Rice Genetics IV - IRRI books - International Rice Research Institute

Sasaki 1997). Such analysis is often referred to as quantitative trait locus (QTL) analysis.Many QTLs have been mapped for many complex traits in rice (McCouch andDoerge 1995, Yano and Sasaki 1997).During the analyses of several quantitative traits by the DNA marker-assistedstrategy, two questions about QTL analysis have been raised: (1) Does a QTL representa single Mendelian locus or a cluster of multiple loci? (2) Is it possible to preciselymap a QTL and identify QTLs at the molecular level using map-based or otherstrategies? To answer these questions, we have performed a series of analyses onheading date as a model for complex traits. This chapter describes a comprehensiveanalysis of QTLs for heading date, including the identification of putative QTLs,characterization and fine mapping of QTLs using near-isogenic lines (NILs), andidentification of genes at QTLs for heading date by the map-based strategy. In addition,we have developed several primary permanent mapping populations and secondarygenetic resources, such as chromosomal segmental substitution lines, to facilitatethe genetic analysis of naturally occurring allelic variations. What we havelearned clearly indicates that naturally occurring allelic variations will be a new resourcefor functional genomics in rice.Launching pad for new genetics in riceThe most important aspect of the genetic dissection of complex traits is the effectiveproduction of genetic markers in the target chromosome regions. Figure 1 summarizespotential resources for the production of chromosomal region-specific markersGenetic linkage mapYAC contigs EST map PAC and BAC contigs Genomic sequences60% genomecoverageRXXXXCXXXSXXXEXXXXXRXXXXCXXXSXXXEXXXXXAbout 5,000clones................................................................GACTGTTCTCCTTACAAATTTATTGCAAAAAAAAAATAGATTCTCTATGGAGAGGCATATTTAACGTTATAGCAGGGCTATAATAAGAAACAGATGGCTCAAAGAAAATGATAAGCAACAAATAACCCATAAAGGACCCATGTCATATATAGATAGGCCTTGCAAACAAACAAAAAAAAGGTATGCAAGGAAATAATAGTTCCTTCAGCAGTTGACCCTCCCTTTCTCTTTTGCAAAAGAATGTGCATAAAGAGG..........................................In progress