Recent advance in carrot genomics

Authors: IORIZZO, M - University Of Wisconsin; ELLISON, S - University Of Wisconsin; VAN DEYNZE, A - University Of California; STOFFEL, K - University Of California; ASHRAFI, H - University Of California; IOVENE, M - National Research Council - Italy; CAVAGNARO, P - Instituto Nacional Tecnologia Agropecuaria; CHENG, SHIFENG - Chinese Academy Of Sciences; ZHENG, PENG - Chinese Academy Of Sciences; ZHENG, ZHIJUN - Chinese Academy Of Sciences; Senalik, Douglas; Spooner, David; Simon, Philipp

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2015
Publication Date: 3/10/2017
Publication URL: http://handle.nal.usda.gov/10113/5678143
Citation: Iorizzo, M., Ellison, S., Van Deynze, A., Stoffel, K., Ashrafi, H., Iovene, M., Cavagnaro, P., Cheng, S., Zheng, P., Zheng, Z., Senalik, D., Spooner, D.M., Simon, P.W. 2017. Recent advance in carrot genomics. Acta Horticulturae. 1153:61-68. doi: 10.17660/ActaHortic.2017.1153.10.

Interpretive Summary: This review summarizes the information available about the carrot genome. It points out that there has been relatively little information available about carrot DNA sequences publicly available until the last 5-6 years. In that time period four new types of methods to locate genes on chromosomes have been developed for carrot. These methods are SSRs (simple sequence repeats), COS markers (conserved orthologous sequences), SNPs (single nucleotide polymorphisms), and DArTs (diversity array technology). They have been developed for many other crops earlier, and with their development for carrot, it will be easier to develop carrot genetic maps and locate genes on carrot chromosomes. These methods are also contributing to an ongoing effort to sequence the carrot genome. This review is of interest to vegetable breeders and geneticists, and to carrot researchers.

Technical Abstract: In recent years there has been an effort towards the development of genomic resources in carrot. The number of available sequences for carrot in public databases has increased recently. This has allowed the design of SSRs markers, COS markers and a high-throughput SNP assay for genotyping. Additional molecular tools include the first high-throughput DArT array and the full sequence of organelle genomes. These molecular resources have been successfully used to gain new insights into carrot genetic diversity, organelle genome evolution and to establish the first dense sequence-based linkage maps. Sequencing of the carrot genome is currently ongoing. Its release, will establish a solid framework for carrot genomic studies, opening a new challenging and exciting era for the carrot scientific community.