ARS | Publication request: Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 1, 2011
Publication Date: August 1, 2011
Citation: Cavagnaro, P.F., Chung, S., Manin, S., Yildiz, M., Ali, A., Alessandro, M.S., Iorizzo, M., Senalik, D.A., Simon, P.W. 2011. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. Biomed Central (BMC) Genomics. 12:386.

Interpretive Summary: Variation in DNA is the foundation for all biological variation, so the availability of tools to identify and follow DNA variation is important in developing our understanding of biological variation for any organism. One such tool to follow DNA variation that is relatively easy to evaluate in the lab and has been developed for humans, many plant, animal and microbe species is referred to as microsatellites or SSRs. We describe a research effort to develop SSRs for carrot for the first time. SSRs of carrot have properties similar to those of other plants, and they were demonstrated to be widely dispersed along carrot chromosomes. This makes carrot SSRs applicable for plant breeders interested in using SSRs to understand genetic variation for plant characteristics they are trying to improve such as productivity, resistance to environmental stress, pests and disease, flavor and nutritional quality. Some carrot SSRs were also demonstrated to be useful by plant taxonomists interested in using SSRs to understand how closely carrot is related to other plants in the same plant family including celery, fennel, cumin, dill, cilantro, parsnip, parsley, and caraway. In addition to carrot breeders and taxonomists, this research is of interest to seed companies in testing genetic purity of seed being sold, and to genomic biologists interested in fundamental questions about how chromosomes and genes are organized.

Technical Abstract: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), would facilitate a number of genetic and breeding purposes in carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development and characterization at various levels of 300 carrot SSR markers. Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.