Rice Genetics IV - IRRI books - International Rice Research Institute

symposium (Li, this volume), here we will focus on major-gene traits. Table 2 lists themajor genes tagged in rice and reported in the available literature to date. Approximatelyhalf of all tagged genes are resistances to biotic factors. This likely reflects notonly the economic importance of these characters and the applicability of markerassistedselection (see below) but also the fact that most resistances are conferred bymajor genes.Upon reviewing the literature of gene-tagging research in rice, several generalizationscan be made:1. While genes have been mapped on all rice chromosomes, it is interesting tonote the large number of genes mapped on chromosomes 11 and 12 relative totheir size in cM.2. For molecular markers, polymerase chain reaction (PCR)-based markers suchas RAPD (random amplified polymorphic DNA), AFLP (amplified fragmentlength polymorphism), and microsatellite or SSR (simple sequence repeat) areincreasingly being applied in gene mapping.3. For the mapping populations, the permanent populations such as DH (doubledhaploid) and RI (recombinant inbred) populations are now more often usedowing to their inherent advantages, although F 2 populations and F 3 familiesare still widely applied to locate interesting loci. Furthermore, althoughintersubspecific crosses are most frequently used to generate mapping populations,intrasubspecific and interspecific crosses have received more attentionrecently. The intrasubspecific crosses can avoid sterility and linkage drag thatresult from wide hybridization and will be favored in terms of practical applicationin plant breeding. Interspecific crosses are especially useful to introgresssome specific traits from a wild source into elite cultivars.Application of markers in breeding and geneticsThree major applications of molecular markers to rice breeding and genetics are (1)identifying allelism of genes that confer identical phenotypes (for example, blast resistancegenes identified in different countries with different isolates), (2) use in markerassistedselection (MAS) or marker-assisted backcrossing (MAB) programs, and (3)use in positional cloning of genes. This chapter focuses on their use in selection programs.Advantages of MAS or MABA general rule when deciding about whether to employ MAS is that, if the gene ofinterest can be scored easily without markers, it will usually not be economical toemploy them. Markers will be more appropriate when (1) the trait is difficult or expensiveto score, (2) several genes are being selected that confer similar phenotypes,or (3) background markers are being used to select against genes from the donorparent.Traits difficult to measure. With MAS, selection can be made without phenotypedata, selection will not be influenced by the environment, and selection is possibleMolecular mapping and marker-assisted selection . . . 139