Rice Genetics IV - IRRI books - International Rice Research Institute

Table 2. The number of detected main-effect QTLs in rice.Trait Number Mean Range Chromosomeof cases adistributionHeading date 29 3.7 1–8 AllPlant height 32 4.1 1–2 AllLodging resistance traits 10 4.6 1–7 All but 5Seedling vigor 10 3.6 2–8 1,2,3,5,6,7,9Tiller and leaf angles 3 5.7 5–6 1,2,3,5,6,7,8,9Leaf traits 14 2.3 0–5 All but 11Resistances to abiotic stresses 25 4.8 0–11 AllResistances to biotic stresses 25 5.1 3–9 AllOther morphological traits 5 5.4 4–7 All but 7,10Anther culturability 9 2.8 1–5 All but 11Grain traits 11 4.2 1–7 All but 6,8,9Panicle traits 36 3.1 0–7 AllGrain quality and nutrients 19 2.0 1–4 All but 10,11Panicles per plant 16 2.0 1–4 All but 6,8Spikelet sterility 13 3.0 0–8 AllGrains per panicle 13 3.6 1–8 All1,000-grain weight 18 4.4 1–10 AllGrain yield per plant 15 3.4 1–10 All but 10Average – 3.8aEach case represents a trait/population/environment combination in a total of 303 cases.former case, the nature and size of mapping populations and use of replications inphenotyping play a key role in reducing phenotyping errors. In the latter case, controlof background genetic variation and inclusion of epistasis and QE interactions in thestatistical models are vital to obtaining more reliable parameter estimates (Zeng 1994,Li 1997, Wang et al 1999, Li 1999).E-QTLsThe second type of QTLs is epistatic QTLs, or E-QTLs. E-QTLs are defined as loci atwhich trait values are determined by interactions between alleles at two or more lociand are detected by associations between trait values and multilocus marker genotypesusing epistatic models (Li 1997, Wang et al 1999, Kao et al 1999). In otherwords, trait values (phenotypes) are associated with specific alleles at single loci forM-QTLs, but with multilocus genotypes for E-QTLs, as shown in Figure 1.Historically, epistasis has been recognized as an important genetic basis underlyingcomplex phenotypes (Wright 1932, 1951, Allard 1988) and founder-effect modelsof speciation (Templeton 1980). Recent results from an experiment and severalmapping studies (Tanksley and Hewitt 1988, Doebley et al 1995, Lark et al 1995, Liet al 1997a,b, Yu et al 1997) have provided strong evidence suggesting that epistasisis an important genetic component determining complex traits. Li et al (1997a) showedthat most of the early QTL mapping studies preferentially identify M-QTLs that eitherhave large effects and/or act independently, and the inability to detect epistasis inmost QTL mapping studies is due largely to the lack of appropriate methodology156 Zhi-Kang Li