In comparison to the classical morphological markers and isozymes, DNA markers are now becoming an essential tool for genetic investigations because of ability to generate and track an unlimited number of loci that can be linked to any trait of interest. Aside from RFLP, a variety of DNA markers such as RAPD (Williams etal. 1990), SSR(LittandLutty 1989), sequence tagged sites (STS) (Olson et al. 1989), sequence characterized amplified region (SCAR) (Martin et al. 1991), CAPS (Koniecyzn and Asubel 1993), and AFLP (Vos et al. 1995) have been developed. Unlike RFLP, most of these recently developed markers are PCR-based with simplified protocols and require minute quantities of DNA. However, the dominant nature of some PCR markers like RAPD and AFLP makes distinguishing homozygotes from heterozygotes difficult. Currently, SSR markers are the most preferred class of markers for marker-assisted selection (MAS) because of its codominant nature, simpler protocols, abundance, and higher level of polymorphism. Due to the availability of considerable amounts of sequence data, single nucleotide polymorphism (SNP) (Brookes 1999) is gaining momentum as an excellent tool to navigate the genome due to its simplicity, abundance, and amenability for automation. A number of softwares such as Mapmaker/QTL (Lincoln et al. 1992), Qgene (Nelson 1997), QTL map per (Wang et al. 1999a), QTL Cartographer (Basten et al. 2001), PLABQTL (Utz and Melchinger 1996), and MQTL (Tinker and Mather 1995) have been developed to detect quantitative trait loci (QTL). DNA markers and their usefulness in crop improvement have been widely reviewed (Paterson et al. 1991; Burrow and Blake 1998; Brar 2002; Subudhi and Nguyen 2004). In this section, we will provide an update on molecular marker utilization to investigate both simple and complex traits in rice.
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