Rice Genetics IV - IRRI books - International Rice Research Institute

1980s have had far-reaching effects on many areas of biological sciences. DNA markersare defined as linear landmarks in DNA molecules or chromosomes where genotypicdifferences arising from point mutations, insertions or deletions, transpositions, etc.,can be detected and visualized by various molecular tools. Several major types ofDNA markers are available, classified largely according to the molecular techniquesby which the DNA differences are detected. These include RFLP (restriction fragmentlength polymorphism), RAPD (randomly amplified polymorphic DNA), CAPS(cleaved amplified polymorphic sequences), STS (sequence tagged sites), AFLP (amplifiedfragment length polymorphism), microsatellites or simple sequence repeats(SSRs), and single nucleotide polymorphisms (SNPs). The most common use of DNAmarkers is to develop comprehensive molecular genetic linkage maps, in which thelinear orders and relative genetic distances of linked DNA markers on individualchromosomes and the whole genome in an organism are determined genetically andrepresented graphically. In rice, several high-density rice molecular linkage mapshave been constructed (Causse et al 1994, Kurata et al 1994, Harushima et al 1998,Shomura et al 1997, Xiong et al 1997, Cho et al 1997). Establishment of these molecularlinkage maps has greatly facilitated efforts in genome mapping of rice. One ofthe most important applications of DNA markers and molecular linkage maps is todissect the genetic variation of quantitative traits into individual Mendelian factorsthrough quantitative trait loci (QTL) mapping analyses.QTL mapping can be defined as the marker-facilitated genetic dissection of variationof complex phenotypes through appropriate experimental design and statisticalanalyses of segregating materials. In QTL mapping, genes controlling genetic variationof quantitative traits in segregating populations are resolved into individual Mendelianfactors by detecting marker-trait associations. The primary objective of a QTLmapping experiment is to understand the genetic basis of specific quantitative traitsby determining the number, locations, gene effects, and actions of loci involved andtheir interactions with other loci (epistasis) and with environments (QTL × environment,or QE, interactions). Another major purpose of QTL mapping is to identifyDNA markers diagnostic for particular phenotypes of interest so that marker-aidedselection (MAS) can be used to efficiently manipulate progenies carrying alleles fortarget traits grown under nontarget environments.In the past 10 years, many rice QTL mapping studies have been conducted andQTLs affecting a wide range of phenotypes have been identified. In this chapter,results from these QTL mapping studies are reviewed with regard to three criticalquestions: the types and number of QTLs involved in specific phenotypes, the behavioror gene action of QTLs, and QE interactions.Types and number of QTLsTo date, QTLs identified in rice can be classified into two major types: main-effectQTLs (M-QTLs) and epistatic QTLs (E-QTLs), based largely on the presence or absenceof epistasis. Distinction of the two types of QTLs is critical to our understandingof the genetic basis of quantitative trait variation in rice.154 Zhi-Kang Li