Euphytica (2006) DOI: 10.1007/s10681-005-9059-2 C  Springer 2006 Identification of two RAPD markers genetically linked to a recessive allele of a Fusarium wilt resistance gene in pigeonpea (Cajanus cajan L. Millsp.) H. Kotresh 1 , B. Fakrudin 1,∗ , S.M. Punnuri 1 , B.K. Rajkumar 1 , M. Thudi 1 , H. Paramesh 2 , H. Lohithaswa 2 , & M.S. Kuruvinashetti 1 1 Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad-580005, India; 2 Agricultural Research Station, Gulbarga, India ( ∗ author for correspondence: e-mail bfakrudin@sancharnet.in) Received 28 June 2005; accepted 15 November 2005 Key words: Pigeonpea, RAPD, linked marker, genetics, segregation, Fusarium wilt Summary Fusarium wilt (Fusarium udum Butler) is a soil borne disease of pigeonpea which causes substantial yield losses. The disease can occur at any stage of plant development, from the young seedling to the pod filling stage. Though resistance is simply inherited, transfer to locally adapted cultivars has been difficult due to linkage drag and difficulty in accurate phenotyping, except in sick plots. An attempt was made to identify RAPD markers associated with wilt phenotype by using F 2 populations derived from contrasting parents; GSl (susceptible) × ICPL87119 (resistant) and GS1 × ICP8863 (resistant). Parents and F 2 s were grown in a national Fusarium sick-plot at Gulbarga, India and phenotyped as resistant or susceptible during the entire crop growth period. In both the crosses, resistance to wilt segregated as a monogenic dominant character. DNA samples extracted from sick plot grown, early seedling stage plants of parents and 254 F 2 plants of GS1 × ICPL87119 were held separately for marker identification. PCR reactions using 340 random decamer primers with genomic DNA of parents resulted in detection of 45 polymorphic amplicons from 39 primers. PCR testing of bulked DNA from subsets of resistant and susceptible plants revealed the presence of two amplicons at 704 bp and 500 bp (OPM03 704 and OPAC11 500 ) with susceptibility. Analysis of individual F 2 plants showed a segregation ratio of 3: 1 for the presence: absence of the amplicon in both crosses. Considering the wilt reaction and susceptibility-linked RAPD marker, it was possible to deduce genotype of every F 2 plant and the genotypic ratio for wilt reaction was 1RR: 2Rr: 1rr, as expected. Introduction Fusarium wilt (Fusarium udum Butler) is an impor- tant soil borne disease of pigeonpea, which causes seri- ous yield losses in susceptible cultivars. In India alone, the loss due to this disease is estimated to be US $71 million (Kannaiyan et al., 1984; Reddy et al., 1993). The fungus enters the host vascular system at root tips through wounds or invasion made by nematodes, lead- ing to progressive chlorosis of leaves, branches, wilting and collapse of the root system (Jain and Reddy, 1995; Butler, 1906). The disease can occur at any stage of the crop and it is rapidly spreading to newer areas in India and other countries (Singh et al., 1998). Resistance to wilt in pigeonpea could be governed either by a sin- gle dominant (Pandey et al., 1996; Singh et al., 1998) or a recessive gene (Jain & Reddy, 1995) in different crosses. More than one gene is also reported in some crosses (Shaw, 1936; Anon, 1946; Joshi, 1957). Long life cycle, out crossing nature, difficulty in accurate phenotyping and linkage drag are some of the problems being faced in conventional breeding efforts for wilt resistance in pigeonpea. The use of genetically linked molecular markers could facilitate marker-assisted se- lection in such cases. A variety of DNA based markers such as RAPD, RFLP, SSR, AFLPs etc. have been employed to con- struct genetic linkage maps and for molecular tagging of various agronomic traits (O’Brien, 1990; Williams et al., 1993; Sandhu et al., 2003; reviewed in Mohan