Merging Carrot Linkage Groups based on Conserved Dominant AFLP Markers in F2 Populations

Santos, C. A. F.; Šimon, Petr

doi:10.21273/jashs.129.2.0211

Cited by 13 publications

(10 citation statements)

References 30 publications

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“…Details concerning the development of the mapping population, plant cultivation, DNA extraction, and detection/scoring of previously mapped AFLP, SCAR, DcM TD ( DcMaster Transposon Display), and gene specific markers were described before [5,8,9,52]. …”

Section: Methodsmentioning

confidence: 99%

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

et al. 2011

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BackgroundThe Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels.ResultsEvaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity.ConclusionsThe addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.

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Section: Methodsmentioning

confidence: 99%

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

et al. 2011

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“…Separate maps were constructed for each parent to avoid problems related to the use of repulsion phase dominant markers, as described previously (Santos and Simon 2004).…”

Section: Plant Materialsmentioning

confidence: 99%

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

Grzebelus

Simon

2008

Genetica

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Transposable elements constitute a significant fraction of plant genomes. Both autonomous and non-autonomous elements of the DcMaster family, residing in the carrot genome, were described previously. DcMaster elements were classified as members of the PIF/Harbinger superfamily. In the present paper we report on the identification of other groups of DcMaster-like elements. Beside the previously described, relatively highly abundant miniature inverted repeat element (MITE) family Krak (ca. 3,600 copies, ca. 80% intra-family similarity), three other families, i.e. 1.1 kb long KrakL1 (ca. 3,000 copies, ca. 98% intra-family similarity), 1.2 kb long KrakL2 (a single identified element, 71.1% similar to KrakL1 consensus), and 2.2 kb long Midi (few elements, 99% intra-family similarity), were revealed. The fact that all members within each of the newly found families were almost identical in their sequence suggests their very recent activity. The families differed in terms of their similarity to the canonical DcMaster element. They also differed in copy number, from just a few copies of Midi to few thousand copies of Krak. A modification of the DcMaster Transposon Display (DcMTD) marker system, targeted specifically towards Krak elements, was used to investigate their insertion polymorphism. It was shown that Krak insertion sites, similarly to those of the DcMaster elements, were highly polymorphic between the wild and the cultivated Daucus carota.

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“…Separate maps were constructed for each parent to avoid problems related to the use of repulsion phase dominant markers, as described previously (Santos and Simon, 2004). The maps were constructed with MAPMAKER 3.0 (Lander et al, 1987).…”

Section: Construction Of Genetic Linkage Mapmentioning

confidence: 99%

The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

Grzebelus

Jagosz

Simon

2007

Gene

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Merging Carrot Linkage Groups based on Conserved Dominant AFLP Markers in F2 Populations

Cited by 13 publications

References 30 publications

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

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