Identification of chromosome regions associated with seedling vigor in rice

Seedling vigor is important for optimum stand establishment in rice cropping. In this paper,a set of 264 F12 recombinant inbred lines (RILs) derived by single seed descent from a cross between Lemont (japonica) and Teqing (indica) was phenotyped for three seedling vigor related traits, including seed germination rate (GR), seedling shoot length and dry weight by the rolled paper towel tests. The phenotype data and a linkage map consisting of 198 DNA markers were combined to map quantitative trait loci (QTL) for seedling vigor by using a computer program QTLMapper1.0. A total of 13 putative main-effect QTL were detected. All of these QTL had much smaller effects on the traits with a mean R2 of 6.2%, ranging from 2.9% to 12.7%. As for digenic interaction, 18 pairs of epistatic loci with R2 > or = 5% were resolved with a mean R2 of 6.9% ,ranging from 5.1% to 11.8%, which was slightly larger than that of the main-effect QTL identified for the traits. The majority of the main-effect and epistatic loci detected for seedling vigor related traits were clustered in a few chromosome regions. Together, seven such chromosome regions (CRs), each with three or more seedling vigor main-effect and epistatic loci, were found to be highly associated with seedling vigor. These CRs can be classified into three types, i.e. M-CRs, E-CRs and ME-CRs. For some CRs just like CR(SV-6), the QTL within one CR were found to interact simultaneously with QTL within more than one other CRs to affect different seedling vigor related traits. The above results revealed that seedling vigor in rice is controlled by many loci, most of which have relatively small effects. Comparatively, epistasis as a genetic factor would be more important than main-effects of QTL for seedling vigor in rice. Nevertheless, the effects of the QTL are still large enough to be detected and in fact several chromosome regions were found to be highly associated with seedling vigor in very different populations as compared with previous studies. Molecular tagging of favorable alleles and marker-aided selection strategy may, therefore, be a promising approach to the improvement of rice seedling vigor.