the microsatellite loci were amplifying the target repeat types except for the loci Eg61 and Embra2002. The locus Eg61 has target repeat of (CAA)(GAT) but the sampled alleles had either (CAA)(GAT) or (GAT) alone. Similarly, the Embra2002 locus was targeting interrupting repeats of (CCA)..(CCA), but the sequenced alleles had repeats of (CCA) with or without interruption. Nevertheless, the allele size estimated in electrophoresis for hybrids was in conformity with that of the parent alleles. This study suggests the need for validation of the repeat characteristics of microsatellites by sequencing of the alleles particularly in cross species amplifi cation.

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Development of 240 novel EST-SSRs in Eucalyptus L’Hérit

Cited by 28 publications

References 21 publications

Transferability of microsatellite markers located in candidate genes for wood properties between Eucalyptus species

Transferability of microsatellite markers located in candidate genes for wood properties between Eucalyptus species

The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa

Microsatellite allele length variations in inter-specific hybrids of Eucalyptus

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