An assessment of genetic diversity within and between populations of Phalaris minor using ISSR markers N McROBERTS*, W SINCLAIR*  , A McPHERSON*, A C FRANKE* à , R P SAHARAN§, R K MALIK§, S SINGH§ & G MARSHALL* *Scottish Agricultural College, Crop & Soil Management Research Group, Edinburgh, UK,  School of Biological & Environmental Sciences, Central Queensland University, Rockhampton, Qld, Australia, àInternational Institute of Tropical Agriculture, Oyo Road, Ibadan, Nigeria, and §CCS Haryana Agricultural University, Agronomy Department, Hisar, India Received 19 November 2002 Revised version accepted 12 August 2005 Summary Intra- and inter-sample similarities for four populations of the annual grass weed Phalaris minor from Haryana state, India, were examined using inter-simple sequence repeat (ISSR) DNA markers. Levels of polymorphism within and between populations were low in comparison with values reported from other grassy weed species. Analysis of inter-population similarities allowed a par- tial differentiation of the four populations and of pairs of populations classified by cropping system. Analysis of the intra-population similarity data showed a weak but consistent and statistically significant negative correla- tion between the molecular similarity of seedlings and the physical distance between their mother plants over distances up to 40 m (the maximum separation tested) in all four populations. The consistency of the observed relationship between molecular similarity and physical separation, and the differences in cultivation practices at the four sites, suggested that the relationship may be a result of localized out-crossing, rather than an effect of localized seed rain. The results of the analyses are discussed in relation to the potential for evolution of multiple traits in the weed in response to changes in the wheat production system in the region. Keywords: Phalaris minor, herbicide resistance, genetic diversity, ISSR markers. MCROBERTS N, SINCLAIR W, MCPHERSON A, FRANKE AC, SAHARAN RP, MALIK RK, SINGH S&MARSHALL G (2005) An assessment of genetic diversity within and between populations of Phalaris minor using ISSR markers. Weed Research 45, 431–439. Introduction Weeds are a persistent problem in world agriculture despite intensive efforts to eradicate them or bring their populations under control. Phenotypic and genotypic diversity are commonly cited as central features in the successful survival of weed populations in the face of concerted control operations by farmers. Genotypic and phenotypic plasticity confer the ability to adapt and survive by exploiting niches which are unsuitable for other plants, particularly crop species (Dekker, 1997). Phalaris minor (Retz.) is a diploid, predominantly in-breeding, annual grass weed which is widely distri- buted on the Indo-Gangetic plains. It may cause yield losses of up to 50% in wheat crops following rice. It has a high competitive ability with wheat. This, combined with its high fecundity, has resulted in the grass colonizing 16 million hectares of wheat cropping land in the region. Its presence in the irrigated rice–wheat system is an ongoing threat to India’s sustainability in food grain production (Singh et al., 1997, 1999; Franke et al., 2003). Although P. minor management in wheat has been problematic in this region for several decades, the situation dramatically worsened with the development of resistance to the commonly used phenyl urea herbicide isoproturon (IPU) in some intensively farmed areas of Haryana, Punjab and Uttar Pradesh in the early 1990s (Malik & Singh, 1993). By 1999, it was estimated that herbicide-resistant biotypes had infested around 1 million hectares in these three states (Yaduraju, 1999). With the introduction in Correspondence: N McRoberts, Scottish Agricultural College, Crop & Soil Research Group, Edinburgh EH9 3JG, UK. Tel: (+44) 1292 520331; Fax: (+44) 1292 525052; E-mail: neil.mcroberts@sac.ac.uk Ó 2005 European Weed Research Society Weed Research 2005 45, 431–439