Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid

Although F(2)s are the most informative populations for genetic analysis, it has been difficult to use F-2 populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to estimate the experimental errors. In this study, we performed a QTL analysis for yield and yield-component traits of an F-2 population based on data from replicated field trials over 2 years using vegetative shoots of ratooned plants, making use of the ratooning habit of rice. The objective of this study was to explore the possibility of conducting QTL analyses directly based on an F-2 population by means of ratooning plants. The experimental population was from a cross between 'Zhenshan 97' and 'Minghui 63', the parents of 'Shanyou 63', an elite rice hybrid widely grown in China. Agenetic linkage map containing 151 molecular markers was constructed for QTL I napping. A total of 20 distinct QTLs were detected. eight of these were detected in both years and remaining 12 in only 1 year. Compared with the results of our previous analysis of the F-2:3 families from the same cross, it was shown that most of the QTLs detected in the ratooned F-2 population were also detected in the F-2:3 population. However, the estimates of both additive and dominant types of genetic effects for many of the QTLs based on F-2 ratoons were substantially larger than those based on F-2:3 families. The results indicate that vegetatively ratooned F-2 populations may have considerable utility in the mapping of QTLs, especially if dominant types of gene actions are of concern, although there were certain technical limitations in making use of such populations in the experiments.