Cross‐species amplification tests and diversity analysis using 56 PCR markers in <i>Dactylis glomerata</i> and <i>Lolium perenne</i>

Litrico, Isabelle; Bech, Nicolas; Flajoulot, Sandrine; Cadier, D.; Talon, C.; Gibelin, Chrystel; Barré, Philippe

doi:10.1111/j.1755-0998.2008.02168.x

Cited by 10 publications

(14 citation statements)

References 11 publications

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“…When orchardgrass SSR markers were tested for amplification in tall fescue and Lolium species herein, less than 50% had clear and repeatable amplification products. This is consistent with previous efforts to take SSR primers from Festuca and Lolium, and amplify those using orchardgrass DNA (Litrico et al 2009). These differences between Festuca and Lolium and orchardgrass suggest a somewhat unique nature of orchardgrass, and further sequence and marker comparisons among these three genera will likely enlighten the cause for lower relative transferability of markers between Dactylis, Festuca, and Lolium.…”

Section: Discussionsupporting

confidence: 91%

“…Previous studies have used a variety of tools: chloroplast and ITS sequences have been used to describe phylogenetic relationships (Lumaret et al 1989;Catalan et al 2004;Stewart and Ellison 2010), dominant markers (e.g., RAPD, ISSR, SRAP) used in discreet studies (Koelliker et al 1999;Tuna et al 2004;Peng et al 2008;Zeng et al 2008), and heterologous markers tested from other forage grass species Litrico et al 2009), However, the openplatform dominant markers generally have the inability to add samples to a study without re-analyzing all previous samples due to the large number of bands genotyped per primer. Heterologous marker transferability also decreases as species diverge (Thiel et al 2003;Zhang et al 2005;Litrico et al 2009), and are accompanied by higher likelihood of homoplasy and polymorphism due to mutations that exist among the species (Thiel et al 2003;Saha et al 2004;Zhang et al 2006). Recently, genomic library-derived SSR markers were used to describe relationships among some Asian germplasm (Xie et al 2010).…”

Section: Introductionmentioning

confidence: 99%

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Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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“…ISSR analysis has been used to assess the genetic diversity of a large number of plant species, including Lolium spp (Dinelli et al, 2004) and Cynodon dactylon (Wang et al, 2013). Both SSRs and ISSRs are powerful and useful tools for genetic studies and have been used in several plant species; however, at present, reports remain P. Madesis et al limited about their use in studies of D. glomerata populations (Litrico et al, 2009;Xie et al, 2010Xie et al, , 2012.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of natural Dactylis glomerata L. populations revealed by morphological and microsatellite-based (SSR/ISSR) markers

Madesis¹,

Abraham²,

Kalivas³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Dactylis glomerata L. is an important forage species in the Mediterranean region, and in other regions with a similar climate. Genetic material from 3 locations in north, central, and south Greece was studied, using morphological traits, SSR, and ISSR molecular markers. Morphological analysis revealed differences among the geographic locations studied for all morphological traits, except the number of reproductive tillers. Moreover, the highest phenotypic variation was observed on the accessions from south, while the lowest was observed on the accessions from the north. Although the results of the molecular marker analysis are indicative, a high level of Morphological and genetic diversity of Dactylis glomerata genetic diversity at the species level was revealed by ISSRs (G ST = 0.291) and SSRs (F ST = 0.186). Analysis of molecular variance showed that a high level of genetic diversity existed for ISSRs and SSRs within populations (62 and 83%, respectively), rather than among populations (38 and 17%, respectively). Cluster analysis divided the 3 populations in 2 groups, with the population originating from the island of Crete forming 1 group, while the populations from north Greece (Taxiarchis) and central Greece (Pertouli) were clustered in a 2nd group. In general, the results indicate that SSRs are more informative compared to ISSRs about the genetic variation within a population, whereas the ISSRs were more informative about the genetic diversity among populations However, a similar trend in diversity (genotypic and phenotypic) was observed in the morphological traits and microsatellite-based (SSR/ISSR) markers at the locations studied.

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“…The average number of alleles per locus was less than those found for Eugenia dysenterica (10.4) (Zucchi et al, 2002) and Festuca arundinacea (7.8) (Elazreg et al, 2011). The observed number of alleles per locus was closer to the values observed for Hymenaea stigonocarpa (6.43) (Ciampi et al, 2008), Dactylis glomerata (5.45), Lolium perenne (4.50) (Litrico et al, 2009) and Blighia sapida (3.7) (Ekué et al, 2009). Albaladejo et al (2008) suggested that the number of alleles per locus observed for microsatellite loci in Pistacia lentiscus (3-13 alleles) provides highly informative content for the loci in population studies.…”

Section: Characterization Of the Polymorphic Ssr Locimentioning

confidence: 75%

“…Several studies have shown that the homology of DNA sequences in microsatellite flanking-region pairs has allowed SSR markers that have been developed for one species to be transferred to another species of the same genus or even different genera (Zucchi et al, 2002;Ciampi et al, 2008;Ekué et al, 2009;Feres et al, 2009;Litrico et al, 2009;Elazreg et al, Use of SSR markers from A. occidentale to A. humile 2011; Cristofani-Yaly et al, 2011). The success of marker transfer is inversely proportional to the evolutionary distance between the 2 species (Schlotterer et al, 1991;Moore et al, 1991;FitzSimmons et al, 1995;Rossetto, 2001).…”

Section: Introductionmentioning

confidence: 99%

Transferability and characterization of simple sequence repeat markers from Anacardium occidentale to A. humile (Anacardiaceae)

Cota¹,

Moreira²,

Menezes³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Use of molecular markers can be limited by the high cost and extensive time required for their development. Transfer of simple sequence repeat (SSR) markers reduces the cost and time limitations and has allowed the use of these markers in a larger number of species. We tested 11 SSR markers previously developed for Anacardium occidentale on A. humile. The 11 loci were successfully amplified in A. humile. All loci were polymorphic and generated a mean of 5.4 alleles per locus. The observed heterozygosity was lower than the expected heterozygosity under Hardy-Weinberg equilibrium for most loci, with mean values of 0.463 and 0.696, respectively. The endogamy coefficients were positive and significant for seven loci. 4609-4616 (2012) However, the combined probability of paternity exclusion was high, and the combined probability of genetic identity was low. None of the pairs of loci were in linkage disequilibrium. The informative power of these loci demonstrates that they are suitable for studies of diversity and genetic structure of natural populations of A. humile. In addition, the loci are suitable for estimating gene flow between populations, assessing species crossing preferences, and performing interspecific comparisons.

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Cross‐species amplification tests and diversity analysis using 56 PCR markers in Dactylis glomerata and Lolium perenne

Cited by 10 publications

References 11 publications

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Genetic diversity and structure of natural Dactylis glomerata L. populations revealed by morphological and microsatellite-based (SSR/ISSR) markers

Transferability and characterization of simple sequence repeat markers from Anacardium occidentale to A. humile (Anacardiaceae)

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