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GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

A Cleaved Amplified Polymorphic Sequence (CAPS) Marker Associated with Root-Knot Nematode Resistance in Sugarbeet

^a USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND 58105
^b USDA-ARS, Crop Improvement and Protection Research Laboratory, Salinas, CA 93905

^* Corresponding author (weilandj{at}fargo.ars.usda.gov).

Resistance to root-knot nematode (Meloidogyne spp.) previously was introgressed into sugar beet (Beta vulgaris L.) from wild beet [B. vulgaris ssp. maritima (L.) Arcang] and was demonstrated to be dominant and simply inherited. Since resistance conferred by this gene was effective against six different Meloidogyne spp. tested, the locus was designated R6m-1. An interpollinated progeny population of resistant heterozygotes segregating for R6m-1, was exposed to nematodes in a greenhouse and rated for root knot disease symptoms. Resistance vs. susceptibility segregated at approximately a 4:1 ratio and 120 resistant roots and 48 susceptible roots were chosen for the generation of molecular markers linked to the resistance trait. Bulked DNA samples prepared from shoots sprouting from the selected plants were subjected to random amplified polymorphic DNA (RAPD) analysis and yielded a marker of 600 base pair (bp) that was highly associated with resistance. Sequence analysis of the 600-bp product led to the design of DNA primers for specific amplification of a 580-bp product, the generation by polymerase chain reaction (PCR) of which occurred in plants both susceptible and resistance to nematode. Comparison between the sequences generated from resistant plants and susceptible plants revealed numerous nucleotide substitutions. One base substitution associated in repulsion with resistance conditioned the existence of a recognition site for cleavage by the restriction endonuclease MseI. Amplification and cleavage of the product with MseI yielded a CAPS marker designated NEM06 that cosegregated with resistance to the root knot nematode. Computer-assisted translation and comparison with sequences in public databases indicates that the marker DNA sequence encodes a protein with high sequence similarity to a plant transcription factor.