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High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

Abstract Carrot (Daucus carota L.) is a versatile vegetable crop and the most economically important member of the Apiaceae family. While there are several important cultivated species in the family such as celery, parsley, cumin, fennel, coriander and parsnip, molecular genetic research in Apiaceae is relatively limited compared to other agriculturally important taxa. In the present work, an in silico approach was employed in order to develop chromosome-anchored simple sequence repeat (SSR) markers from the carrot genome assembly. A total of 55,386 markers were developed and marker loci that correspond to protein coding sequences were determined. In silico mapping analysis predicted that 51,160 of these were single-locus markers and 4,226 amplified more than one locus. Cross-species transferability of the markers was assessed using the fennel (Foeniculum vulgare Mill.) draft genome sequence, resulting in the identification of 578 low-copy transferable markers. These markers can serve for the purposes of interspecific genomic synteny studies and comparative gene identification/cloning. A subset of 50 markers was evaluated on DNA from 17 accessions of carrot. As a result, 46 (92%) produced amplicons from all genotypes, of which 28 (61%) displayed polymorphisms among the 17 carrot accessions, confirming the potential of the newly developed markers to reveal genotypic diversity in cultivated carrot. With the present work, carrot chromosomes were saturated with sequence-specific markers, which constitute a physical map of the carrot genome. The collection of markers will serve as practical molecular tools for germplasm characterization, gene tagging and molecular breeding studies in this important crop species.