Development of new simple sequence repeat markers for pearl millet

Abstract

Availability of good numbers of polymerase chain reaction (PCR)-compatible markers is a prerequisite for their application in marker assisted breeding (MAB) for the genetic improvement of agricultural crops. Simple sequence repeats (SSRs) or microsatellites, which consist of a variable number of tandem repeats of a simple motif sequence, typically a mono-, di-, tri- or tetranucleotide repeat, are very useful markers for a number of plant species. The main advantages of SSRs are that they are abundant, reproducible, co-dominant, widely distributed in crop genomes and require a small quantity of DNA for PCR to detect polymorphisms. Because of these properties, SSRs are suitable markers for use in breeding programs, which essentially require high throughput markers as breeders need to screen a large number of breeding lines and segregating progenies. Like other crops, MAB has potential application in pearl millet (Pennisetum glaucum), which is a very important grain crop in the arid and semi-arid parts of Africa and South Asia. Pearl millet is confronted by a number of biotic (mainly diseases) and abiotic (drought, heat, salinity and low nutrient supply) constraints to its production. Selecting this crop for better tolerance to these stresses has been an important objective in its breeding programs. Marker assisted selection (MAS) offers a considerable advantage over conventional breeding methods in terms of precise and quick improvement in hard-to-screen traits like drought tolerance and downy mildew resistance (Hash and Witcombe 2002). Recently, there has been a tremendous progress in developing SSR markers for a number of grain crops like rice (Oryza sativa) (McCouch et al. 2002), wheat (Triticum aestivum) (Gupta and Varshney 2000), barley (Hordeum vulgare) (Varshney et al. 2007) and sorghum (Sorghum bicolor) (Menz et al. 2004). Compared to these crops, however, the number of available SSR markers in pearl millet is much lower and many more are required to produce a linkage map with high marker density to facilitate MAS. Previously, approximately 150 SSRs have been developed for use in pearl millet (Allouis et al. 2001, Qi et al. 2001, 2004, Budak et al. 2003, Senthilvel et al. 2004,Mariac et al. 2006). Development of many of these SSRs was very costly as it involved library construction, hybridization screening and clone sequencing. Currently, large public expressed sequence tags (EST) databases exist for several grass species which can be utilized for identification and development of SSR for orphan crops like pearl millet. Senthilvel et al. (2004) and Mariac et al. (2006) used this approach to design SSR markers. We report here designing and development of additional SSR markers for pearl millet.