Development And Characterization Of Novel SSR Markers In Carrot (Daucus carota L.) And Their Application For Mapping And Diversity Analysis In Apiaceae

CAVAGNARO, P. F.; CHUNG, S.-M.; ALI, A.; YILDIZ, M.; ALESSANDRO, M. S.; SIMON, P. W.

San Diego

Conferencia; Plant & Animal Genomes XVII Conference; 2009

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 carrot genetic maps constructed to date (mainly using anonymous dominant markers) and aid in the genotyping of carrot and perhaps 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 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 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 more distantly related non-Daucus species the SSRs performance varied greatly depending on the species and the SSR. The frequency of carrot SSRs in BAC-end sequence was estimated to be 1 every 7.6 kb.