Efficiency of different marker systems for molecular characterization of subtropical carrot germplasm T.JHANG 1 , M. KAUR 1 , P. KALIA 2 AND T.R. SHARMA 1 * 1 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India 2 Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 110012, India (Revised MS received 17 September 2009; First published online 22 January 2010) SUMMARY Genetic variability in carrots is a consequence of allogamy, which leads to a high level of inbreeding depression, affecting the development of new varieties. To understand the extent of genetic variability in 40 elite indigenous breeding lines of subtropical carrots, 48 DNA markers consisting of 16 inter simple sequence repeats (ISSRs), 10 universal rice primers (URPs), 16 random amplification of poly- morphic DNA (RAPD) and six simple sequence repeat (SSR) markers were used. These 48 markers amplified a total of 591 bands, of which 569 were polymorphic (0 . 96). Amplicon size ranged from 200 to 3500 base pairs (bp) in ISSR, RAPD and URPs markers and from 100 to 300 bp in SSR markers. The ISSR marker system was found to be most efficient with (GT) n motifs as the most abundant SSR loci in the carrot genome. The unweighted pair group method with arithmetic mean (UPGMA) analysis of the combined data set of all the DNA markers obtained by four marker systems classified 40 genotypes in two groups with 0 . 45 genetic similarity with high Mantel matrix correlation (r=0 . 92). The principal component analysis (PCA) of marker data also explained 0 . 55 of the variation by first three components. Molecular diversity was very high and non-structured in these open-pollinated genotypes. The study demonstrated for the first time that URPs can be used successfully in genetic diversity analysis of tropical carrots. In addition, an entirely a new set of microsatellite markers, derived from the expressed sequence tags (ESTs) sequences of carrots, has been developed and utilized successfully. INTRODUCTION Carrots (Daucus carota L., Apiaceae) are cultivated worldwide, with Asia accounting for 0 . 38 of global production. India produces 350 000 metric tonnes of carrots annually from an area of 24 000 ha with 14 . 6 t/ha productivity (FAO 2004). It forms an im- portant component of the human diet owing to its unique flavouring, textural, medicinal, fibre and nu- tritional characteristics. The carrot is classified by the International Board for Plant Genetic Resources in priority group 4 (IBPGR 1981). Based on physiology and reproductive biology, the carrot is categorized as either tropical or temperate. Tropical carrots have purple and red coloured roots, pubescent leaves and are quick to reproduce (i.e. are early bolting), while temperate carrots have orange coloured roots, less pubescent leaves and late or no bolting until pro- longed exposure to low temperature. Carrot genotypes are available in distinct colours, viz., dark red, red, orange, yellow, purple and black. The major pigments, e.g. alpha and beta-carotene in orange, lycopene in red, lutein in yellow and antho- cynin in purple and black carrots, have a significant role in nutrition and carotenoids are known to have an anti-cancerous genetic effect (Simon 1996). The genetic background and nutritional information, such as improved flavours and more diverse pigments, are of immense importance for the vegetable industry and consumers (Simon 2000). In the early 18th century, carrots were the first allogamous vegetable to under- go intensive selection breeding (Stein & Nothnagel 1995). Over the last two centuries, open-pollinated carrot varieties have been bred by mass selection and * To whom all correspondence should be addressed. Email : trsharma@nrcpb.org Journal of Agricultural Science (2010), 148, 171–181. f Cambridge University Press 2010 171 doi:10.1017/S0021859609990591