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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

Title: Development of 304 new microsatellite markers for carrot. Analysis of their potential for linkage mapping, assessment of genetic diversity and cross-taxa utilization

Authors
item Simon, Philipp
item Cavagnaro, Pablo - UW MADISON
item Chung, Sang-Min - DONGGUK UNIV S KOREA
item Ali, Aamir - UNIV-SARGODHA PAKISTAN
item Yildiz, Mehtap - YUZUNCU YIL UNIV TURKEY
item Alesandro, Maria - INST NACI TECN ARGENTINA

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: November 2, 2008
Publication Date: January 17, 2009
Citation: Simon, P.W., Cavagnaro, P.F., Chung, S., Ali, A., Yildiz, M., Alesandro, M.S. 2009. Development of 304 new microsatellite markers for carrot. Analysis of their potential for linkage mapping, assessment of genetic diversity and cross-taxa utilization [abstract]. 33rd International Carrot Conference. Paper No. BG-103.

Technical Abstract: Two different approaches were used 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 more 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 successfully 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, as resolved by high-resolution agarose electrophoresis, ranged from 34-45% for GSSRs, and 25-34% for BSSRs. More than 80% of the SSR markers amplified DNA in Daucus species other than carrot, whereas in the more distantly related non-Daucus species the SSRs performance varied greatly depending on the species and the SSR. To assess genetic relatedness among 90 cultivated and wild Daucus accessions 24 selected SSRs were used and resolved by 6% polyacrilamide gel electrophoresis, and 1 marker (GSSR4) was sequence-analyzed. Sequence analysis of GSSR4 revealed novel size and sequence polymorphisms (e.g., indels and SNPs) beyond the microsatellite region, thus increasing its discriminatory power. The addition of codominant SSR to the carrot maps will allow their integration and therefore improve their potential for map-based cloning.

Last Modified: 8/27/2014