Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice ( Oryza sativa L.)

Abstract

Seedling-vigor is important for optimum stand establishment and increasing weed competitive ability in rice cropping systems. In the current study, three seedling-vigor-related traits, seed germination rate, seedling shoot length and dry matter weight, were investigated by the paper-roll tests with rice recombinant inbred lines derived from a cross between Lemont ( japonica) and Teqing ( indica). The phenotype data, together with a linkage map consisting of 198 marker loci, was used to conduct composite interval mapping by QTLMapper 1.0 to simultaneously map both main-effect and epistatic QTLs for seedling-vigor in rice. Totally, 13 putative main-effect QTLs and 19 pairs of epistatic loci with R 2 ≥ 5% were identified. Almost all of these QTLs or interactions individually explained only around 5–10% of the phenotypic variation. The majority (68%) of these main-effect and epistatic loci were clustered in seven chromosome regions, each spanning 12–28 cM (centi-Morgan) and containing three or more detectable loci. When detectable for the multiple seedling-vigor-related traits, either the main-effect QTLs or the epistatic interactions sharing the same map location had their additive or epistatic effects in the same direction, which agreed well with the positive correlations among the traits. The results demonstrated that seedling-vigor in rice could be controlled by many loci, most of which had small effects, but, relatively, epistasis as a genetic factor was much more important than main-effects of QTLs. Along with the results reported previously, this study revealed the extensive genetic diversity for seedling-vigor in rice. In addition, the QTL q SV-7 on chromosome 7 was found to have the largest main-effects on multiple seedling-vigor-related traits and therefore could be used as a potential target to be genetically manipulated by marker-assisted selection in rice seedling-vigor breeding programs.