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Research Project:
ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY
Location: Vegetable Crops Research Unit
Title: Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae
Authors
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Simon, Philipp
| | Cavagnaro, Pablo - UW MADISON | | Chung, Sang-Min - DONGGUK UNIV S KOREA | | Ali, Aamir - UNIV SARGODHA PARKISTAN | | Yildiz, Mehtap - YUZUNCU YIL UNIV TURKEY | | Alesandro, Maria - INSI NAC DE TEC ARGENTINA |
Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 20, 2008
Publication Date: January 17, 2009
Citation: Simon, P.W., Cavagnaro, P.F., Chung, S., Ali, A., Yildiz, M., Alesandro, M.S. 2009. Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae. Plant and Animal Genome Conference [abstract]. Plant and Animal Genome Conference. p. 132.
Technical Abstract:
Genomic resources in carrot and other Apiaceae are relatively underdeveloped. The availability of a large set of pcr-based codominant markers, such as simple sequence repeats (SSR), would allow integration of the different carrot genetic maps constructed to date (mainly using anonymous dominant markers) and aid in the genotyping of carrot and related taxa. We used two different approaches to isolate carrot SSRs; 1) Construction and analysis of a genomic DNA library enriched for SSR loci (GSSRs) and 2) Bioinformatic mining for SSR motifs in a 1.7 Mb BAC-end sequence database (BSSR). The SSR-enriched library yielded microsatellites with higher number of repeats but shorter motifs than the BAC-end sequence derived SSRs. The most abundant motifs found were di- (47%) and tetranucleotides (40%) for GSSRs, and tri- (43%) and tetranucleotides (25%) for BSSRs. A total of 304 SSRs (158 GSSRs and 146 BSSRs) were succesfuly characterized in a subset (16 plants/population) of 5 F2 carrot mapping populations, and in 16 different Apiaceae. The percentage of potentially mapable markers (codominant or dominant) in the F2 families ranged from 34-45 and 25-34 among GSSRs and BSSRs, respectively. More than 80 % of the SSR markers amplified DNA in Daucus species other than carrot, whereas in the further related non-Daucus species the SSRs performance varied greatly depending on the species and the SSR. In general, the type of motif class, motif length and repeat were not indicative of polymorphisms. The frequency of carrot SSRs in BAC-end sequence was estimated to be 1 every 7.6 kb.
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