Phenomic networks reveal largely independent root and shoot adjustment in waterlogged plants of Lotus japonicus.

Waterlogging imposes severe stress to the plant, and the interplay between root and aerial organs in the adjustment to this stress is poorly understood. A set of recombinant inbred lines (RILs) of Lotus japonicus (Gifu B-129 × Miyakojima MG-20) was subjected to control and waterlogging conditions for 21 d, and 12 traits related to leaf physiological functioning, root aerenchyma formation, shoot and root morphology, and dry mass accumulation were assessed to generate phenomic networks. The phenomic network became more complex under waterlogging as a result of the incorporation of root aerenchyma and dark-adapted Fv/Fm. Significant waterlogging-induced variation was found for stomatal conductance, dark-adapted Fv/Fm and aerenchyma. The RILs with stronger induction of aerenchyma in response to waterlogging tended to show reduced negative impact of this stress on root growth but suffered average impact on shoot growth. The RILs that retained higher stomatal conductance under waterlogging tended to retain higher dark-adapted Fv/Fm and shoot growth under waterlogging conditions but showed average impact on root traits. We propose a model where, although the stress experienced by the roots during waterlogging is transmitted to the shoot, shoots and roots deal with waterlogging in a less interdependent manner than often assumed.

Simulation of population size and genome saturation level for genetic mapping of recombinant inbred lines (RILs)

Various population sizes and number of markers have been used to obtain genetic maps. However, the precise number of individuals and markers needed for obtaining reliable maps is not known. We used data simulation to determine the influence of population size, the effect of the degree of marker saturation of the genome, and the number of individuals required for mapping of recombinant inbred lines (RILs). Three genomes with 11 linkage groups were generated with saturation levels of 5, 10 and 20 cM. For each saturation level populations were generated with 50, 100, 154, 200, 300, 500 and 800 individuals with 100 replications for each population size. A total of 2100 populations was generated and mapped. Small marker numbers and small population sizes produced maps with more than 11 linkage groups. As population size and marker saturation increased, marker inversion and non-linked markers decreased, moreover, between-marker distance estimates were improved. In this study, a minimum size of 200, 300 and 500 individuals were necessary for obtaining reliable maps when they were evaluated over the saturation levels of 5, 10 and 20 cM, respectively.