Rice Genetics IV - IRRI books - International Rice Research Institute

clear alignment of major factors controlling agronomic traits with genes in wheat,maize, or rice for which the physiological, biochemical, and genetic control has alreadybeen well studied (Wang et al 2001).Gene predictionThe predictive power of the comparative alignments works extremely well for biochemicalgenes and genes controlling morphological traits. Figure 1 shows the comparativelocations of a few such genes. These include major structural loci, such asthe waxy genes, and classical mutants, such as genes for liguleless and dwarfism.Often, major genes in one species are aligned with QTLs for the same trait in another,as is the case with the domestication-related shattering genes in wheat and rice, whichare aligned with QTLs for the same trait in both maize genomes. It has been suggestedthat some genes, such as those controlling disease resistance, find themselvesunder such intense selection pressure that colinearity, particularly involving copynumbers, may quickly be lost (Leister et al 1998).Cross-genome gene isolationStrong colinearity between the genomes of the different cereals opens up new possibilitiesfor gene isolation. For example, until recently, wheat genes were consideredto be well beyond the reach of conventional map-based cloning technology, becausethe genomic tools were not available and because of the large genome size. Clearly,however, the homoeologues of the same genes in rice are far more tractable to use inmap-based cloning, even before the complete rice DNA sequence becomes availablefrom the commercial and public programs. The tools—very dense genetic maps, largeEST collections, large-insert BAC, P1-derived artificial chromosome (PAC), and YAClibraries—are already available and in use in most cereal genetics laboratories.This approach is being used to isolate the wheat Ph gene, which controls chromosomepairing by limiting it to homologues, rather than homoeologues (Riley andChapman 1964). Detailed maps of the critical regions on wheat chromosome 5B andrice chromosome 9 show a very high level of conserved colinearity (Foote et al 1997).However, because allelic variation is not known at the locus in wheat, let alone inrice, a new approach has been developed. Rather than use genetic recombination tonarrow down the region that contains Ph, Roberts et al (1999) developed a set ofoverlapping deletions, induced by fast-neutron mutagenesis, spanning the region of5BL carrying the gene. The 300-kb region of the rice YAC contig corresponding tothe section of wheat 5B containing Ph has been sequenced and the painstaking functionalgenomics exercise to identify the roles of the 20 or so open reading frames inthe region has begun. This strategy should be applicable to any gene in any crop inwhich the null phenotype can be clearly recognized. Allelic variation is not a prerequisiteand large recombinant populations are not necessary. Availability of the completerice genomic sequence could make map-based cloning by deletions an evenmore popular approach.Rice: a central genome for the genetics of all cereals 85