Functional markers in plants

Andersen, Jeppe Reitan; Lübberstedt, Thomas

doi:10.1016/j.tplants.2003.09.010

Cited by 681 publications

(415 citation statements)

References 68 publications

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“…Unlike markers derived from genomic DNA, a putative function can be deduced for gene-/EST-derived markers (Varshney et al 2005a). Therefore, they represent a functional class of molecular markers (Andersen and Lü bberstedt 2003). The functional SSR markers include earlier published genic SSR markers (Saghai Maroof et al 1994;Becker and Heun 1995;Pillen et al 2000) and recently developed EST-derived SSR markers (Thiel et al 2003;Rostoks et al 2005;Varshney et al 2006a;Marcel et al 2007).…”

Section: Functional Ssr Markersmentioning

confidence: 99%

A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

311

234

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Section: Functional Ssr Markersmentioning

confidence: 99%

A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

311

234

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“…This goal has been significantly aided by the explosive growth of large-scale expressed sequence tag (EST) sequencing projects (e.g., Lunde et al 2003;Ronning et al 2003). EST libraries generated by these projects have proven to be excellent resources for gene discovery, molecular marker development, analysis of gene expression at the level of the whole genome, and identification of candidate genes for phenotypes of interest (Andersen and Lubberstedt 2003;Clarke et al 2003;Gupta and Rustgi 2004). The EST approach has been particularly useful in taxa whose whole genome sequences remain unavailable or are otherwise limited in their genetic resources, e.g., the Compositae.…”

Section: Introductionmentioning

confidence: 99%

Identification and mapping of SNPs from ESTs in sunflower

et al. 2005

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More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from droughtand salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion-deletion polymorphism (SNP) variation in silico, had apparent tissuespecific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 × RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.

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“…They are based on the increasing amount of sequence information and marker density in the genomes of important crop species, as well as progress in knowledge of the physiological background of the interaction of the plant with the environment: (a) Instead of linked markers, functional markers move into the focus of interest. Here, the difference in the sequence is not only linked to the marker with the specific trait expression, but directly responsible for the change in trait (Andersen and Lübberstedt 2003). Thus, linkage between marker and trait cannot be lost and the marker is fairly independent from the genetic background.…”

Section: What Have Markers To Offer?mentioning

confidence: 99%

The role of molecular markers and marker assisted selection in breeding for organic agriculture

et al. 2010

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Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder's perspectives and perspectives seen from the organic sector's standpoint. Clear strengths were identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/ or conventional agriculture, such as the increasing competition and cost investments to get access to marker technology, and the need for bridging the gap between phenotyping and genotyping especially with complex and quantitative inherited traits such as nutrient-efficiency. A major conclusion of the authors is that more interaction and mutual understanding between organic and molecular oriented breeders is necessary and can benefit both research communities.

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Functional markers in plants

Cited by 681 publications

References 68 publications

A high density barley microsatellite consensus map with 775 SSR loci

A high density barley microsatellite consensus map with 775 SSR loci

Identification and mapping of SNPs from ESTs in sunflower

The role of molecular markers and marker assisted selection in breeding for organic agriculture

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