A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

Syed, Naeem H.; Sørensen, A.; Antonise, Rudie; Wiel, C.C.M. van de; Linden, C. Gerard van der; Westende, Wendy van ‘t; Hooftman, Danny A. P.; Nijs, H. C. M. den; Flavell, Andrew J.

doi:10.1007/s00122-005-0155-4

Cited by 53 publications

(40 citation statements)

References 41 publications

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“…S-SAP, a technique of revealing the genetic distribution of retrotransposons in a genome, is a combination of the general principle of amplified fragment length polymorphism (AFLP) and sequence-specific polymerase chain reaction (PCR). Compared with conventional molecular marker systems such as AFLP, random amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), and simple sequence repeat (SSR), the S-SAP method produces a higher density of polymorphisms, a more even distribution across the genome, and a better quality of amplification products Berenyi et al 2002;Syed et al 2005;Tam et al 2005;Lou and Chen 2007). Furthermore, it is worth mentioning that S-SAP is effective for identifying variation among somaclones (Breto et al 2001;Tahara et al 2004;Venturi et al 2006Venturi et al , 2009, which could not be done by conventional molecular markers (Wünsch and Hormaza 2002).…”

Section: Introductionmentioning

confidence: 99%

Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji

Zhao

Hirata

Liu

et al. 2009

Tree Genetics & Genomes

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Retrotransposon-based molecular markers are a powerful tool for mapping and diversity studies. The scarcity of retrotransposon long terminal repeat (LTR) sequences limits the application of retrotransposon-based molecular marker systems. Here, we isolated two novel complete Ty1-copia retrotransposons (CTcrm1 and CTcrm2) in apple using a genome walking strategy. The CTcrm retrotransposons are nearly 5 kb long, and they have all the features of Ty1-copia retrotransposons. The differences in gene organization and nucleotide sequence length between the CTcrm retrotransposons and other reported complete retrotransposons in apple showed that CTcrm1 and CTcrm2 are the first two distinct complete Ty1-copia retrotransposons in the apple genome. To investigate the potential utility of the two retrotransposons as molecular markers, primers complementary to the CTcrm LTRs were designed to develop sequence-specific amplification polymorphism markers for discriminating bud sports of Fuji apple. Multiple polymorphisms corresponding to CTcrm1 and CTcrm2 were detected and could easily be used to discriminate bud sports from their Fuji progenitor, as well as from each other.

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Section: Introductionmentioning

confidence: 99%

Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji

Zhao

Hirata

Liu

et al. 2009

Tree Genetics & Genomes

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“…This approach has been successfully used for genetic mapping, diversity and evolutionary studies in many plant species Lou and Chen 2007;Pearce et al 2000;Queen et al 2004;Sanz et al 2007;Syed et al 2005Syed et al , 2006Tam et al 2005;Vukich et al 2009;Waugh et al 1997).…”

Section: Introductionmentioning

confidence: 99%

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

et al. 2010

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Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

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“…The anonymous methods (SSAP, IRAP and REMAP) have been used for variety fingerprinting and to develop genetic maps in barley (Waugh et al, 1997), pea , bread wheat and its wild relatives (Gribbon et al, 1999), oat (Yu and Wise, 2000), Medicago sativa L. (Porceddu et al, 2002), tomato (Tam et al, 2005), apple (Venturi et al, 2006), globe artichoke (Lanteri et al, 2006) and lettuce (Syed et al, 2006). These methods have also been applied in gene mapping projects in barley (Manninen et al, 2000), oat (Tanhuanpää et al, 2006(Tanhuanpää et al, , 2007 and in the D-genome of bread wheat (Aegilops tauschii Coss.…”

Section: Diversity Analysis With Retrotransposon Markersmentioning

confidence: 99%

Analysis of plant diversity with retrotransposon-based molecular markers

et al. 2010

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Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.

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A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

Cited by 53 publications

References 41 publications

Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji

Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

Analysis of plant diversity with retrotransposon-based molecular markers

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