Rice Genetics IV - IRRI books - International Rice Research Institute

the remaining parts of the linkage map. The majority of the QTLs were found tointeract with at least one other locus and many of the QTLs interacted with three ormore loci (Table 1).Analyzing the genetic basis of heterosisusing an “immortalized” F 2 populationIt is well known that the F 2 generation theoretically provides the most complete andmost informative population for genetic analysis (Allard 1956). However, it is verydifficult to use the F 2 for genetic analysis of quantitative traits, as each genotype isrepresented by only a single individual, which makes it difficult to get replicatedmeasurements of the same genotype. Also, the population is in a transient state; thus,the experiment cannot be repeated. Although genetic analyses using the F 2:3 type ofpopulations can produce a considerable amount of useful information on the geneticcomponents underlying heterosis, such analyses suffer from several shortcomings thatare inherent in the data generated from the populations. First, F 3 families are geneticallyheterogeneous; thus, it is impossible to have exact replications in the field trials. Second,an additional cycle of meiosis would result in gene combinations that are differentfrom those in the F 2 generation; thus, the genotypes of F 2:3 families do not correspondexactly with those of F 2 individuals. And, third, one generation of self-fertilization theoreticallyreduces the level of heterozygosity by half; thus, data from the F 2:3 type ofpopulations underestimate dominant types of genetic effects, such as dominance andoverdominance at the single-locus level and dominant types of interaction at the twolocuslevel. To overcome these shortcomings, we designed a new mating scheme thatgenerated an “immortalized” F 2 population, using a population of 240 recombinantinbred lines (RILs) produced by the single-seed descent method from the Zhenshan 97/Minghui 63 cross.Experimental design and data collectionIn this design, crosses were made between the RILs chosen by random permutations ofthe 240 RILs. In each round of permutation, the 240 RILs were randomly divided intotwo groups and the lines in the two groups were paired at random without replacementto provide parents for 120 crosses. This procedure can be repeated as many times asdesired and each round of permutation will pair the parents for 120 crosses. Such amating scheme would result in a population consisting of crosses in multiples of 120.For heterosis study, such a population possesses several distinct advantages. First,the genotypes and their proportions in this population are similar to those of an F 2 population(i.e., 1:2:1 for single-locus genotypes and 1:2:1:2:4:2:1:2:1 for two-locus combinations),thus allowing for more complete and direct analyses of the genetic components.Second, instead of only one individual per genotype represented in an F 2 population,each genotype in this population is represented by as many plants as desired, thuspermitting replicated trials. The whole population can be recreated when needed, eitherin exactly the same way or by different permutation schemes. Thus, the field experimentcan be repeated in multiple environments. Third, plants in each of the lines are178 Qifa Zhang et al