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.

中文翻译：

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高通量简单序列重复 (SSR) 挖掘使胡萝卜 (Daucus carota L.) 基因组具有染色体锚定标记

摘要 胡萝卜（Daucus carota L.）是一种用途广泛的蔬菜作物，是伞形科最重要的经济成员。虽然该科中有几个重要的栽培物种，如芹菜、欧芹、小茴香、茴香、香菜和欧洲防风草，但与其他农业上重要的分类群相比，伞形科的分子遗传研究相对有限。在目前的工作中，采用计算机方法从胡萝卜基因组组装中开发染色体锚定的简单序列重复 (SSR) 标记。总共开发了 55,386 个标记，并确定了对应于蛋白质编码序列的标记位点。计算机映射分析预测，其中 51,160 个是单基因座标记，4,226 个扩增了一个以上的基因座。使用茴香 (Foeniculum vulgare Mill.) 草图基因组序列评估标记的跨物种可转移性，从而鉴定出 578 个低拷贝可转移标记。这些标记可用于种间基因组同线性研究和比较基因鉴定/克隆的目的。对来自 17 个胡萝卜材料的 DNA 评估了 50 个标记的子集。结果，46 个 (92%) 产生了来自所有基因型的扩增子，其中 28 个 (61%) 在 17 个胡萝卜种质中显示出多态性，证实了新开发的标记在揭示栽培胡萝卜基因型多样性方面的潜力。在目前的工作中，胡萝卜染色体充满了序列特异性标记，构成了胡萝卜基因组的物理图谱。