36th International Carrot Conference Abstract

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

Massimo Iorizzo¹, Douglas Senalik^1,2, Shelby Ellison¹, Dariusz Grzebelus³, Pablo Cavagnaro⁴, David Spooner², Allen Van Deynze⁵ and Philipp Simon^1,2

¹ Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706. USA

² USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA

³ Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland

⁴ CONICET, Fac. Ciencias Agrarias – Universidad Nacional de Cuyo, and INTA EEA La Consulta, CC8 La Consulta (5567), Mendoza, Argentina

⁵ Seed Biotechnology Center, University of California, 1 Shields Ave, Davis, CA, 95616-8816, USA

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.

Last updated Thursday, 25-Jul-2013 11:53:40 CDT