Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.).

IORIZZO, M.; SENALIK, D.; ELLISON, S.; GRZEBELUS, D.; CAVAGNARO, P. F.; SPOONER, D.M.; VAN DEYNZE, A.; SIMON, P. W.

madison

Congreso; 36th International Carrot Conference; 2013

University of Wisconsin

The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access these technologies. Here, we designed 4,000 Single Nucleotide Polymorphisms markers (SNPs) from carrot transcriptome sequences data to characterize the genetic diversity in a geographically well dispersed subset of wild and cultivated carrots using the Kbioscience (Hoddesdon, England) platform. Overall, 3636 SNPs (91%) produced distinct genotypic clusters. Analysis of allelic diversity of SNP data revealed no reduction of genetic diversity in cultivated vs. wild accessions. Structure and phylogenetic analysis indicated a clear separation between wild and cultivated accessions as well as between eastern and western cultivated carrot. Among the wild carrots, those from Central Asia were genetically most similar to cultivated accessions. Furthermore, we found that wild carrots from North America were most closely related to European wild accessions. Evaluation of seven mapping populations revealed that the rate of polymorphism ranged from 24.9% to 47.9%. Mapping data from three populations allowed us to develop an integrated map of 1,242 SNPs. This study provides the first genome wide molecular characterization of genetic diversity in carrot. Integration of the SNP map and previously mapped markers and phenotypic traits is ongoing. This will provide a framework for the upcoming carrot genome sequence analysis.