Development and use of statistical and bioinformatic tools for the analysis of linkage disequilibrium in plant populations

This thesis is on the development and application of tools for the analysis of plant genomes and populations. Essentially the work is divided in two parts. In the first part it is presented Nuragen, a software developed to facilitate the analysis of linkage disequilibrium (LD) in multiple populations. The software implements several statistics that could be useful to describe patterns and to understand the contribution of demographic and selective forces in shaping the structure of LD within and among populations and at genome level. Moreover, some routines facilitate the use of the software in conjunction with other already available programs that allow simulations of genetic diversity under different evolutionary scenarios. In the second part of the thesis, as a case of study, the structure of LD in Sardinian landrace populations of cultivated barley is investigated. In particular, the software is used to investigate the impact of water deficit on the population structure of LD and to look for signature of epistatic (balancing and divergent) selection. Despite it seems that genetic drift and population subdivision are the main causes of the observed pattern, data suggests that ecological differences among population sampling sites have an impact on the genetic structure of this landraces. Moreover, we identify some loci (and pair of loci) displaying non-neutral patterns of genetic diversity LD with convincing evidences of balancing and divergent selection.